diff --git a/manuscript/Snakefile b/manuscript/Snakefile index 1713a71b..bbf1cfc3 100644 --- a/manuscript/Snakefile +++ b/manuscript/Snakefile @@ -69,6 +69,7 @@ rule concat_HDBSCAN_tables: "sars-cov-2-nextstrain/results/optimal_cluster_accuracy_and_parameters_for_Nextclade_pango_collapsed.csv", "sars-cov-2-nextstrain-2022-2023/results/full_HDBSCAN_metadata_for_Nextstrain_clade.csv", "sars-cov-2-nextstrain-2022-2023/results/full_HDBSCAN_metadata_for_Nextclade_pango_collapsed.csv", + "sars-cov-2-nextstrain/results/single_clade/cluster_accuracy_t-sne_for_Nextclade_pango_collapsed.csv", ] output: fullKDE = "manuscript/tables/total_HDBSCAN_table.csv", @@ -83,6 +84,7 @@ rule concat_HDBSCAN_tables: "early SARS-CoV-2 (2020-2022)", "late SARS-CoV-2 (2022-2023)", "late SARS-CoV-2 (2022-2023)", + "SARS-CoV-2 21J (Delta) only", ], genetic_group_types = [ "Nextstrain clade", @@ -93,6 +95,7 @@ rule concat_HDBSCAN_tables: "Pango", "Nextstrain clade", "Pango", + "Pango", ], conda: "../cartography.yml" shell: diff --git a/manuscript/cartography.tex b/manuscript/cartography.tex index 84d311ce..85a276b6 100644 --- a/manuscript/cartography.tex +++ b/manuscript/cartography.tex @@ -436,6 +436,16 @@ \subsection{SARS-CoV-2 clusters recapitulate broad genetic groups corresponding With the exception of t-SNE's performance, these results replicate the patterns we observed with early SARS-CoV-2 data where clusters from embeddings more effectively represented broader genetic diversity than the finer resolution diversity denoted by Pango lineages. Unlike the Pango lineages in the early SARS-CoV-2 data, the lineages from the later data exhibited fewer pairwise genetic distances between samples in each lineage than samples in Nextstrain clades or any embedding cluster (Supplementary Fig.~S\ref{S_Fig_sarscov2_within_between_group_distances}). +To understand whether t-SNE clusters could capture Pango-resolution genetic groups within a single Nextstrain clade, we evenly sampled approximately 2,000 sequences from a dominant Nextstrain clade with many Pango lineages, 21J (Delta), and identified clusters from a t-SNE embedding of those data. +Within the 1,992 sequences sampled from 21J (Delta), we found 38 Pango lineages after collapsing lineages with fewer than 10 sequences into their parent lineages. +We found 28 t-SNE clusters representing 1,806 sequences (91\%) with 186 sequences (9\%) assigned to the unclustered ``-1'' label (Supplementary Fig.~\ref{S_Fig_sarscov2_single_clade_embeddings_tsne_counts}). +The VI distance between Pango lineages and all clusters (including the unclustered group) was 0.17 (Supplementary Table~\ref{S_Table_optimal_cluster_parameters}). +This distance was consistent with the distance of 0.14 between Pango lineages and t-SNE clusters from both the full early and late SARS-CoV-2 datasets. +The VI distance between Pango lineages and clusters without the unclustered sequences was 0.13, confirming that one quarter of the distance between t-SNE clusters and Pango lineages above came from unclustered sequences. +Of the 38 Pango lineages with a t-SNE cluster, 30 lineages (79\%) had a single corresponding t-SNE cluster, seven lineages (18\%) had two or three t-SNE clusters, and one lineage (B.1.617.2) had five t-SNE clusters (Supplementary Fig.~\ref{S_Fig_sarscov2_single_clade_embeddings_tsne_counts}). +Of the 28 t-SNE clusters, 21 clusters (75\%) had a single corresponding Pango lineage, six (21\%) mapped to two or three Pango lineages, and one (cluster 27) mapped to 18 Pango lineages with most sequences from B.1.617.2 and AY.4. +These results suggest that clusters from t-SNE embeddings can capture more Pango-resolution genetic groups by analyzing sequences within a specific Nextstrain clade. + \subsection{Distance-based embeddings reflect SARS-CoV-2 recombination events} Finally, we tested the ability of sequence embeddings to place known recombinant lineages of SARS-CoV-2 between their parental lineages in Euclidean space. @@ -482,7 +492,8 @@ \subsection{Limitations of methods and analysis} Despite the promise of these simple methods to answer important public health questions about human pathogenic viruses, these methods and our analyses suffer from inherent limitations. The lack of an underlying biological model is both a strength and the clearest limitation of the dimensionality reduction methods we considered here. -For example, embeddings of SARS-CoV-2 genomes cannot capture the same fine-grained genetic resolution as Pango lineage annotations. +For example, embeddings of SARS-CoV-2 genomes that represent the complete circulating diversity at a given time cannot capture the same fine-grained genetic resolution as Pango lineage annotations. +Only t-SNE clusters of SARS-CoV-2 genomes within a single Nextstrain clade get close to defining Pango-resolution genetic groups. Each method provides only a few parameters to tune its embeddings and these parameters have little effect on the qualitative outcome. In maintaining a linear relationship between Euclidean and genetic distances, MDS sacrifices the ability to form more accurate genetic clusters for viruses with large genomes like SARS-CoV-2. Neither t-SNE nor UMAP maintain a linear relationship between pairwise Euclidean and genetic distances across the observed range of genetic distances. diff --git a/manuscript/cartography_supplement.tex b/manuscript/cartography_supplement.tex index dfe6a21b..fe031839 100644 --- a/manuscript/cartography_supplement.tex +++ b/manuscript/cartography_supplement.tex @@ -209,6 +209,13 @@ \section*{Supplementary data} \caption{{\bf Number of late SARS-CoV-2 strains per combination of recombinant Pango lineage and t-SNE cluster where the count was at least 10 strains.}}\label{S_Fig_sarscov2_late_embeddings_tsne_recombinant_counts} \end{figure} +\begin{figure}[!h] +\includegraphics[width=\columnwidth]{figures/sarscov2-single-clade-lineages-and-clusters-counts.png} +\caption{{\bf Number of SARS-CoV-2 sequences from Nextstrain clade 21J (Delta) per combination of Pango lineage and t-SNE cluster showing the degree to which clusters of sequences from a single Nextstrain clade can capture Pango-resolution genetic groups.} + The size of each circle represents the number of sequences associated with each pair of t-SNE cluster and Pango lineage. + The cluster label ``-1'' represents sequences that could not be assigned to a cluster.}\label{S_Fig_sarscov2_single_clade_embeddings_tsne_counts} +\end{figure} + \begin{figure}[!h] \includegraphics[width=0.75\columnwidth]{figures/sarscov2-test-mds-reassortment-XE-BA1-BA2.png}\\ \includegraphics[width=0.75\columnwidth]{figures/sarscov2-test-mds-reassortment-XAS-BA2-BA5.png} diff --git a/manuscript/figures/sarscov2-single-clade-lineages-and-clusters-counts.png b/manuscript/figures/sarscov2-single-clade-lineages-and-clusters-counts.png new file mode 100644 index 00000000..4741422a Binary files /dev/null and b/manuscript/figures/sarscov2-single-clade-lineages-and-clusters-counts.png differ diff --git a/manuscript/tables/accuracy_table.tex b/manuscript/tables/accuracy_table.tex index fab7fdf9..4e371703 100644 --- a/manuscript/tables/accuracy_table.tex +++ b/manuscript/tables/accuracy_table.tex @@ -42,5 +42,6 @@ & & MDS & 18 & 0.37 & \\ & & genetic & 15 & 0.43 & \\ & & PCA & 7 & 0.46 & \\ + SARS-CoV-2 21J (Delta) only & Pango & t-SNE & 28 & 0.17 & \\ \botrule \end{tabular} diff --git a/manuscript/tables/total_HDBSCAN_table.csv b/manuscript/tables/total_HDBSCAN_table.csv index 60f1f469..9b3867ed 100644 --- a/manuscript/tables/total_HDBSCAN_table.csv +++ b/manuscript/tables/total_HDBSCAN_table.csv @@ -39,3 +39,4 @@ 37,MDS,0.37,18,,, 38,genetic,0.43,15,,, 39,PCA,0.46,7,,, +40,t-SNE,0.17,28,,SARS-CoV-2 21J (Delta) only,Pango diff --git a/notebooks/scripts/concat_KDE_tables.py b/notebooks/scripts/concat_KDE_tables.py index db6cebbe..d35fcf55 100644 --- a/notebooks/scripts/concat_KDE_tables.py +++ b/notebooks/scripts/concat_KDE_tables.py @@ -42,8 +42,9 @@ df = df.loc[:, [column for column in columns_to_use if column != "distance_threshold"]].copy() df["distance_threshold"] = "" - df["Pathogen Dataset"] = [pathogen] + [""] * (len(embedding_name_by_abbreviation) - 1) - df["Genetic Group Type"] = [genetic_group_type] + [""] * (len(embedding_name_by_abbreviation) - 1) + number_of_methods = df["method"].drop_duplicates().shape[0] + df["Pathogen Dataset"] = [pathogen] + [""] * (number_of_methods - 1) + df["Genetic Group Type"] = [genetic_group_type] + [""] * (number_of_methods - 1) tables.append(df) df = pd.concat(tables, ignore_index=True) diff --git a/sars-cov-2-nextstrain/Snakefile b/sars-cov-2-nextstrain/Snakefile index 3edc8a50..512e0101 100644 --- a/sars-cov-2-nextstrain/Snakefile +++ b/sars-cov-2-nextstrain/Snakefile @@ -17,6 +17,11 @@ rule sarscov2: "auspice/cartography_ncov-2020-2022.json", expand("sars-cov-2-nextstrain/results/mutation_table_for_{clade_membership}.csv", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), "sars-cov-2-nextstrain/results/monophyletic_clusters.csv", + "sars-cov-2-nextstrain/results/single_clade/cluster_accuracy_t-sne_for_Nextclade_pango_collapsed.csv", + "sars-cov-2-nextstrain/results/single_clade/cluster_accuracy_without_unclustered_t-sne_for_Nextclade_pango_collapsed.csv", + "sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters_counts.tsv", + "sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters_counts_without_unclustered.tsv", + "manuscript/figures/sarscov2-single-clade-lineages-and-clusters-counts.png", rule sarscov2_download_filtered_metadata: output: @@ -960,3 +965,243 @@ rule sarscov2_get_authors_for_accessions: | csvtk rename -l -t -f "Isolate Lineage" -n "Virus Name" \ | csvtk mutate2 -l -t -n "dataset" -e "'sars-cov-2-2020-2022'" > {output.authors} """ + +rule sarscov2_subsample_single_clade: + input: + metadata="sars-cov-2-nextstrain/data/filtered_metadata.tsv.zst", + outliers="sars-cov-2-nextstrain/config/exclude.txt", + output: + strains="sars-cov-2-nextstrain/data/single_clade/strains.txt", + params: + random_seed=RANDOM_SEED, + single_clade="21J (Delta)", + conda: "../cartography.yml" + shell: + """ + augur filter \ + --metadata {input.metadata} \ + --exclude {input.outliers} \ + --min-date 2020-01-01 \ + --max-date 2022-01-01 \ + --query "Nextstrain_clade == '{params.single_clade}'" \ + --group-by region year month \ + --subsample-max-sequences 2000 \ + --subsample-seed {params.random_seed} \ + --output-strains {output.strains} + """ + +rule sarscov2_extract_subsampled_data_for_single_clade: + input: + metadata="sars-cov-2-nextstrain/data/filtered_metadata.tsv.zst", + alignment="sars-cov-2-nextstrain/data/all_aligned.fasta.zst", + strains="sars-cov-2-nextstrain/data/single_clade/strains.txt", + output: + metadata="sars-cov-2-nextstrain/data/single_clade/metadata.tsv", + alignment="sars-cov-2-nextstrain/data/single_clade/aligned.fasta", + conda: "../cartography.yml" + shell: + """ + augur filter \ + --metadata {input.metadata} \ + --sequences {input.alignment} \ + --exclude-all \ + --include {input.strains} \ + --output-metadata {output.metadata} \ + --output-sequences {output.alignment} + """ + +rule sarscov2_collapse_pango_lineages_for_single_clade: + input: + metadata="sars-cov-2-nextstrain/data/single_clade/metadata.tsv", + output: + metadata="sars-cov-2-nextstrain/data/single_clade/metadata_Pango_collapsed.tsv", + conda: "../cartography.yml" + log: + "logs/sars-cov-2-nextstrain/collapse_pango_lineages_for_single_clade.txt", + params: + min_samples=10, + pango_column="Nextclade_pango", + new_column="Nextclade_pango_collapsed", + shell: + """ + python3 notebooks/scripts/collapse_pango_lineages.py \ + --metadata {input.metadata} \ + --min-samples {params.min_samples} \ + --pango-column {params.pango_column} \ + --new-column {params.new_column} \ + --output {output.metadata} 2>&1 | tee {log} + """ + +rule sarscov2_create_distance_matrix_for_single_clade: + input: + alignment="sars-cov-2-nextstrain/data/single_clade/aligned.fasta", + output: + output="sars-cov-2-nextstrain/results/single_clade/distance_matrix.csv", + conda: "../cartography.yml" + shell: + """ + pathogen-distance \ + --alignment {input.alignment} \ + --indel-distance \ + --output {output.output} + """ + +rule sarscov2_embed_tsne_for_single_clade: + input: + alignment="sars-cov-2-nextstrain/data/single_clade/aligned.fasta", + distance_matrix="sars-cov-2-nextstrain/results/single_clade/distance_matrix.csv", + parameters="simulations/coronavirus-like/moderate-recombination-rate/t-sne_parameters.csv", + output: + dataframe="sars-cov-2-nextstrain/results/single_clade/embed_t-sne.csv", + params: + random_seed=RANDOM_SEED, + conda: "../cartography.yml" + shell: + """ + pathogen-embed \ + --alignment {input.alignment} \ + --distance-matrix {input.distance_matrix} \ + --embedding-parameters {input.parameters} \ + --random-seed {params.random_seed} \ + --output-dataframe {output.dataframe} \ + t-sne \ + --pca-encoding simplex + """ + +rule sarscov2_cluster_for_single_clade: + input: + embedding="sars-cov-2-nextstrain/results/single_clade/embed_t-sne.csv", + parameters="sars-cov-2-nextstrain/results/optimal_cluster_accuracy_and_parameters_for_Nextclade_pango_collapsed.csv", + output: + clustered_embedding="sars-cov-2-nextstrain/results/single_clade/cluster_embed_t-sne_for_Nextclade_pango_collapsed.csv", + params: + min_size=CLUSTER_MIN_SIZE, + min_samples=CLUSTER_MIN_SAMPLES, + conda: "../cartography.yml" + shell: + """ + pathogen-cluster \ + --embedding {input.embedding} \ + --min-size {params.min_size} \ + --min-samples {params.min_samples} \ + --distance-threshold "$(csvtk filter2 -f '$method=="t-sne"' {input.parameters} | csvtk cut -f distance_threshold | csvtk del-header)" \ + --label-attribute "t-sne_label_for_Nextclade_pango_collapsed" \ + --output-dataframe {output.clustered_embedding} + """ + +rule sarscov2_cluster_accuracy_for_single_clade: + input: + metadata="sars-cov-2-nextstrain/data/single_clade/metadata_Pango_collapsed.tsv", + clusters="sars-cov-2-nextstrain/results/single_clade/cluster_embed_t-sne_for_Nextclade_pango_collapsed.csv", + output: + dataframe="sars-cov-2-nextstrain/results/single_clade/cluster_accuracy_t-sne_for_Nextclade_pango_collapsed.csv", + params: + ignored_clusters="unassigned", + conda: "../cartography.yml" + shell: + """ + python3 notebooks/scripts/metadata_HDBSCAN.py \ + --method "t-sne" \ + --true-clusters {input.metadata} \ + --true-clusters-column "Nextclade_pango_collapsed" \ + --predicted-clusters {input.clusters} \ + --predicted-clusters-column "t-sne_label_for_Nextclade_pango_collapsed" \ + --ignored-clusters {params.ignored_clusters:q} \ + --output {output.dataframe} + """ + +rule sarscov2_cluster_accuracy_without_unclustered_for_single_clade: + input: + metadata="sars-cov-2-nextstrain/data/single_clade/metadata_Pango_collapsed.tsv", + clusters="sars-cov-2-nextstrain/results/single_clade/cluster_embed_t-sne_for_Nextclade_pango_collapsed.csv", + output: + dataframe="sars-cov-2-nextstrain/results/single_clade/cluster_accuracy_without_unclustered_t-sne_for_Nextclade_pango_collapsed.csv", + params: + ignored_clusters=["unassigned", "-1"], + conda: "../cartography.yml" + shell: + """ + python3 notebooks/scripts/metadata_HDBSCAN.py \ + --method "t-sne" \ + --true-clusters {input.metadata} \ + --true-clusters-column "Nextclade_pango_collapsed" \ + --predicted-clusters {input.clusters} \ + --predicted-clusters-column "t-sne_label_for_Nextclade_pango_collapsed" \ + --ignored-clusters {params.ignored_clusters:q} \ + --output {output.dataframe} + """ + +rule sarscov2_select_lineages_for_single_clade: + input: + metadata="sars-cov-2-nextstrain/data/single_clade/metadata_Pango_collapsed.tsv", + output: + lineages="sars-cov-2-nextstrain/results/single_clade/lineages.tsv", + conda: "../cartography.yml" + shell: + """ + tsv-select -H -f strain,Nextclade_pango_collapsed {input.metadata} > {output.lineages} + """ + +rule sarscov2_select_clusters_for_single_clade: + input: + clusters="sars-cov-2-nextstrain/results/single_clade/cluster_embed_t-sne_for_Nextclade_pango_collapsed.csv", + output: + clusters="sars-cov-2-nextstrain/results/single_clade/clusters.tsv", + conda: "../cartography.yml" + shell: + """ + tsv-select -d "," -H -f 'strain','t\-sne_label_for_Nextclade_pango_collapsed' {input.clusters} \ + | csv2tsv > {output.clusters} + """ + +rule sarscov2_merge_lineages_and_clusters_for_single_clade: + input: + lineages="sars-cov-2-nextstrain/results/single_clade/lineages.tsv", + clusters="sars-cov-2-nextstrain/results/single_clade/clusters.tsv", + output: + table="sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters.tsv", + conda: "../cartography.yml" + shell: + """ + tsv-join -H -f {input.lineages} -k strain -a Nextclade_pango_collapsed {input.clusters} > {output.table} + """ + +rule sarscov2_summarize_lineages_and_clusters_for_single_clade: + input: + table="sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters.tsv", + output: + counts="sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters_counts.tsv", + conda: "../cartography.yml" + shell: + """ + tsv-summarize -H -g 'Nextclade_pango_collapsed','t\-sne_label_for_Nextclade_pango_collapsed' --count {input.table} > {output.counts} + """ + +rule sarscov2_filter_lineages_and_clusters_for_single_clade: + input: + counts="sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters_counts.tsv", + output: + counts="sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters_counts_without_unclustered.tsv", + conda: "../cartography.yml" + shell: + """ + tsv-filter -H --str-ne "t\-sne_label_for_Nextclade_pango_collapsed:-1" {input.counts} > {output.counts} + """ + +rule sarscov2_plot_lineages_and_clusters_for_single_clade: + input: + counts="sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters_counts.tsv", + output: + counts_plot="manuscript/figures/sarscov2-single-clade-lineages-and-clusters-counts.png", + conda: "../cartography.yml" + params: + lineage_column="Nextclade_pango_collapsed", + cluster_column="t-sne_label_for_Nextclade_pango_collapsed", + shell: + """ + python3 sars-cov-2-nextstrain/scripts/plot-single-clade-lineage-and-cluster-counts.py \ + --counts {input.counts} \ + --lineage-column {params.lineage_column:q} \ + --cluster-column {params.cluster_column:q} \ + --output {output.counts_plot} + """ diff --git a/sars-cov-2-nextstrain/results/single_clade/cluster_accuracy_t-sne_for_Nextclade_pango_collapsed.csv b/sars-cov-2-nextstrain/results/single_clade/cluster_accuracy_t-sne_for_Nextclade_pango_collapsed.csv new file mode 100644 index 00000000..71f3d76e --- /dev/null +++ b/sars-cov-2-nextstrain/results/single_clade/cluster_accuracy_t-sne_for_Nextclade_pango_collapsed.csv @@ -0,0 +1,2 @@ +method,predicted_clusters_column,normalized_vi,n_predicted_clusters,n_predicted_cluster_samples,n_ignored_predicted_clusters,n_true_cluster_samples,n_ignored_true_clusters,n_vi_cluster_samples +t-sne,t-sne_label_for_Nextclade_pango_collapsed,0.17,28,1992,0,1992,0,1992 diff --git a/sars-cov-2-nextstrain/results/single_clade/cluster_accuracy_without_unclustered_t-sne_for_Nextclade_pango_collapsed.csv b/sars-cov-2-nextstrain/results/single_clade/cluster_accuracy_without_unclustered_t-sne_for_Nextclade_pango_collapsed.csv new file mode 100644 index 00000000..bc373a63 --- /dev/null +++ b/sars-cov-2-nextstrain/results/single_clade/cluster_accuracy_without_unclustered_t-sne_for_Nextclade_pango_collapsed.csv @@ -0,0 +1,2 @@ +method,predicted_clusters_column,normalized_vi,n_predicted_clusters,n_predicted_cluster_samples,n_ignored_predicted_clusters,n_true_cluster_samples,n_ignored_true_clusters,n_vi_cluster_samples +t-sne,t-sne_label_for_Nextclade_pango_collapsed,0.13,28,1806,186,1992,0,1806 diff --git a/sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters.tsv b/sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters.tsv new file mode 100644 index 00000000..cede273b --- /dev/null +++ b/sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters.tsv @@ -0,0 +1,1993 @@ +strain t-sne_label_for_Nextclade_pango_collapsed Nextclade_pango_collapsed +BRA/SP-NVBS6920GENOV828076619274/2021 1 AY.99.2 +USA/TX-CDC-LC0056011/2021 27 B.1.617.2 +England/LOND-YYBNF59/2022 27 AY.4.2 +LC752099 16 AY.29 +BHR/400215521_S32_L001/2021 27 B.1.617.2 +OY530201 27 AY.4 +England/NORW-13DACBA/2021 27 AY.4 +Northern_Ireland/NIRE-0050d0/2021 27 AY.4 +USA/MN-CDC-ASC210453623/2021 18 AY.3 +BHR/21342818722_S65_L001/2021 15 AY.3 +CHL/AR-UFRO-0421/2021 11 AY.101 +SouthAfrica/NHLS-UCT-GS-F132/2021 26 AY.45 +Switzerland/SO-ETHZ-33760694/2021 21 AY.43 +England/NORT-YYBGBS/2021 27 AY.4 +OV115124 27 AY.33 +NZL/21MV0277/2021 27 AY.4 +NZL/21CV0251/2021 9 AY.39.1.1 +USA/NC-CDC-STM-000069068/2021 27 B.1.617.2 +Japan/SZ-NIG-Y211710/2021 16 AY.29 +IND/hospital_2_130/2021 27 B.1.617.2 +OY628730 27 AY.4 +NZL/21MV1536/2021 9 AY.39.1.1 +NZL/21MV1298/2021 9 AY.39.1.1 +NZL/21MV1215/2021 9 AY.39.1.1 +England/NEWC-202DDC4/2021 27 AY.4 +BRA/ILMD2200125/2021 11 AY.101 +USA/MN-CDC-IBX711673689055/2021 2 AY.44 +BRA/BA-NVBS7150GENOV045616267287/2021 27 B.1.617.2 +BRA/PR-NVBS2685GENOV45371166115/2021 11 AY.101 +BRA/PR-NVBS4508GENOV827964198877/2021 11 AY.101 +BRA/RJ-NVBS6623GENOV828104289868/2021 1 AY.99.2 +BRA/ILMD2200096/2021 1 AY.99.2 +OY342278 27 AY.4 +OY382565 27 AY.4.2 +OY501555 27 AY.4 +NZL/21MV1387/2021 -1 AY.98 +NZL/21MV1933/2021 9 AY.39.1.1 +LAO/LOMWRU-1375/2021 3 AY.1 +IND/CWS_0011_49330959/2021 27 B.1.617.2 +BRA/RJ-NVBS5528GENOV827972782105/2021 1 AY.99.2 +LAO/LOMWRU-0826/2021 5 AY.85 +USA/SC-COVID21-5260/2021 22 AY.103 +DJI/NAMRU3_F397/2021 -1 AY.127 +England/ALDP-1633654/2021 27 AY.4 +England/MILK-179B06A/2021 27 AY.6 +England/PHEC-3J089J73/2021 27 AY.4 +IND/hospital_2_125/2021 27 B.1.617.2 +Scotland/QEUH-15D489C/2021 27 AY.4 +USA/CO-CDC-MMB09185280/2021 23 AY.25 +BRA/RJ-NVBS5406GENOV827934953444/2021 1 AY.99.2 +SouthAfrica/NHLS-UCT-GS-AE23/2021 26 AY.45 +NZL/21MV2839/2021 8 AY.39.1.1 +NZL/21MV2962/2021 8 AY.39.1.1 +NZL/21CH0644/2021 8 AY.39.1.1 +NZL/21CH0505/2021 9 AY.39.1.1 +NZL/21MV2031/2021 8 AY.39.1.1 +LAO/LOMWRU-1051/2021 3 AY.1 +DJI/NAMRU3_G907/2021 12 AY.100 +NZL/21MV1578/2021 9 AY.39.1.1 +OU517713 27 AY.4 +USA/MA-CDCBI-CRSP_O7KATHJL3WNZPUTM/2021 2 AY.44 +BGD/Laila_180/2021 27 B.1.617.2 +Scotland/SCOT-2944/2022 27 AY.4.2 +IND/407MN908947.3/2021 27 B.1.617.2 +England/NORT-1BF6E50/2021 27 AY.4 +IND/GBRC619/2021 27 B.1.617.2 +England/ALDP-1546A53/2021 27 AY.4 +USA/DE-CDC-LC0388304/2021 2 AY.44 +BGD/Laila_251/2021 14 AY.122 +BHR/342331334/2021 27 B.1.617.2 +England/PLYM-17A54BC/2021 27 AY.4 +England/PLYM-189E93E/2021 27 AY.4 +USA/CA-CDC-ASC210110103/2021 27 B.1.617.2 +NZL/21MV0511/2021 -1 AY.46 +NZL/21MV1513/2021 9 AY.39.1.1 +NZL/21MV1365/2021 9 AY.39.1.1 +IND/562MN908947.3/2021 27 B.1.617.2 +KEN/SS2359/2021 -1 AY.46 +USA/MA-CDCBI-CRSP_VJQPYHLNI7SM7XDS/2021 18 AY.3 +USA/CO-CDPHE-2101609275/2021 2 AY.44 +UGA/MUWRP-KIR210124S/2021 27 AY.46 +NZL/21MV2408/2021 9 AY.39.1.1 +BGD/B_210626_07.fasta/2021 27 B.1.617.2 +BRA/RS-NVBS7208GENOV68128515101/2021 1 AY.99.2 +NZL/21MV1697/2021 9 AY.39.1.1 +OV104402 27 AY.46.6 +OV104452 -1 B.1.617.2 +USA/KY-CDC-LC0325862/2021 9 AY.39 +SouthAfrica/NHLS-UCT-GP-N180/2021 4 AY.32 +USA/OR-UW-22010154609/2022 24 AY.103 +USA/CO-CDC-MMB11540784/2021 2 AY.44 +England/ALDP-2BE6685/2021 27 AY.4 +LAO/LOMWRU-1512/2021 3 AY.1 +LAO/LOMWRU-1185/2021 3 AY.1 +NZL/21MV0614/2021 -1 B.1.617.2 +NZL/21MV1333/2021 9 AY.39.1.1 +USA/CA-LACPHL-AF03772/2021 24 AY.103 +England/ALDP-203CB22/2021 27 AY.4 +SouthAfrica/NHLS-UCT-LA-Z537/2021 4 AY.32 +Japan/SZ-NIG-212480/2021 16 AY.29 +LAO/LOMWRU-1273/2021 3 AY.1 +OV543090 17 AY.126 +BHR/21342751271_S30_L001/2021 7 AY.33 +USA/CA-CDC-FG-108324/2021 2 AY.44 +THA/CONI-1760/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-GS-AE87/2021 20 AY.91 +SouthAfrica/NHLS-UCT-GP-K618/2021 27 AY.107 +Japan/SZ-NIG-Y211958/2021 16 AY.29 +USA/NM-UNM-ED00988/2022 23 AY.25 +England/NORW-30902CC/2021 27 AY.4 +England/MILK-29D2615/2021 27 AY.4 +THA/CONI-1640/2021 27 B.1.617.2 +OV649901 -1 AY.4 +England/NEWC-1D1FB2B/2021 27 AY.4 +UGA/MUWRP-KIR210118S/2021 27 AY.46 +NZL/21MV3213/2021 8 AY.39.1.1 +England/MILK-2820330/2021 -1 AY.98 +Denmark/DCGC-256085/2021 27 B.1.617.2 +England/MILK-17AF41C/2021 27 AY.4 +BRA/RJ-NVBS5276GENOV827942410366/2021 1 AY.99.2 +BRA/PR-NVBS5715GENOV045374597145/2021 11 AY.101 +BHR/21921622772/2021 27 B.1.617.2 +BRA/EPI_ISL_8890165/2021 1 AY.99.2 +SouthAfrica/NHLS-UCT-GS-D150/2021 4 AY.32 +MRT/394421/2021 10 AY.34.1 +OY409223 27 AY.46 +USA/TN-SPHL-0204/2021 23 AY.25 +NZL/21CV0954/2021 -1 AY.39.1.1 +NZL/21MV2853/2021 8 AY.39.1.1 +USA/OKPHL0025522/2021 24 AY.103 +USA/UT-UPHL-210609601897/2021 2 AY.44 +USA/CO-CDC-MMB08875794/2021 2 AY.44 +England/ALDP-157FECE/2021 27 AY.4 +USA/MD-CDC-LC0338756/2021 23 AY.25 +BRA/EPI_ISL_8890043/2021 1 AY.99.2 +OY434175 27 AY.4 +OY335678 27 AY.5 +OY516379 -1 AY.4 +UGA/MUWRP-KIR210120S/2021 27 AY.46 +HongKong/HKU-220213-217/2021 27 B.1.617.2 +BRA/SP-NVBS10911GENOV701284878537/2021 1 AY.99.2 +BRA/PI-NVBS9779GENOV701341436076/2021 1 AY.99.2 +BRA/SP-NVBS6730GENOV828077847546/2021 1 AY.99.2 +BRA/RJ-NVBS3731GENOV827835016927/2021 1 AY.99.2 +LAO/LOMWRU-0480/2021 5 AY.85 +Scotland/QEUH-1687F47/2021 27 AY.4 +Scotland/QEUH-15DED84/2021 27 AY.4 +USA/IL-CDC-STM-000070452/2021 27 B.1.617.2 +NGA/CV4780/2021 6 AY.36 +BHR/342326038/2021 27 B.1.617.2 +England/RAND-1955FB8/2021 27 AY.4 +USA/CA-CDPH-3000258352/2021 27 AY.20 +BHR/21921795622_S81_L001/2021 7 AY.33 +OY432978 27 AY.4 +OV504854 27 AY.122 +USA/WA-UW-21052765778/2021 -1 B.1.617.2 +IND/GBRC629a/2021 27 B.1.617.2 +BRA/ILMD2101235/2021 10 B.1.617.2 +BRA/ILMD2101432/2021 1 AY.99.2 +USA/CO-CDPHE-2101937541/2021 12 AY.100 +OV103948 21 AY.43 +NZL/21CV0543/2021 9 AY.39.1.1 +NZL/21MV1331/2021 2 AY.44 +BHR/21342702121/2021 7 AY.33 +USA/MA-CDCBI-CRSP_2EVA2B7AU2T77RSV/2021 -1 AY.127 +NZL/21CH0045/2021 27 AY.4 +NZL/21CV0246/2021 9 AY.39.1.1 +NZL/21CV0412/2021 9 AY.39.1.1 +England/PLYM-20917BE/2021 -1 AY.4 +NZL/21MV0571/2021 13 AY.23 +NZL/21MV0812/2021 9 AY.39.1.1 +NZL/21MV0950/2021 9 AY.39.1.1 +OU858094 -1 B.1.617.2 +NGA/CV2822/2021 6 AY.36 +USA/NC-CDC-ASC210464998/2021 27 B.1.617.2 +USA/UT-UPHL-210721332314/2021 2 AY.44 +IND/CWS_0019_47812264/2021 27 B.1.617.2 +Scotland/QEUH-1641E6A/2021 27 AY.4 +LAO/LOMWRU-1002/2021 3 AY.1 +FRA/IHUCOVID-028147_Nova1/2021 21 AY.43 +USA/CA-CDPH-2000052704/2021 23 AY.25.1 +USA/MI-CDC-STM-76462R3JA/2021 24 AY.103 +England/ALDP-15EA5C9/2021 27 AY.4 +England/NORT-1BE1B06/2021 27 AY.98 +BEN/MTMC_35_094/2021 27 B.1.617.2 +USA/B011888/2021 24 AY.103 +SouthAfrica/NHLS-UCT-LA-Z660/2021 27 AY.6 +England/MILK-2874F0C/2021 27 AY.4 +KEN/SS7131/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-AM-Z062/2021 26 AY.45 +SouthAfrica/NHLS-UCT-GS-C909/2021 4 AY.32 +USA/FL-CDC-QDX25472414/2021 18 AY.3 +BRA/ILMD2200159/2021 1 AY.99.2 +Japan/SZ-NIG-Y212025/2021 16 AY.29 +OV374282 27 AY.4 +OY706184 27 AY.4 +LAO/LOMWRU-1328/2021 3 AY.1 +BGD/IEDCR-OIS-242/2021 27 B.1.617.2 +USA/FL-CDC-LC0073561/2021 2 AY.44 +USA/NE-TESTNE_A1KVV71/2021 24 AY.103 +USA/CA-OC-FG-233046/2021 -1 AY.103 +USA/Mayo9809/2021 23 AY.25 +OY569698 27 AY.6 +OY550434 27 AY.4 +SouthAfrica/NHLS-UCT-GS-C002/2021 4 AY.32 +BRA/SP-NVBS11534GENOV828501895365/2021 -1 AY.46 +SYC/SS4702/2021 19 AY.122 +Japan/SZ-NIG-Y212133/2021 16 AY.29 +NZL/21MV1675/2021 8 AY.39.1.1 +KEN/C97296/2021 27 AY.116 +BHR/21921749402_S93_L001/2021 27 B.1.617.2 +JPN/HiroC117c/2021 16 AY.29 +BRA/SC-NXBS4749GENOV045615834268/2021 11 AY.101 +BRA/RJ-NVBS3542GENOV700921341489/2021 1 AY.99.2 +NGA/CV4746/2021 6 AY.36 +IND/NIB148384/2021 27 B.1.617.2 +BRA/PR-NVBS4514GENOV827962987770/2021 11 AY.101 +England/PHEC-U30AU1C4/2021 27 B.1.617.2 +England/MILK-15E050F/2021 27 AY.4 +IND/GBRC1218/2021 27 B.1.617.2 +England/MILK-188D862/2021 27 AY.4 +USA/ME-CDC-ASC210565432/2022 18 AY.3 +USA/CO-CDC-MMB08717562/2021 23 AY.25 +NGA/CV4259/2021 6 AY.36 +LAO/LOMWRU-1782/2021 3 AY.1 +England/QEUH-2DE8205/2021 -1 AY.98 +Scotland/QEUH-1852A06/2021 27 AY.4 +USA/MA-CDC-QDX24476850/2021 27 B.1.617.2 +England/HSLL-1532CBE/2021 27 AY.122 +USA/AZ-CDC-ASC210089808/2021 2 AY.44 +USA/CT-1137/2021 23 AY.25 +KEN/C103161/2021 27 AY.116 +NZL/21CV0231/2021 13 AY.23 +NZL/21MV0524/2021 27 B.1.617.2 +USA/OKPHL0024763/2022 27 AY.103 +NZL/21MV0489/2021 27 B.1.617.2 +NZL/21MV0758/2021 9 AY.39.1.1 +NZL/21MV0597/2021 -1 B.1.617.2 +IND/532MN908947.3/2021 27 B.1.617.2 +BRA/SP-NVBS11361GENOV701800592213/2021 21 AY.43 +USA/GA-CDC-STM-000711405/2021 27 B.1.617.2 +England/ALDP-15B57A3/2021 27 AY.4 +USA/KS-CDC-2-4567468/2021 2 AY.44 +England/ALDP-15DA92A/2021 27 AY.4 +England/MILK-174C411/2021 27 AY.4 +BRA/DF-NVBS9953GENOV828374567161/2021 1 AY.99.2 +USA/GA-CDC-MMB09516331/2021 -1 AY.39 +SouthAfrica/NHLS-UCT-GS-F574/2021 4 AY.32 +USA/CA-LACPHL-AF04675/2021 23 AY.25 +NZL/21MV0636/2021 25 AY.120 +BHR/400216326_S30_L001/2021 27 B.1.617.2 +BGD/Laila_73/2021 27 B.1.617.2 +OV103798 27 AY.4 +England/ALDP-2B9984F/2021 27 AY.4.2 +England/MILK-15C987C/2021 27 AY.5 +USA/NJ-CDC-QDX24840221/2021 27 B.1.617.2 +Wales/PHWC-PY4TGW/2021 27 AY.4 +NZL/21MV0564/2021 27 AY.4 +NZL/21CV0275/2021 9 AY.39 +SYC/SS3569/2021 -1 AY.122 +BTN/RCDC0012-SV210150/2020 27 B.1.617.2 +KEN/SS5010/2021 27 AY.46 +NZL/21MV0488/2021 27 B.1.617.2 +OU857748 21 AY.43 +BRA/RJ-NVBS11963GENOV700965959145/2021 1 AY.99.2 +USA/TG1061579/2021 12 AY.100 +BRA/SP-NVBS11284GENOV828486877240/2021 -1 AY.46 +USA/MA-CDCBI-CRSP_HMU2UOIZJYFAE46L/2021 18 AY.3 +BHR/21921864481/2021 27 B.1.617.2 +IND/CWS_0006_49088398/2021 27 B.1.617.2 +England/ALDP-15F5CE4/2021 27 AY.4 +FRA/IHUCOVID-055223-Nova1/2021 21 AY.43 +BRA/SP-NVBS11471GENOV828485403754/2021 21 AY.43 +BRA/RJ-NVBS3541GENOV827851232646/2021 1 AY.99.2 +NZL/21MV1292/2021 9 AY.39.1.1 +UZB/UZB-332/2021 27 AY.122 +USA/NV-CDC-QDX26116121/2021 2 AY.44 +NZL/21CH0280/2021 8 AY.39.1.1 +OV104284 21 AY.43 +BRA/RJ-NVBS9684GENOV828368479265/2021 1 AY.99.2 +BRA/BA-NVBS5373GENOV700931114141/2021 1 AY.99.2 +NZL/21MV3143/2021 9 AY.39.1.1 +England/ALDP-1540813/2021 27 AY.4 +UGA/MUWRP-MUL210273/2021 27 AY.46 +USA/FL-CDC-ASC210032824/2021 27 B.1.617.2 +KEN/C106199/2021 27 AY.116 +Japan/SZ-NIG-3-C12636/2021 16 AY.29 +USA/CO-CDPHE-2102651133/2022 24 AY.103 +England/MILK-2D45B38/2021 27 AY.4 +England/PHEC-Y306YA90/2021 -1 B.1.617.2 +BRA/EPI_ISL_8890379/2021 1 AY.99.2 +England/BRBR-1C71627/2021 27 AY.4 +OY528028 27 AY.4 +NZL/21MV3110/2021 9 AY.39.1.1 +USA/CO-CDC-ASC210179974/2021 18 AY.3 +USA/PA-CDC-LC0305532/2021 23 AY.25.1 +NGA/BCVL-26967/2021 6 AY.36 +USA/MA-CDCBI-CRSP_ATUA5QY57ZPIRS2E/2021 -1 B.1.617.2 +LAO/LOMWRU-1525/2021 5 AY.85 +LAO/LOMWRU-1394/2021 3 AY.1 +USA/UT-UPHL-210621699831/2021 2 AY.44 +England/ALDP-168C3CE/2021 27 AY.4 +NZL/21MV0487/2021 27 AY.4 +NZL/21MV1555/2021 9 AY.39.1.1 +KEN/C98276/2021 27 AY.116 +BRA/21894987DMN/2021 1 AY.99.2 +England/HSLL-15193B8/2021 14 AY.122 +BTN/RCDC0020-SV210158/2021 27 B.1.617.2 +USA/CO-CDC-ASC210065360/2021 2 AY.44 +SouthAfrica/NHLS-UCT-GS-C911/2021 26 AY.45 +PAK/153181/2021 27 B.1.617.2 +USA/UT-UPHL-210921586575/2021 23 AY.25.1 +England/MILK-1C90C11/2021 25 AY.120 +BRA/SP-NVBS11661GENOV828510730435/2021 10 AY.34.1 +BRA/PE-NVBS8421GENOV828251057495/2021 1 AY.99.2 +IND/hospital_2_320/2021 27 B.1.617.2 +England/QEUH-1D7657F/2021 27 AY.4 +OY509844 27 AY.4 +Denmark/DCGC-223472/2021 21 AY.43 +USA/LA-BIE-BP254/2022 -1 AY.39 +England/ALDP-2D817E1/2021 27 AY.4.2 +BRA/RS-NVBS7211GENOV19426656501/2021 1 AY.99.2 +FRA/IHUCOVID-0027109_Nova1/2020 -1 B.1.617.2 +SYC/SS3973/2021 19 AY.122 +MRT/397636/2021 10 AY.34.1 +USA/MA-CDC-LC0466718/2022 24 AY.103 +USA/TN-CDC-ASC210107804/2021 2 AY.44 +USA/WA-CDC-UW21051982399/2021 -1 B.1.617.2 +BHR/921069396/2021 27 B.1.617.2 +BRA/ILMD2200168/2021 1 AY.99.2 +BRA/SP-NVBS11872GENOV828512594288/2021 10 AY.34.1 +BRA/SP-NVBS10154GENOV130640662327/2021 21 AY.43 +BRA/RJ-NVBS6511GENOV700940553214/2021 1 AY.99.2 +USA/NM-UNM-TRL_2J2022_111/2022 18 AY.3 +OY350231 27 AY.98 +OY481497 27 AY.4 +OY564815 27 AY.4 +USA/TX-CDC-LC0334074/2021 18 AY.3 +USA/GA-CDC-MMB09835834/2021 -1 AY.39 +England/NORT-YYBI4W/2021 27 AY.4 +BHR/21921819264/2021 7 AY.33 +England/QEUH-29F05F6/2021 27 AY.6 +BRA/EPI_ISL_8890105/2021 1 AY.99.2 +BHR/21922022252_S40_L001/2021 -1 AY.4 +OV103942 -1 AY.122 +LAO/LOMWRU-1751/2022 3 AY.1 +KEN/SS4437/2021 -1 AY.46 +USA/TX-CDC-FG-203316/2021 23 AY.25 +Switzerland/GE-HUG-36608772/2022 17 AY.126 +England/MILK-30C1BE3/2022 27 AY.4.2 +USA/MO-CDC-ASC210470623/2021 24 AY.103 +OV019321 -1 AY.43 +NZL/21MV1708/2021 9 AY.39.1.1 +BHR/21100206582_S63_L001/2021 15 AY.3 +USA/OKPHLCOV0008237/2021 2 AY.44 +USA/UT-UPHL-220109420824/2021 24 AY.103 +USA/MO-UMGC-7403/2021 18 AY.3 +USA/MN-CDC-ASC210160024/2021 24 AY.103 +NGA/CV2496/2021 6 AY.36 +KEN/SS10670/2021 27 B.1.617.2 +BEN/528720/2021 6 AY.36 +SYC/SS2592/2021 19 AY.122 +USA/PA-CDC-STM-000732892/2021 23 AY.25.1 +England/NORT-YYWTNN/2021 27 AY.4.2 +Japan/SZ-NIG-3-C11857/2021 16 AY.29 +England/MILK-2CBEE9C/2021 27 AY.4.2 +OY712859 27 AY.4 +BRA/SP-NVBS11541GENOV828488900366/2021 10 AY.46 +Japan/SZ-NIG-3-C11398/2021 16 AY.29 +England/NORT-1BF0F53/2021 27 AY.4 +OV104177 -1 AY.98 +NGA/CV3476/2021 6 AY.36 +NGA/CV4741/2021 27 B.1.617.2 +Wales/ALDP-161020E/2021 27 AY.4 +England/ALDP-17FF77E/2021 27 AY.4 +BRA/SP-NXBS4941GENOV827935574174/2021 1 AY.99.2 +BRA/RJ-NVBS5479GENOV700932292138/2021 1 AY.99.2 +BRA/RJ-NXBS1903GENOV807674328719/2021 1 AY.99.2 +BRA/RJ-NVBS3523GENOV827824550272/2021 1 AY.99.2 +IND/GBRC605a/2021 27 AY.122 +SYC/SS4669/2021 19 AY.122 +Japan/SZ-NIG-213383/2021 16 AY.29 +USA/NM-UNM-ED00952/2021 22 AY.103 +USA/MI-MDHHS-SC31451/2021 27 AY.119 +NZL/21MV0609/2021 14 AY.122 +USA/GA-CDC-MMB10169455/2021 24 AY.103 +USA/2112269/2022 23 AY.25.1 +MEX/CMX-2_358/2021 27 AY.20 +USA/NM-UNM-TRL_2J2022_176/2022 27 B.1.617.2 +England/MILK-1DE46F1/2021 27 AY.4 +USA/CO-CDPHE-2101378528/2021 2 AY.44 +USA/MA-CDCBI-CRSP_LIUJR7AKQI25Y2KZ/2021 27 AY.119 +England/HSLL-15194C4/2021 14 AY.122 +USA/CO-CDC-MMB09298708/2021 23 AY.25 +England/MILK-17ADF95/2021 27 AY.4 +THA/MTM_01_045/2021 5 AY.85 +THA/MTM_01_009/2021 5 AY.85 +FRA/IHUCOVID-057750-Nova1M/2020 21 AY.43 +USA/MO-CDC-QDX24326395/2021 27 B.1.617.2 +USA/FL-CDC-QDX30129743/2021 2 AY.44 +USA/TX-CDC-QDX30410688/2021 12 AY.100 +KEN/SS8067/2021 27 AY.46 +BRA/RJ-NVBS8689GENOV828208798570/2021 1 AY.99.2 +BRA/SP-NVBS7085GENOV828106674938/2021 0 AY.99 +USA/CA-OC-1431/2021 27 B.1.617.2 +USA/WI-CDC-ASC210636259/2021 24 AY.103 +OV653499 17 AY.126 +NZL/21CV3110/2021 9 AY.39.1.1 +CHL/AR-UFRO-0444/2021 21 AY.43 +Japan/SZ-NIG-3-C12825/2021 16 AY.29 +Japan/SZ-NIG-Y21931/2021 16 AY.29 +Japan/SZ-NIG-Y21745/2021 16 AY.29 +MNG/202107046/2021 -1 AY.107 +JAM/202112026/2021 -1 AY.107 +USA/MN-CDC-IBX365054916151/2021 18 AY.3 +SouthAfrica/NHLS-UCT-AM-Z036/2021 4 AY.32 +Denmark/DCGC-225342/2021 27 AY.122 +USA/AL-CDC-LC0211576/2021 24 AY.103 +USA/MA-CDCBI-CRSP_K7PMJZZ44ADDME7V/2021 27 AY.119 +NZL/21CV0523/2021 9 AY.39.1.1 +USA/PA-CDC-STM-000731938/2021 24 AY.103 +England/MILK-1FEF9EC/2021 27 AY.4 +USA/MN-CDC-IBX989416244184/2021 24 AY.103 +NZL/21CH0070/2021 13 AY.23 +NZL/21MV1096/2021 9 AY.39.1.1 +BHR/21410356779/2021 27 AY.122 +England/QEUH-164AF8C/2021 27 AY.4 +USA/CO-CDC-MMB11311783/2021 24 AY.103 +USA/NJ-CDC-LC0389108/2021 -1 AY.39 +BHR/21342796161_S58_L001/2021 7 AY.33 +England/MILK-2B38B49/2021 27 AY.6 +NZL/21CH0059/2021 13 AY.23 +NZL/21MV1177/2021 9 AY.39.1.1 +KEN/C97160/2021 27 AY.116 +Japan/SZ-NIG-Y21760/2021 16 AY.29 +BRA/BA-NVBS5802GENOV828062975926/2021 1 AY.99.2 +BRA/PR-NVBS4479GENOV827973639217/2021 11 AY.101 +England/MILK-1557A6E/2021 14 AY.122 +USA/TG1298343/2020 12 AY.100 +BRA/EPI_ISL_4273424/2021 1 AY.99.2 +USA/OH-CDC-ASC210083928/2021 9 AY.39 +NZL/21MV1729/2021 9 AY.39.1.1 +KEN/SS4390/2021 27 B.1.617.2 +LC752088 16 AY.29 +USA/CA-CDPH-1002012163/2020 22 AY.103 +OL966453 27 B.1.617.2 +NZL/21MV2372/2021 9 AY.39.1.1 +NGA/CV4796/2021 6 AY.36 +USA/CO-CDPHE-2102651239/2022 27 AY.3 +LAO/LOMWRU-1682/2021 5 AY.85 +Switzerland/VD-CHUV-GEN6565/2021 21 AY.43 +BHR/921227846/2021 -1 B.1.617.2 +USA/MD-CDC-LC0192073/2021 -1 B.1.617.2 +England/NORW-13F3969/2021 27 AY.4 +NGA/CV3076/2021 6 AY.36 +KEN/C97622/2021 27 AY.116 +SYC/SS4733/2021 19 AY.122 +USA/MN-CDC-IBX243968500097/2021 12 AY.100 +KEN/SS4154/2021 27 AY.46 +NZL/21MV1370/2021 9 AY.39.1.1 +KEN/C97982/2021 27 AY.116 +USA/1780926/2021 9 AY.39 +OV019320 27 B.1.617.2 +USA/CO-CDPHE-2101290842/2021 23 AY.25 +USA/CO-CDC-FG-027338/2021 2 AY.44 +South_Africa/UW21070329826/2021 20 AY.91 +USA/CA-CDPH-3000149110/2021 27 AY.116 +England/ALDP-272641A/2021 -1 AY.4 +BRA/21899718ECS/2021 1 AY.99.2 +England/MILK-1926C6E/2021 27 AY.6 +USA/IL-CDC-ASC210035698/2021 27 B.1.617.2 +England/NORW-13F8560/2021 27 AY.4 +BRA/SP-NVBS7110GENOV828108722880/2021 -1 AY.46 +BRA/PR-NVBS5874GENOV828086932035/2021 1 AY.99.2 +USA/UT-CDC-LC0052754/2021 2 AY.44 +USA/CO-CDC-FG-034634/2021 2 AY.44 +OY558333 27 AY.4 +England/QEUH-15748F8/2021 27 AY.4 +LAO/LOMWRU-1788/2021 3 AY.1 +BHR/342314247/2021 27 B.1.617.2 +USA/IN-CDC-LC0141533/2021 24 AY.103 +USA/NY-CDC-QDX27085435/2021 2 AY.44 +BHR/342372540/2021 27 B.1.617.2 +IND/CWS_0016_47131542/2021 27 B.1.617.2 +USA/WA-CDC-UW21090828566/2021 2 AY.44 +BRA/SP-NVBS11396GENOV500278615246/2021 10 AY.34.1 +Denmark/DCGC-276130/2021 27 B.1.617.2 +USA/MN-CDC-IBX980583181908/2021 18 AY.3 +BGD/Laila_216/2021 12 B.1.617.2 +NZL/21MV0256/2021 27 B.1.617.2 +England/ALDP-1EB477E/2021 27 AY.4 +England/ALDP-174C52D/2021 27 AY.4 +OU515782 27 AY.4 +SouthAfrica/NHLS-UCT-LA-Z707/2021 4 AY.32 +SouthAfrica/NHLS-UCT-GS-I837/2021 20 AY.91 +USA/CA-CDPH-3000261185/2021 18 AY.3 +USA/CA-CDPH-3000261192/2021 23 AY.25 +England/ALDP-1A42876/2021 27 AY.4 +HongKong/HKPU-00195/2021 13 AY.23 +England/PLYM-1C15A0B/2021 25 AY.120 +OV017503 27 B.1.617.2 +LAO/LOMWRU-0947/2021 5 AY.85 +CHL/AR-UFRO-0196/2021 21 AY.43 +OX317126 27 B.1.617.2 +THA/CONI-0903/2021 5 AY.85 +KEN/C94833/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-GS-9714/2021 -1 AY.107 +USA/MI-CDC-QDX32187701/2021 24 AY.103 +NGA/CV2371/2021 6 AY.36 +LAO/LOMWRU-0462/2021 3 AY.1 +USA/1998300/2021 27 B.1.617.2 +USA/WA-UW-21041954910/2021 27 B.1.617.2 +BRA/PR-NVBS5873GENOV828101236612/2021 11 AY.101 +KEN/SS1194/2021 27 AY.46 +USA/NV-CDC-QDX28508566/2021 27 AY.20 +England/BRBR-1E24DE0/2021 27 AY.4 +GAB/7192_Gabon/2021 10 B.1.617.2 +USA/2078211_BB1L13/2021 -1 AY.25 +NGA/CV3275/2021 6 AY.36 +NZL/21MV1835/2021 8 AY.39.1.1 +SouthAfrica/NHLS-UCT-GS-C003/2021 4 AY.32 +IND/GBRC1264/2021 25 AY.120 +USA/FL-CDC-LC0139720/2021 27 AY.119 +USA/NJ-PHEL-V21035335/2021 -1 AY.103 +Scotland/QEUH-2A565C0/2021 27 AY.4 +Switzerland/SH-ETHZ-34896003/2021 27 B.1.617.2 +NGA/CV2812/2021 6 AY.36 +Japan/SZ-NIG-3-C11444/2021 16 AY.29 +USA/NY-CDC-ASC210424754/2021 23 AY.25 +OV107421 27 B.1.617.2 +SouthAfrica/NHLS-UCT-GS-AF24/2021 27 B.1.617.2 +England/LOND-13706A9/2021 27 AY.4 +HongKong/HKU-220213-211/2021 27 AY.4.2 +BRA/RJ-NXBS5123GENOV827947814084/2021 1 AY.99.2 +Japan/SZ-NIG-Y21573/2021 13 AY.23 +OV104214 -1 AY.122 +England/ALDP-2B8A225/2021 27 AY.4 +LAO/LOMWRU-1179/2021 3 AY.1 +USA/CA-OC-1710/2022 24 AY.103 +NZL/21MV0864/2021 9 AY.39.1.1 +NZL/21MV2596/2021 8 AY.39.1.1 +IND/GBRC1280/2021 25 AY.120 +USA/ALTCOV-NIZ34D4DTP6QT4DV/2021 -1 B.1.617.2 +USA/UT-UPHL-210710299852/2021 2 AY.44 +BHR/342472311/2021 -1 B.1.617.2 +BRA/SP-NVBS8189GENOV45616668244/2021 21 AY.43 +IND/GBRC726/2021 27 AY.122 +England/ALDP-157F8B1/2021 25 AY.120 +USA/GA-CDC-LC0141827/2021 -1 AY.103 +USA/GA-CDC-LC0138191/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-GP-6643/2021 4 AY.32 +NGA/CV4721/2021 6 AY.36 +LAO/LOMWRU-1143/2021 3 AY.1 +USA/CO-CDC-MMB08679857/2021 23 AY.25 +IND/NIB149780/2021 27 B.1.617.2 +England/NORW-30926B6/2021 27 AY.4 +SouthAfrica/NHLS-UCT-GP-6555/2021 4 AY.32 +SouthAfrica/NHLS-UCT-LA-Z625/2021 26 AY.45 +THA/CONI-1393/2021 5 AY.85 +OX115864 21 AY.43 +SouthAfrica/NHLS-UCT-GP-M982/2021 20 AY.91 +IND/CWS_0084_52220027/2021 27 B.1.617.2 +USA/NC-CDC-LC0078599/2021 -1 AY.103 +NZL/21MV0525/2021 27 B.1.617.2 +NZL/21MV0425/2021 14 AY.122 +KEN/C99737/2021 27 AY.116 +Japan/SZ-NIG-3-C11159/2021 16 AY.29 +Japan/SZ-NIG-3-C11059/2021 16 AY.29 +Switzerland/BE-IFIK-5610-8586/2022 27 AY.46.6 +BRA/SP-NVBS11376GENOV828509995951/2021 1 AY.99.2 +SouthAfrica/NHLS-UCT-GS-C101/2021 20 AY.91 +England/QEUH-1B259FD/2021 27 AY.4 +USA/UT-UPHL-210612642370/2021 2 AY.44 +USA/OR-UW-21072091446/2021 9 AY.39 +England/ALDP-1D983D7/2021 27 AY.98 +IND/GBRC1275/2021 27 B.1.617.2 +England/NORT-1BE9AF2/2021 27 AY.4 +Japan/SZ-NIG-3-C11713/2021 16 AY.29 +LAO/LOMWRU-1558/2021 3 AY.1 +IND/INSACOG-GBRC1622/2021 27 B.1.617.2 +BHR/921069369/2021 27 B.1.617.2 +England/BRBR-1A846BA/2021 27 AY.98 +Scotland/QEUH-15A47B6/2021 27 AY.4 +Scotland/QEUH-17C5D9D/2021 27 AY.4 +NZL/21MV1042/2021 9 AY.39.1.1 +USA/WA-S12602/2021 18 AY.3 +BRA/RJ-NVBS6187GENOV828082890933/2021 1 AY.99.2 +BRA/DF-NVBS5940GENOV828103043522/2021 1 AY.99.2 +BRA/RJ-NVBS3545GENOV827840132544/2021 1 AY.99.2 +USA/CA-CDPH-3000265066/2021 12 AY.100 +USA/UT-UPHL-220204596804/2022 12 AY.100 +SouthAfrica/NHLS-UCT-GS-I299/2021 4 AY.32 +SouthAfrica/NHLS-UCT-GS-B937/2021 -1 AY.120 +SouthAfrica/NHLS-UCT-GS-AD22/2021 26 AY.45 +USA/CO-CDC-MMB08964531/2021 23 AY.25 +England/ALDP-154D791/2021 27 AY.4 +England/PHEC-30AE09/2021 27 B.1.617.2 +USA/CA-LACPHL-AF04823/2021 2 AY.44 +Northern_Ireland/NIRE-008d27/2021 27 AY.4 +BHR/21922022597_S29_L001/2021 27 B.1.617.2 +USA/MN-CDC-ASC210362440/2021 24 AY.103 +OU937022 27 AY.122 +OU932144 21 AY.43 +DJI/NAMRU3_E932/2021 25 AY.120 +LAO/LOMWRU-1391/2021 3 AY.1 +England/NEWC-202C6AC/2021 27 AY.4 +NGA/CV2364/2021 6 AY.36 +Denmark/DCGC-230595/2021 27 AY.122 +OU266496 14 AY.122 +USA/CO-CDC-ASC210719057/2021 -1 AY.39 +OV103742 -1 B.1.617.2 +England/MILK-152462A/2021 27 AY.6 +OV103611 21 AY.43 +OV103774 -1 B.1.617.2 +NZL/21MV0651/2021 21 AY.43 +BHR/21342685363/2021 -1 B.1.617.2 +BHR/21921943599_S68_L001/2021 21 AY.43 +DJI/NAMRU3_E302/2021 -1 AY.127 +England/MILK-16646B4/2021 27 AY.5 +CHL/AR-UFRO-0462/2021 21 AY.43 +Denmark/DCGC-146141/2021 27 AY.122 +SouthAfrica/NHLS-UCT-GS-AE66/2021 4 AY.32 +SouthAfrica/NHLS-UCT-AM-Z020/2021 4 AY.32 +England/ALDP-15F0E01/2021 27 AY.4 +IND/CWS_0012_49330960/2021 27 B.1.617.2 +IND/CWS_0077_55316183/2021 27 B.1.617.2 +USA/UT-UPHL-210723596488/2021 2 AY.44 +Northern_Ireland/NIRE-01333f/2021 27 AY.4.2 +USA/IL-CDC-ASC210638202/2021 -1 AY.39 +Japan/SZ-NIG-3-C11430/2021 16 AY.29 +USA/UT-UPHL-220107540011/2021 23 AY.25.1 +IND/hospital_2_324/2021 27 B.1.617.2 +IND/GBRC1291/2021 27 B.1.617.2 +IND/GBRC1235/2021 27 B.1.617.2 +England/ALDP-1578214/2021 27 AY.4 +England/ALDP-15D1A99/2021 27 AY.4 +England/MILK-17A9E14/2021 -1 B.1.617.2 +USA/OH-CDC-LC0396211/2021 -1 AY.39 +USA/MN-CDC-ASC210527555/2021 -1 AY.39 +USA/MN-CDC-IBX667917487612/2021 23 AY.25 +OV104488 21 AY.43 +England/PHEC-34E698/2021 27 AY.4 +England/MILK-1E6A470/2021 27 AY.4 +BRA/SC-NVBS11656GENOV045617307432/2021 1 AY.99.2 +BRA/RJ-NVBS3499GENOV827812865777/2021 1 AY.99.2 +SouthAfrica/NHLS-UCT-GS-B992/2021 4 AY.32 +THA/CONI-1026/2021 5 AY.85 +BHR/921228968/2021 27 B.1.617.2 +BTN/RCDC0013-SV210151/2020 27 B.1.617.2 +Scotland/QEUH-1738E1A/2021 27 AY.4 +England/MILK-17FFFEF/2021 27 AY.4 +BRA/SP-NVBS4822GENOV130639240437/2021 21 AY.43 +UGA/MUWRP-KIR210109S/2021 27 AY.46 +England/MILK-1544F29/2021 14 AY.122 +USA/CO-CDC-MMB09425171/2021 2 AY.44 +England/ALDP-1AE8AD6/2021 27 AY.4 +England/PLYM-2FDEE2A/2021 27 AY.4.2 +England/MILK-30C8F0E/2022 27 AY.4 +OY351191 27 AY.4 +ZAF/NHLS-UCT-GS-C441/2021 4 AY.32 +BRA/PR-NVBS996GENOV44905645850/2021 11 AY.101 +BRA/SP-NVBS3161GENOV701236642773/2021 1 AY.99.2 +NZL/21CH0118/2021 9 AY.39.1.1 +OY484127 27 AY.4 +NGA/CV3128/2021 6 AY.36 +USA/SC-COVID21-3352/2021 18 AY.3 +OY373549 27 AY.4 +MEX/CMX-2_274/2021 27 AY.20 +BRA/SP-NVBS6904GENOV828104303823/2021 -1 AY.46 +USA/CO-CDPHE-40849569/2021 2 AY.44 +NZL/21MV1293/2021 9 AY.39.1.1 +NZL/21CV0821/2021 8 AY.39.1.1 +USA/CO-CDC-MMB08964627/2021 23 AY.25 +NZL/21MV0352/2021 12 B.1.617.2 +SouthAfrica/NHLS-UCT-GS-B974/2021 4 AY.32 +NGA/CV4789/2021 6 AY.36 +SouthAfrica/NHLS-UCT-LA-Z628/2021 4 AY.32 +NZL/21MV1339/2021 9 AY.39.1.1 +England/MILK-2092595/2021 27 AY.4.2 +Scotland/QEUH-27C1BC1/2021 27 AY.4 +SYC/SS4697/2021 19 AY.122 +SYC/SS4654/2021 19 AY.122 +SouthAfrica/NHLS-UCT-GS-AE99/2021 4 AY.32 +USA/GA-CDC-ASC210205271/2021 24 AY.103 +BHR/921451322/2021 27 B.1.617.2 +NZL/21CV0417/2021 9 AY.39.1.1 +LAO/LOMWRU-1494/2021 5 AY.85 +NZL/21CV2651/2021 8 AY.39.1.1 +USA/GA-CDC-LC0205636/2021 23 AY.25 +KEN/C107900/2021 27 AY.116 +BRA/ILMD2101185/2021 11 AY.101 +England/NORT-YY6Z9P/2021 27 AY.4 +NGA/CV2652/2021 6 AY.36 +USA/KY-LMDC-21071800/2021 23 AY.25 +BRA/DF-NVBS9887GENOV828395315901/2021 1 AY.99.2 +BRA/RJ-NVBS9688GENOV700957368290/2021 1 AY.99.2 +BRA/RJ-NVBS9390GENOV828346957549/2021 1 AY.99.2 +BRA/PR-NVBS5666GENOV827961803675/2021 11 AY.101 +BRA/MT-NVBS6057GENOV070982350110/2021 1 AY.99.2 +BHR/21342736020/2021 -1 B.1.617.2 +England/QEUH-157752B/2021 27 AY.4 +IND/GBRC828/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-GS-D866/2021 20 AY.91 +GAB/24922-22C_Gabon/2021 10 B.1.617.2 +KEN/SS7231/2021 27 AY.46 +KEN/SS2209/2021 27 AY.46 +Pakistan/UHS2-Pak-463/2021 27 B.1.617.2 +BHR/21921908372/2021 -1 B.1.617.2 +OV020422 27 AY.20 +USA/CA-CDPH-3000281289/2021 24 AY.103 +IND/177405/2021 27 B.1.617.2 +OV103587 21 AY.43 +OV104007 -1 B.1.617.2 +BHR/21342810901_S68_L001/2021 15 AY.3 +England/MILK-2C9D76B/2021 27 AY.4.2 +BTN/RCDC0017-SV210155/2021 27 B.1.617.2 +BRA/DF-NVBS9226GENOV828214905184/2021 1 AY.99.2 +LAO/LOMWRU-1414/2021 5 AY.85 +USA/1992435/2022 24 AY.103 +USA/UT-UPHL-210603476432/2021 2 AY.44 +BRA/PR-NVBS4591GENOV827974141368/2021 11 AY.101 +Denmark/DCGC-265968/2021 27 AY.5 +NGA/CV3430/2021 6 AY.36 +NGA/CV2283/2021 6 AY.36 +USA/MN-CDC-IBX759049469323/2021 18 AY.3 +OU516489 -1 AY.43 +OV020045 27 AY.46.6 +SouthAfrica/NHLS-UCT-LA-Z569/2021 26 AY.45 +UZB/UZB-325/2021 17 AY.126 +BHR/21342805901_S40_L001/2021 27 B.1.617.2 +USA/CO-CDPHE-2103153337/2022 12 AY.100 +BRA/SP-NVBS6842GENOV828075919375/2021 11 AY.101 +BRA/RJ-NVBS8614GENOV828216058161/2021 1 AY.99.2 +BRA/RJ-NVBS5614GENOV827978550685/2021 1 AY.99.2 +NZL/21MV2033/2021 9 AY.39.1.1 +NZL/21CH0539/2021 8 AY.39.1.1 +NZL/21CH0593/2021 8 AY.39.1.1 +Scotland/QEUH-15A3C21/2021 27 AY.4 +England/MILK-1552AEB/2021 14 AY.122 +LC752097 16 AY.29 +LAO/LOMWRU-1456/2021 5 AY.85 +LAO/LOMWRU-1147/2021 3 AY.1 +USA/Mayo5427/2021 24 AY.103 +MYS/M_C15843/2021 27 B.1.617.2 +KEN/SS312/2021 27 B.1.617.2 +SYC/SS3514/2021 19 AY.122 +USA/FL-CDC-ASC210449920/2021 23 AY.25 +FRA/IHUCOVID-043594_Nova1/2021 -1 B.1.617.2 +BHR/21921666712_S46_L001/2021 27 B.1.617.2 +USA/CA-CDC-FG-145893/2021 27 B.1.617.2 +USA/CA-CDPH-3000132180/2021 2 AY.44 +NGA/CV4281/2021 6 AY.36 +NGA/CV4988/2021 6 AY.36 +BHR/21342801887_S86_L001/2021 27 AY.122 +England/ALDP-1537C04/2021 27 B.1.617.2 +OX122596 27 AY.46.6 +USA/KY-CDC-LC0193969/2021 18 AY.3 +NZL/21CV1083/2021 8 AY.39.1.1 +NZL/21CV0622/2021 9 AY.39.1.1 +NZL/21CH0206/2021 8 AY.39.1.1 +IND/GBRC785/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-AM-Z018/2021 4 AY.32 +SouthAfrica/NHLS-UCT-GS-AF03/2021 -1 AY.91 +USA/CA-CDPH-3000266961/2021 -1 AY.119 +BRA/SC-NVBS11261GENOV045617224869/2021 11 AY.101 +NZL/21MV0556/2021 27 B.1.617.2 +USA/MN-CDC-IBX128780380628/2021 23 AY.25 +BHR/21342697772_S75_L001/2021 7 AY.33 +USA/CO-CDPHE-2103139266/2021 18 AY.3 +LAO/LOMWRU-0479/2021 5 AY.85 +USA/PA-CDC-STM-000726722/2021 27 AY.4 +USA/MA-CDCBI-CRSP_TZS7YQKRFOV6MMQ2/2021 -1 B.1.617.2 +Scotland/QEUH-1E6E52E/2021 27 AY.4 +Switzerland/BE-IFIK-210906_os-89/2021 27 B.1.617.2 +England/ALDP-1EAA034/2021 27 AY.4 +LAO/LOMWRU-1556/2021 5 AY.85 +BHR/342515176_S348_L001/2021 27 B.1.617.2 +USA/MA-CDCBI-CRSP_XL5APY7FRJX2DYSB/2021 2 AY.44 +England/HSLL-1E5C4F9/2021 27 AY.4 +USA/NM-UNM-ED00397/2021 2 AY.44 +BGD/Laila_219/2021 27 B.1.617.2 +OV114052 27 AY.4 +OV111672 21 AY.43 +Japan/SZ-NIG-Y212067/2021 16 AY.29 +England/MILK-2EA3715/2021 27 AY.4.2 +USA/PA-CDC-ATM-337GFSRF2/2021 9 AY.39 +SYC/SS4682/2021 19 AY.122 +England/QEUH-18449BF/2021 27 AY.4 +NZL/21MV0720/2021 9 AY.39.1.1 +NZL/21MV0496/2021 -1 AY.46 +NZL/21MV1594/2021 9 AY.39.1.1 +NZL/21MV2049/2021 8 AY.39.1.1 +NZL/21MV2640/2021 9 AY.39.1.1 +England/PHEP-YYNF4TZ/2021 27 AY.4 +LAO/LOMWRU-0907/2021 3 AY.1 +LAO/LOMWRU-1264/2021 3 AY.1 +USA/MO-CDC-ASC210614243/2021 -1 AY.39 +JAM/202112025/2021 -1 AY.107 +OV652944 27 AY.4 +USA/WV127177/2021 2 AY.44 +USA/CO-CDC-FG-121886/2021 27 B.1.617.2 +USA/2078211/2021 -1 AY.25 +England/ALDP-154E11A/2021 27 AY.4 +BRA/DF-NVBS9049GENOV828244122353/2021 1 AY.99.2 +BRA/RJ-NVBS3346GENOV700921167171/2021 0 AY.99 +THA/MTM_01_050/2021 5 AY.85 +MEX/CHP-5_2173/2021 27 AY.20 +BRA/SP-NVBS11592GENOV828493983927/2021 21 AY.43 +BRA/PE-NVBS8325GENOV828220042538/2021 1 AY.99.2 +JPN/JP_HiroFH212c/2021 16 AY.29 +SouthAfrica/NHLS-UCT-GS-AA42/2021 26 AY.45 +BRA/RJ-NVBS3668GENOV827825030162/2021 1 AY.99.2 +USA/CO-CDPHE-2103153151/2022 2 AY.44 +KEN/SS3725/2021 27 AY.46 +USA/FL-CDC-QDX30567031/2021 23 AY.25.1 +IND/177124/2021 27 B.1.617.2 +BRA/SC-NVBS10248GENOV045616872016/2021 1 AY.99.2 +USA/MD-CDC-MMB12191405/2021 22 AY.103 +USA/KY-LMDC-21071776/2021 23 AY.25 +USA/TX-CDC-QDX24365294/2021 27 B.1.617.2 +England/ALDP-154DD71/2021 14 AY.122 +OV019325 -1 AY.43 +OY382162 27 AY.4 +BHR/921366267_S359_L001/2021 27 B.1.617.2 +OY356769 27 AY.4 +NZL/21MV1507/2021 9 AY.39.1.1 +OY520791 -1 AY.4 +BRA/MS-NVBS9622GENOV700957382685/2021 0 AY.99 +KEN/SS4388/2021 -1 AY.46 +Japan/SZ-NIG-3-C11633/2021 16 AY.29 +England/MILK-2DFD971/2021 27 AY.122 +England/LOND-1358021/2021 -1 AY.4 +USA/NY-CDC-FG-039300/2021 -1 AY.107 +THA/AFRIMS-COV8779/2021 5 AY.85 +BRA/EPI_ISL_3696684/2021 1 AY.99.2 +BRA/ILMD2100982/2021 11 AY.101 +IND/GBRC1217/2021 27 AY.122 +England/PLYM-1CAB9A3/2021 27 AY.4 +SYC/SS3420/2021 -1 AY.122 +England/NEWC-27EE4A5/2021 27 AY.4.2 +BRA/SE-NVBS11133GENOV701348990731/2021 1 AY.99.2 +BRA/RJ-NVBS6452GENOV700939817440/2021 1 AY.99.2 +BRA/MT-NVBS7114GENOV828114678102/2021 1 AY.99.2 +BRA/RJ-NVBS3708GENOV827844313185/2021 1 AY.99.2 +USA/TX-CDC-FG-124030/2021 18 AY.3 +KEN/SS954/2021 27 AY.116 +USA/FL-CDC-ASC210249203/2021 18 AY.3 +USA/TX-CDC-LC0222937/2021 2 AY.44 +England/NORW-301FB21/2021 27 AY.4 +USA/OKPHLCOV0009270/2022 -1 AY.103 +BRA/EPI_ISL_3696775/2021 1 AY.99.2 +SouthAfrica/NHLS-UCT-GS-C964/2021 26 AY.45 +South_Africa/UW21070492184/2021 26 AY.45 +BEN/MTMC_35_254/2021 27 AY.122 +BHR/342331430/2021 27 B.1.617.2 +NGA/BCVL-26830/2021 6 AY.36 +NZL/21MV1383/2021 9 AY.39.1.1 +NZL/21CV0274/2021 9 AY.39.1.1 +USA/NY-CDC-FG-136746/2021 27 B.1.617.2 +BHR/21342656627_S66_L001/2021 7 AY.33 +Scotland/QEUH-2726F28/2021 27 AY.4.2 +Switzerland/LU-UHB-43144767/2021 27 AY.46.6 +KEN/SS4097/2021 27 AY.46 +OV104373 21 AY.43 +NGA/CV2697/2021 0 AY.99 +THA/CONI-0792/2021 5 AY.85 +BRA/DF-NVBS9186GENOV828254390100/2021 1 AY.99.2 +BRA/RJ-NVBS6256GENOV828066010654/2021 1 AY.99.2 +BRA/RJ-NVBS8599GENOV828214785342/2021 1 AY.99.2 +BRA/RJ-NVBS3529GENOV827840216930/2021 1 AY.99.2 +SYC/SS1024/2021 19 AY.122 +BTN/RCDC0026-SV210164/2021 27 B.1.617.2 +BRA/ILMD2200229/2021 1 AY.99.2 +England/PHEC-3504B7/2021 27 AY.98 +USA/TX-DSHS-7507/2021 27 AY.119 +USA/TX-CDC-QDX27272181/2021 23 AY.25 +USA/NE-NCOV21-23758/2021 -1 AY.103 +BHR/920858661/2021 27 B.1.617.2 +KEN/SS11674/2021 17 AY.126 +MRT/MLT02/2021 10 AY.34.1 +BRA/DF-NVBS10798GENOV828390622615/2021 1 AY.99.2 +BRA/PB-NVBS8402GENOV701336318226/2021 1 AY.99.2 +BRA/RJ-NVBS5499GENOV700931948814/2021 1 AY.99.2 +BRA/RS-NVBS7204GENOV29783383801/2021 1 AY.99.2 +BRA/PE-NVBS4452GENOV827979462390/2021 1 AY.99.2 +BEN/528580/2021 27 B.1.617.2 +USA/OR-CDC-LC0337176/2021 -1 B.1.617.2 +BHR/21921891893/2021 -1 B.1.617.2 +NGA/CV4749/2021 6 AY.36 +Switzerland/BS-UHB-42947018/2021 27 AY.5 +NGA/CV4800/2021 27 B.1.617.2 +USA/TN-CDC-ASC210535299/2021 9 AY.39 +OV104204 21 AY.43 +SYC/SS3607/2021 27 AY.122 +USA/WA-CDC-UW21111908055/2021 -1 AY.39 +England/PLYM-2FC4917/2021 -1 AY.4.2 +KAZ/36_02/2021 27 B.1.617.2 +LAO/LOMWRU-1761/2021 3 AY.1 +SouthAfrica/NHLS-UCT-GP-N079/2021 26 AY.45 +BRA/ILMD2101341/2021 21 AY.43 +KEN/SS4919/2021 27 AY.46 +USA/TG1063431/2021 2 AY.44 +BRA/SP-NVBS10166GENOV130640652632/2021 21 AY.43 +BRA/GO-NVBS9062GENOV700800148345/2021 -1 AY.46 +BRA/RJ-NVBS3338GENOV827846636008/2021 1 AY.99.2 +OV103573 -1 B.1.617.2 +NZL/21CH0060/2021 13 AY.23 +SYC/SS2583/2021 19 AY.122 +USA/TX-CDC-LC0310937/2021 23 AY.25 +OU857892 21 AY.43 +Japan/SZ-NIG-Y211440/2021 16 AY.29 +USA/NM-UNM-ED00987/2022 12 AY.100 +USA/CO-CDPHE-2102650227/2022 24 AY.103 +OV656252 21 AY.43 +Scotland/QEUH-31D302A/2022 27 AY.4.2 +THA/AFRIMS-COV8000/2021 5 AY.85 +LAO/LOMWRU-1319/2021 3 AY.1 +USA/FL-CDC-QDX26258036/2021 27 B.1.617.2 +England/MILK-17B1866/2021 27 AY.4 +England/MILK-2BABCB7/2021 27 AY.4 +England/NORW-3165450/2022 -1 AY.127 +NZL/21MV0517/2021 -1 AY.46 +USA/AL-CDC-ASC210284864/2021 9 AY.39 +OU857714 21 AY.43 +England/NORW-306189D/2021 27 AY.46 +BHR/21922011162/2021 15 AY.3 +UZB/UZB-336/2021 17 AY.126 +USA/MN-CDC-ASC210713559/2021 9 AY.39 +BGD/Laila_41/2021 27 B.1.617.2 +IND/GBRC820/2021 27 B.1.617.2 +IND/GBRC605b/2021 27 AY.122 +THA/AFRIMS-COV8430/2021 5 AY.85 +England/MILK-30D9034/2022 27 AY.4 +OV653198 21 AY.43 +Denmark/DCGC-278360/2021 27 AY.4 +USA/MN-CDC-IBX211329159312/2021 24 AY.103 +USA/MN-CDC-ASC210532875/2021 22 AY.103 +NGA/CV3468/2021 6 AY.36 +SYC/SS3944/2021 19 AY.122 +BGD/Laila_100/2021 27 B.1.617.2 +KEN/SS4918/2021 27 AY.46 +USA/CO-CDPHE-2102573326/2022 27 AY.119 +SouthAfrica/NHLS-UCT-GS-D664/2021 4 AY.32 +GAB/7177_Gabon/2021 10 B.1.617.2 +NZL/21MV0754/2021 3 AY.1 +England/MILK-1FD3532/2021 25 AY.120 +England/ALDP-27A4BD3/2021 27 AY.4.2 +OX113378 21 AY.43 +USA/KY-GD_01768/2021 22 AY.103 +SouthAfrica/NHLS-UCT-GS-H972/2021 4 AY.32 +BHR/21921952120_S89_L001/2021 27 AY.4 +USA/NV-CDC-QDX30764943/2021 -1 AY.39 +BRA/ILMD2101097/2021 21 AY.43 +USA/TN-CDC-ASC210029984/2021 27 AY.1 +BRA/PR-NVBS5675GENOV045375655776/2021 27 AY.116 +NGA/CV3053/2021 6 AY.36 +NZL/21MV2444/2021 8 AY.39.1.1 +USA/CA-CDC-FG-029327/2021 27 B.1.617.2 +OV104025 -1 B.1.617.2 +SYC/SS4679/2021 19 AY.122 +USA/WI-CDC-LC0408919/2021 24 AY.103 +BGD/Laila_142/2021 14 AY.122 +KEN/SS4133/2021 27 AY.46 +BRA/RJ-NVBS3750GENOV807840691111/2021 1 AY.99.2 +NGA/CV3334/2021 6 AY.36 +South_Africa/UW21021798418/2021 26 AY.45 +England/LSPA-1E44C92/2021 27 AY.4 +BRA/RJ-NVBS3725GENOV827839191002/2021 1 AY.99.2 +USA/MI-CDC-ASC210457373/2021 24 AY.103 +BGD/Laila_107/2021 -1 B.1.617.2 +OV103578 21 AY.43 +BRA/ILMD2101369/2021 21 AY.43 +BRA/SP-NVBS10273GENOV045616875406/2021 1 AY.99.2 +USA/CO-CDPHE-2103164375/2022 27 AY.20 +NZL/21CV0323/2021 9 AY.39.1.1 +NGA/CV2706/2021 0 AY.99 +IND/NIB148365/2021 27 B.1.617.2 +BHR/21922063300_S7_L001/2021 15 AY.3 +Pakistan/UHS2-Pak-97/2021 27 B.1.617.2 +England/ALDP-15CD5DB/2021 27 AY.4 +NZL/21MV0439/2021 27 B.1.617.2 +NZL/21MV1384/2021 9 AY.39.1.1 +USA/NV-CDC-LC0313865/2021 27 AY.20 +USA/IN-CDC-LC0304230/2021 24 AY.103 +England/ALDP-20CEF1A/2021 27 AY.4 +USA/VA-VTVAS3-GSC30922/2022 27 AY.46 +Wales/PHWC-PYP75A/2021 27 AY.98 +OY381764 27 AY.4 +BRA/EPI_ISL_4273567/2021 6 AY.36 +KEN/SS4398/2021 27 AY.46 +OX448570 -1 B.1.617.2 +USA/UT-UPHL-210820649962/2021 2 AY.44 +BRA/ILMD2101129/2021 27 AY.119 +USA/CO-CDC-FG-030533/2021 2 AY.44 +BRA/ILMD2200165/2021 1 AY.99.2 +BRA/BA-NVBS11493GENOV045617240371/2021 1 AY.99.2 +BEN/611975/2021 27 AY.122 +USA/CA-CDC-FG-054168/2021 24 AY.103 +BRA/SP-NXBS4934GENOV821442047961/2021 1 AY.99.2 +BRA/RJ-NVBS3695GENOV807845536264/2021 1 AY.99.2 +USA/CO-CDPHE-2101112583/2021 2 AY.44 +OV385217 17 AY.126 +MEX/CMX-4_1125/2021 27 AY.20 +BHR/921385685_S196_L001/2021 27 B.1.617.2 +England/PHEC-334941/2021 25 AY.120 +USA/CA-CDC-FG-039128/2021 14 AY.122 +UGA/MUWRP-KIR210128S/2021 27 AY.46 +NZL/21CH0395/2021 8 AY.39.1.1 +OY354551 27 AY.46 +BRA/RJ-NVBS8904GENOV828243374159/2021 1 AY.99.2 +KEN/SS7249/2021 27 AY.46 +LAO/LOMWRU-1380/2021 3 AY.1 +England/PLYM-17A52C1/2021 27 AY.4 +USA/TX-DSHS-12334/2021 24 AY.103 +OV104196 21 AY.43 +OV103918 21 AY.43 +IND/GBRC614b/2021 27 AY.122 +SouthAfrica/NHLS-UCT-GP-M986/2021 20 AY.91 +USA/CT-CDC-2-5380624/2021 24 AY.103 +USA/TX-CDC-QDX31492332/2021 12 AY.100 +BGD/Laila_77/2021 27 B.1.617.2 +USA/CA-CDC-ASC210634990/2021 23 AY.25.1 +OV113566 27 AY.122 +OV104100 17 AY.126 +USA/TX-CDC-FG-041191/2021 23 AY.25 +IND/hospital_2_291/2021 27 B.1.617.2 +IND/GBRC1263/2021 27 B.1.617.2 +England/MILK-1B602FB/2021 25 AY.120 +NGA/CV2809/2021 6 AY.36 +NGA/CV3088/2021 6 AY.36 +Japan/SZ-NIG-Y211943/2021 16 AY.29 +MYS/M_C15537/2021 27 B.1.617.2 +NZL/21MV2694/2021 8 AY.39.1.1 +England/PHEC-31EDC9/2021 27 AY.4 +England/PHEC-M30AM55F/2021 27 AY.4 +England/PHEC-YYBYNZA1/2021 27 AY.4 +England/PHEC-Y308Y041/2021 27 AY.4 +USA/NC-CDC-LC0260468/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-GS-E175/2021 26 AY.45 +OY324690 -1 AY.4.2 +ZAF/NHLS-UCT-GS-C205/2021 4 AY.32 +Denmark/DCGC-257785/2021 27 AY.122 +NZL/21MV2275/2021 8 AY.39.1.1 +NZL/21CH0801/2021 8 AY.39.1.1 +USA/CO-CDPHE-2103164247/2022 12 AY.100 +BRA/SP-NVBS11710GENOV828538410678/2021 11 AY.101 +BRA/RJ-NVBS8695GENOV828222366724/2021 1 AY.99.2 +BRA/SP-NVBS8046GENOV828209335293/2021 1 AY.99.2 +USA/NE-TESTNE_A1KUW3K/2021 9 AY.39 +NZL/21MV0485/2021 -1 AY.107 +IND/544MN908947.3/2021 -1 B.1.617.2 +BHR/21342703575/2021 7 AY.33 +Switzerland/ZH-ETHZ-34696348/2021 17 AY.126 +England/MILK-2BAF4CA/2021 21 AY.43 +NZL/21MV0617/2021 27 AY.4 +LAO/LOMWRU-1614/2021 3 AY.1 +KEN/C101699/2021 27 AY.116 +England/NEWC-1B36443/2021 27 AY.4 +USA/MA-CDCBI-CRSP_YFUCKPY6HZQYXR7O/2021 18 AY.3 +Japan/SZ-NIG-Y21733/2021 16 AY.29 +OV110675 27 AY.4 +THA/CONI-0909/2021 5 AY.85 +Switzerland/BS-UHB-43238627/2021 -1 B.1.617.2 +USA/WA-UW-21042294873/2021 27 AY.122 +USA/WA-UW-21060924846/2021 27 AY.122 +UGA/MUWRP-KIR210154S/2021 27 AY.46 +VNM/OUCRU-NHTD352/2021 27 AY.6 +England/NEWC-1DA1432/2021 27 AY.4 +USA/MI-MDHHS-SC33350/2021 24 AY.103 +SYC/SS3935/2021 19 AY.122 +OY371882 27 AY.98 +DJI/NAMRU3_A459/2021 15 AY.3 +COL/SEC-1542H/2021 23 AY.25.1 +Wales/PHWC-PYPETB/2021 27 AY.4 +England/PHWC-PYSPKA/2021 27 AY.4 +OV104478 21 AY.43 +SouthAfrica/NHLS-UCT-GS-C732/2021 4 AY.32 +SouthAfrica/NHLS-UCT-GS-AE80/2021 26 AY.45 +IND/GBRC806a/2021 -1 B.1.617.2 +BHR/21921957746_S13_L001/2021 -1 AY.4 +England/MILK-29B1755/2021 27 AY.4 +England/HSLL-15BA999/2021 27 AY.5 +BGD/icddrb-CMOSH-CU-2552588/2021 27 B.1.617.2 +BRA/SP-NVBS11685GENOV828516649984/2021 21 AY.43 +USA/TX-CDC-ASC210235203/2021 12 AY.100 +England/ALDP-1D32AE9/2020 27 AY.4 +England/ALDP-1C7DA10/2021 27 AY.4 +England/QEUH-1C2B8AE/2021 27 AY.5 +NZL/21CH0256/2021 8 AY.39.1.1 +BHR/342182425/2021 27 B.1.617.2 +BRA/DF-NVBS9089GENOV070984991809/2021 1 AY.99.2 +BRA/DF-NVBS6039GENOV828100253702/2021 1 AY.99.2 +FRA/IHUCOVID-057745_Nova1/2022 27 AY.122 +OV111674 21 AY.43 +England/ALDP-194A3E7/2021 27 AY.4 +NGA/CV2915/2021 6 AY.36 +NGA/CV3042/2021 27 B.1.617.2 +IND/NIB148287/2021 27 B.1.617.2 +NZL/21CH0229/2021 8 AY.39.1.1 +IND/GBRC780/2021 14 AY.122 +BRA/21895821JCS/2021 1 AY.99.2 +BRA/SP-NVBS7062GENOV701259967853/2021 10 AY.34.1 +USA/UT-UPHL-210612896933/2021 2 AY.44 +LAO/LOMWRU-1363/2021 3 AY.1 +BTN/RCDC0019-SV210157/2021 27 B.1.617.2 +USA/MN-MDH-20650/2022 24 AY.103 +USA/CT-1154/2021 18 AY.3 +NZL/21CV0788/2021 8 AY.39.1.1 +USA/FL-CDC-2-5313842/2021 24 AY.103 +KEN/SS4381/2021 27 AY.46 +England/ALDP-30B86C0/2022 27 AY.4.2 +England/PLYM-15B9262/2021 27 AY.4 +IND/CWS_0056_55110146/2021 27 B.1.617.2 +USA/VA-Noblis-S558B57/2021 27 B.1.617.2 +OV331715 -1 AY.122 +BRA/EPI_ISL_8890097/2021 1 AY.99.2 +England/PHEC-30F51E/2021 27 AY.4 +IND/NIB148355/2021 14 AY.122 +BHR/21922020691_S46_L001/2021 27 B.1.617.2 +OV104015 27 B.1.617.2 +BRA/RJ-NVBS6514GENOV700939719454/2021 1 AY.99.2 +BRA/RJ-NVBS3676GENOV827851781519/2021 1 AY.99.2 +OV104436 -1 AY.122 +CHL/AR-UFRO-0344/2021 21 AY.43 +SouthAfrica/NHLS-UCT-GS-C018/2021 -1 AY.120 +SouthAfrica/NHLS-UCT-GS-C505/2021 0 AY.99 +IND/GBRC841/2021 27 B.1.617.2 +USA/ALTCOV-QPWIDVZ43LCNIOQX/2021 22 AY.103 +USA/JW1728/2021 9 AY.39 +USA/MN-UMGC-4326/2021 18 AY.3 +NZL/21MV0600/2021 -1 B.1.617.2 +NZL/21MV1670/2021 9 AY.39.1.1 +SYC/SS468/2021 27 AY.122 +Switzerland/LU-ETHZ-671076/2021 27 B.1.617.2 +England/NEWC-2720DBB/2021 27 AY.4 +KEN/SS10882/2021 27 AY.46 +USA/WA-UW-2021041224321/2021 27 B.1.617.2 +NZL/21CH0056/2021 13 AY.23 +England/ALDP-1EAEBB7/2021 27 AY.4 +SouthAfrica/NHLS-UCT-GP-K533/2021 27 AY.6 +USA/TX-CDC-QDX25930634/2021 23 AY.25 +Denmark/DCGC-280363/2021 27 B.1.617.2 +England/ALDP-28FD712/2021 27 AY.4 +LC646473 27 B.1.617.2 +CHL/AR-UFRO-0411/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-GS-E173/2021 4 AY.32 +GAB/7283L_Gabon/2021 10 B.1.617.2 +USA/OKPHLCOV0001609/2021 27 AY.122 +MNG/10011935/2021 17 AY.126 +BGD/Laila_131/2021 -1 B.1.617.2 +SouthAfrica/NHLS-UCT-GP-N004/2021 26 AY.45 +USA/AZ-CDC-STM-TEQZ6DHNZ/2021 12 AY.100 +OV019324 21 AY.43 +SouthAfrica/NHLS-UCT-GP-M995/2021 26 AY.45 +IND/GBRC808b/2021 -1 AY.122 +OV020066 27 AY.4 +NZL/21CV0539/2021 9 AY.39.1.1 +KEN/C98728/2021 27 AY.116 +BHR/21922066020_S10_L001/2021 15 AY.3 +OV104415 21 AY.43 +IND/GBRC1267/2021 27 B.1.617.2 +England/NORW-30A0375/2021 27 AY.4 +USA/CT-1142/2021 -1 B.1.617.2 +England/MILK-2975508/2021 21 AY.43 +USA/GA-CDC-QDX25988512/2021 18 AY.3 +OY641911 27 AY.122 +THA/CONI-1404/2021 5 AY.85 +NGA/CV3451/2021 6 AY.36 +England/BRBR-1BD2388/2021 27 AY.4 +Denmark/DCGC-139368/2021 -1 AY.98 +USA/MN-UMGC-8982/2021 23 AY.25 +BRA/SP-NVBS8184GENOV828254959468/2021 -1 AY.46 +BRA/RJ-NVBS8941GENOV700949860559/2021 -1 B.1.617.2 +BRA/PR-NVBS8492GENOV828245431614/2021 11 AY.101 +NGA/CV2663/2021 27 B.1.617.2 +OV020060 27 AY.4 +NZL/21MV0591/2021 1 AY.99.2 +NZL/21MV1458/2021 21 AY.43 +KEN/C101335/2021 27 AY.116 +England/NEWC-2729532/2021 -1 AY.98 +BRA/SP-NVBS7637GENOV828215713863/2021 1 AY.99.2 +OV103954 21 AY.43 +USA/MA-CDCBI-CRSP_E5GTW3OQF36KD2BQ/2021 27 AY.20 +England/NORW-309F9F0/2021 27 AY.4 +OV104104 21 AY.43 +SouthAfrica/NHLS-UCT-GS-AE96/2021 4 AY.32 +USA/CA-LACPHL-AF09230/2022 24 AY.103 +UZB/hCoV-19-Uzb-CGB-43/2021 27 AY.122 +BRA/SP-NVBS10225GENOV828345031448/2021 1 AY.99.2 +BHR/21024243002/2021 -1 AY.4 +BGD/Laila_76/2021 27 AY.127 +NZL/21CH0057/2021 13 AY.23 +NZL/21MV0519/2021 27 B.1.617.2 +Switzerland/SG-ETHZ-673703/2022 21 AY.43 +BRA/RN-NVBS11454GENOV045952881277/2021 10 AY.34.1 +BRA/RJ-NVBS5586GENOV700932232400/2021 1 AY.99.2 +BRA/SP-NVBS3305GENOV827846888872/2021 11 AY.101 +NZL/21MV0570/2021 27 AY.122 +NZL/21MV0942/2021 9 AY.39.1.1 +THA/AFRIMS-COV4251/2021 5 AY.85 +NGA/CV2909/2021 6 AY.36 +USA/DE-CDC-LC0195911/2021 22 AY.103 +England/PLYM-30AD3D6/2022 27 AY.46 +NZL/21MV0629/2021 -1 B.1.617.2 +NZL/21CV0566/2021 9 AY.39.1.1 +OY546743 27 AY.4 +Scotland/QEUH-1A5F5CA/2021 27 AY.4 +USA/TN-SPHL-0541/2021 18 AY.3 +NZL/21CV0666/2021 8 AY.39.1.1 +NZL/21CV2208/2021 8 AY.39.1.1 +USA/IN-CDC-LC0427107/2021 24 AY.103 +OY453713 -1 AY.4 +BHR/21922070702_S15_L001/2021 27 B.1.617.2 +SYC/SS4714/2021 19 AY.122 +KEN/SS4311/2021 27 AY.116 +England/MILK-2E4535D/2021 27 AY.122 +England/ALDP-2FC27E2/2021 27 AY.4 +BHR/21922010797/2021 15 AY.3 +USA/VA-DCLS-11192/2021 12 AY.100 +BTN/RCDC0029-SV210167/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-GS-C745/2021 4 AY.32 +NZL/21MV3020/2021 8 AY.39.1.1 +NZL/21MV2604/2021 8 AY.39.1.1 +NZL/21CV0600/2021 9 AY.39.1.1 +England/ALDP-152D797/2021 27 AY.4 +England/ALDP-15345DF/2021 27 AY.4 +England/ALDP-15EFA6B/2021 27 AY.4 +USA/NY-CDCBI-CRSP_DIJLMNTYPK7Z3WRF/2021 -1 B.1.617.2 +USA/MA-CDC-LC0466729/2022 18 AY.3 +USA/MP-CDC-2-5374628/2021 23 AY.25 +NGA/CV2654/2021 6 AY.36 +Japan/SZ-NIG-Y211373/2021 10 AY.34.1 +England/HSLL-17C246E/2021 27 B.1.617.2 +BRA/SP-NVBS11847GENOV828505220644/2021 1 AY.99.2 +BRA/PR-NVBS9998GENOV045388421528/2021 11 AY.101 +USA/CA-CDPH-3000265759/2021 -1 AY.119 +SouthAfrica/NHLS-UCT-GP-6638/2021 4 AY.32 +SouthAfrica/NHLS-UCT-GP-6592/2021 27 AY.6 +OY500306 27 AY.4.2 +USA/NV-NSPHL-LV377290/2021 2 AY.44 +IND/CWS_0020_47813148/2021 27 B.1.617.2 +England/ALDP-18B1452/2021 27 AY.4 +NGA/CV2598/2021 6 AY.36 +KAZ/63_02/2021 27 AY.122 +NZL/21CH0440/2021 -1 AY.39.1.1 +FRA/IHUCOVID-056678_Nova2/2021 -1 AY.4.2 +USA/MA-CDCBI-CRSP_NBBQDVTKS3PUAHYG/2021 18 AY.3 +BHR/921092988/2021 27 B.1.617.2 +England/ALDP-17CCA53/2021 27 AY.4 +England/ALDP-15CC1BA/2021 27 AY.4 +USA/CO-CDC-MMB09226346/2021 2 AY.44 +USA/CO-CDC-MMB11463387/2021 24 AY.103 +OV104408 -1 AY.4 +OV240665 27 AY.122 +NZL/21CV3009/2021 9 AY.39.1.1 +IND/177961/2021 14 AY.122 +OV103966 17 AY.126 +VNM/OUCRU-NHTD231/2021 27 B.1.617.2 +NZL/21MV2813/2021 8 AY.39.1.1 +NZL/21MV0313/2021 27 B.1.617.2 +USA/MN-CDC-IBX245583909121/2021 24 AY.103 +England/ALDP-208E5C9/2021 27 AY.6 +NZL/21MV1684/2021 9 AY.39.1.1 +England/MILK-2D9E365/2021 27 AY.4.2 +OV665686 21 AY.43 +USA/MS-CDC-LC0082458/2021 18 AY.3 +IND/GBRC809/2021 27 AY.122 +BRA/RJ-NVBS8663GENOV700948755436/2021 0 AY.99 +USA/MN-CDC-IBX411845989336/2021 18 AY.3 +COM/SS3800/2021 27 B.1.617.2 +USA/KY-GD_00290/2021 18 AY.3 +OV017673 17 AY.126 +England/NORT-1BF4BE2/2021 27 AY.4 +England/ALDP-17CAB61/2021 25 AY.120 +USA/NJ-PHEL-V21014787/2021 -1 AY.103 +BHR/21922082495_S30_L001/2021 15 AY.3 +England/ALDP-2AD8335/2021 27 AY.4 +BHR/21921810873/2021 -1 B.1.617.2 +SouthAfrica/NHLS-UCT-GP-6556/2021 4 AY.32 +SouthAfrica/NHLS-UCT-GS-B912/2021 -1 AY.120 +BGD/Laila_220/2021 14 AY.122 +KEN/SS4145/2021 27 B.1.617.2 +OV104094 21 AY.43 +USA/CO-CDPHE-40849573/2021 2 AY.44 +USA/NM-CDC-ASC210154710/2021 27 AY.46 +USA/2006267/2021 24 AY.103 +IND/hospital_2_304/2021 27 B.1.617.2 +THA/MTM_01_005/2021 5 AY.85 +England/ALDP-1DC0A4A/2021 27 AY.4 +USA/FL-CDC-STM-000711604/2021 9 AY.39 +USA/NJ-PHEL-V21029122/2021 23 AY.25 +USA/PA-CDC-ASC210360725/2021 22 AY.103 +BRA/PR-NVBS7590GENOV828218833315/2021 1 AY.99.2 +BRA/RJ-NVBS9462GENOV828389971830/2021 1 AY.99.2 +BRA/RJ-NVBS6531GENOV828113790881/2021 1 AY.99.2 +BRA/RJ-NVBS10150GENOV701288802316/2021 10 AY.34.1 +BGD/B_210627_203.fasta/2021 27 B.1.617.2 +BRA/PR-NVBS5665GENOV045375179166/2021 11 AY.101 +USA/NV-CDC-QDX25762876/2021 2 AY.44 +USA/NV-CDC-LC0044049/2021 14 AY.122 +IND/hospital_2_307/2021 27 B.1.617.2 +USA/MI-CDC-ASC210480980/2021 24 AY.103 +OV104553 -1 B.1.617.2 +USA/WA-UW-21042185581/2021 27 B.1.617.2 +LAO/LOMWRU-1493/2021 3 AY.1 +USA/MD-CDC-ASC210032991/2021 27 B.1.617.2 +HongKong/HKU-220213-201/2021 21 AY.43 +USA/CA-CDPH-500024963/2021 24 AY.103 +USA/FL-CDC-QDX32535094/2022 24 AY.103 +England/NORT-YYS1XD/2020 27 AY.4 +BRA/21893644FMN/2021 1 AY.99.2 +NZL/21MV0618/2021 27 B.1.617.2 +BHR/T095319700_S41_L001/2021 27 B.1.617.2 +BRA/SP-NVBS6681GENOV828071538808/2021 1 AY.99.2 +SouthAfrica/NHLS-UCT-GS-AC33/2021 4 AY.32 +USA/FL-CDC-ASC210203833/2021 2 AY.44 +OU857626 21 AY.43 +Japan/SZ-NIG-Y211380/2021 16 AY.29 +NZL/21MV0631/2021 23 AY.25.1 +NZL/21MV0555/2021 27 B.1.617.2 +NZL/21CV0312/2021 9 AY.39.1.1 +KEN/C109666/2021 27 B.1.617.2 +England/MILK-1FB3556/2021 27 AY.6 +OY686619 27 AY.4.2 +IND/GBRC787/2021 27 B.1.617.2 +England/ALDP-16681A0/2021 27 AY.4 +USA/AR-UNM-ACHV00314/2021 2 AY.44 +USA/JW4103/2022 23 AY.25 +MNG/202107040/2021 -1 AY.107 +Wales/MILK-2CD7273/2021 10 AY.34.1 +KEN/SS308/2021 27 B.1.617.2 +BRA/DF-NVBS9927GENOV828344970946/2021 1 AY.99.2 +Japan/SZ-NIG-3-C12683/2021 16 AY.29 +USA/WV128607/2022 27 AY.46 +BHR/21922081976_S31_L001/2021 15 AY.3 +BGD/Laila_25/2021 27 B.1.617.2 +BGD/Laila_7/2021 27 B.1.617.2 +OV103988 27 AY.4 +Japan/SZ-NIG-3-C12446/2021 16 AY.29 +Japan/SZ-NIG-212700/2021 16 AY.29 +England/ALDP-2D6FCAE/2021 27 AY.4.2 +England/PHEC-30AEFA/2021 27 B.1.617.2 +THA/MTM_01_002/2021 5 AY.85 +IND/GBRC712b/2021 27 AY.122 +England/NORW-13F67E4/2021 27 AY.4 +FRA/IHUCOVID-057748_Nova1/2022 21 AY.43 +SouthAfrica/NHLS-UCT-LA-Z736/2021 27 AY.122 +SouthAfrica/NHLS-UCT-GS-D626/2021 26 AY.45 +NGA/CV4725/2021 6 AY.36 +KEN/C103163/2021 27 AY.116 +USA/FL-CDC-ASC210117175/2021 2 AY.44 +MNG/202107044/2021 -1 AY.107 +BRA/SP-NVBS8090GENOV828254969603/2021 21 AY.43 +BRA/PR-NVBS5864GENOV828111066735/2021 11 AY.101 +USA/CA-MCPHL-MC02743/2021 18 AY.3 +USA/WI-CDC-ASC210656631/2021 12 AY.100 +SYC/SS3937/2021 19 AY.122 +BHR/21400264073_S82_L001/2021 27 AY.4 +BGD/Laila_295/2021 27 B.1.617.2 +OY607800 27 AY.4 +England/MILK-1CD5919/2021 27 AY.4 +USA/CO-CDC-MMB09001774/2021 2 AY.44 +NZL/21MV0560/2021 27 AY.4 +NZL/21CV0573/2021 9 AY.39.1.1 +NZL/21MV1286/2021 9 AY.39.1.1 +BRA/BA-NVBS6227GENOV828102166994/2021 1 AY.99.2 +BRA/SP-NVBS4788GENOV827960809135/2021 1 AY.99.2 +KEN/SS4157/2021 -1 AY.46 +USA/NJ-PHEL-V21035431/2021 24 AY.103 +England/MILK-2C1F37C/2021 27 AY.4 +KEN/SS4308/2021 27 AY.116 +MNG/202107050/2021 27 AY.122 +England/MILK-2D4C9BF/2021 -1 AY.4 +SYC/SS3980/2021 19 AY.122 +OV107470 -1 AY.4 +USA/MD-CDC-ASC210237008/2021 27 AY.122 +EGY/CCHE57357_W4_A035/2021 27 B.1.617.2 +BRA/SP-NVBS11411GENOV828511457423/2021 1 AY.99.2 +BRA/SP-NVBS10418GENOV828373800160/2021 1 AY.99.2 +BRA/RJ-NVBS6402GENOV828065310106/2021 1 AY.99.2 +BRA/RS-NVBS7215GENOV67970515101/2021 1 AY.99.2 +SYC/SS3549/2021 19 AY.122 +Wales/MILK-27FC40E/2021 -1 AY.4 +THA/CONI-1153/2021 5 AY.85 +THA/CONI-1071/2021 5 AY.85 +OW046953 21 AY.43 +NZL/21CH0291/2021 8 AY.39.1.1 +USA/OH-CDC-LC0054844/2021 27 B.1.617.2 +USA/NE-NCOV21-22900/2021 24 AY.103 +England/PHEP-YYNWZJC/2021 27 AY.4 +England/PHEC-U308U445/2021 27 B.1.617.2 +USA/CA-CDPH-1002012115/2020 2 AY.44 +USA/WI-CDC-ASC210067150/2021 23 AY.25 +LAO/LOMWRU-1483/2021 5 AY.85 +NZL/21CH0080/2021 27 AY.5 +SYC/SS2504/2021 19 AY.122 +LAO/LOMWRU-1692/2021 5 AY.85 +Northern_Ireland/NIRE-00447e/2021 27 AY.4 +USA/IL-CDC-LC0162545/2021 24 AY.103 +KAZ/37_02/2021 27 AY.122 +NGA/CV2543/2021 6 AY.36 +KEN/SS4406/2021 27 AY.46 +OY629193 27 AY.4 +LAO/LOMWRU-0987/2021 3 AY.1 +LAO/LOMWRU-1531/2021 5 AY.85 +OV104441 21 AY.43 +OV104417 -1 B.1.617.2 +OV103623 27 B.1.617.2 +BHR/21921891910/2021 -1 B.1.617.2 +OV017671 17 AY.126 +USA/CA-CDPH-3000112495/2021 24 AY.103 +DJI/NAMRU3_E445/2021 -1 AY.127 +IND/hospital_2_293/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-GS-C744/2021 20 AY.91 +BHR/33_S33_L001/2021 7 AY.33 +England/QEUH-2EB6D1D/2021 21 AY.43 +KEN/SS4150/2021 27 AY.46 +USA/MI-CDC-ASC210453221/2021 23 AY.25 +OV103962 21 AY.43 +USA/CO-CDC-FG-030342/2021 2 AY.44 +BRA/PR-NVBS7542GENOV828232402245/2021 11 AY.101 +NZL/21MV2687/2021 8 AY.39.1.1 +USA/WI-CDC-IBX351320921173/2021 27 B.1.617.2 +IND/RGCB-LMMD-5/2020 27 B.1.617.2 +SouthAfrica/NHLS-UCT-GS-C464/2021 26 AY.45 +USA/CA-CDC-FG-090772/2021 2 AY.44 +KEN/SS941/2021 27 AY.116 +USA/NY-CDC-FG-096646/2021 18 AY.3 +Switzerland/TI-EOC-26098876/2021 27 B.1.617.2 +Pakistan/UHS2-Pak-362/2021 27 B.1.617.2 +USA/CO-CDC-MMB11411301/2021 -1 AY.103 +IND/GBRC1211/2021 27 B.1.617.2 +USA/MN-CDC-STM-000064330/2021 27 B.1.617.2 +NZL/21MV2089/2021 9 AY.39.1.1 +Scotland/QEUH-15CF339/2021 27 AY.4 +BTN/RCDC0023-SV210161/2021 27 B.1.617.2 +OY386082 27 B.1.617.2 +FRA/IHUCOVID-043067_Nova1/2021 21 AY.43 +IND/GBRC1219/2021 27 B.1.617.2 +NGA/CV2507/2021 6 AY.36 +BRA/RJ-NVBS8701GENOV828259155735/2021 1 AY.99.2 +OY543624 27 AY.4 +ZAF/NHLS-UCT-GP-N266/2021 20 AY.91 +USA/2003356/2021 18 AY.3 +USA/MN-CDC-IBX119954553086/2021 23 AY.25.1 +BGD/Laila_694/2022 27 B.1.617.2 +OV518446 21 AY.43 +England/ALDP-279318A/2021 27 AY.4 +USA/CO-CDPHE-40849550/2021 2 AY.44 +OV653534 27 AY.4 +FRA/IHUCOVID-054540-Nova1M/2021 27 B.1.617.2 +USA/CA-CDPH-3000252964/2021 27 AY.20 +BHR/21921779003_S16_L001/2021 27 AY.4 +BRA/RJ-NVBS9708GENOV828356793922/2021 21 AY.43 +NZL/21CH0455/2021 8 AY.39.1.1 +NZL/21MV0607/2021 27 AY.46 +NZL/21CH0069/2021 13 AY.23 +KEN/SS2410/2021 -1 AY.46 +England/ALDP-1553BD8/2021 27 AY.4 +England/ALDP-15697CC/2021 14 AY.122 +NZL/21MV2716/2021 9 AY.39.1.1 +NZL/21KV0765/2021 8 AY.39.1.1 +NZL/21CV3348/2021 9 AY.39.1.1 +OX112123 -1 AY.122 +IND/CWS_0015_49899483/2021 27 B.1.617.2 +Scotland/QEUH-1793CF5/2021 27 AY.4 +England/NEWC-1F0625D/2021 27 AY.4 +BGD/Laila_36/2021 14 AY.122 +OV242550 27 AY.46.6 +BGD/Laila_102/2021 14 AY.122 +OV103952 27 AY.4 +OV239694 27 AY.122 +OV302139 21 AY.43 +England/ALDP-15C0848/2021 27 AY.4 +NZL/21CV0221/2021 13 AY.23 +NZL/21CV0254/2021 9 AY.39.1.1 +USA/UT-UPHL-211016608777/2021 2 AY.44 +NZL/21CH0063/2021 13 AY.23 +NZL/21MV1391/2021 9 AY.39.1.1 +USA/SEARCH-100752/2021 27 B.1.617.2 +Japan/SZ-NIG-213462/2021 16 AY.29 +England/MILK-1C447B1/2021 27 AY.4 +USA/AR-UNM-UAMS112MD115/2021 2 AY.44 +SouthAfrica/NHLS-UCT-AM-Z032/2021 4 AY.32 +SouthAfrica/NHLS-UCT-LA-Z721/2021 27 AY.6 +USA/SRL_331883056/2022 18 AY.3 +England/ALDP-2AC4985/2021 27 AY.4 +SouthAfrica/NHLS-UCT-GS-C782/2021 26 AY.45 +SouthAfrica/NHLS-UCT-GS-C775/2021 26 AY.45 +USA/MO-CDC-QDX25806316/2021 18 AY.3 +USA/NJ-CDC-LC0206567/2021 24 AY.103 +USA/UT-CDC-QDX26380700/2021 2 AY.44 +Pakistan/UHS2-Pak-140/2021 27 B.1.617.2 +NZL/21MV0660/2021 27 B.1.617.2 +THA/AFRIMS-COV7471/2021 5 AY.85 +USA/OH-CDC-QDX28508736/2021 18 AY.3 +England/MILK-1C51EE9/2021 27 AY.6 +England/PLYM-1A03D18/2021 27 AY.4 +OY353171 27 AY.4 +SYC/SS4681/2021 19 AY.122 +England/MILK-2D8F200/2021 27 AY.4 +OV665150 21 AY.43 +NZL/21MV2282/2021 8 AY.39.1.1 +USA/CA-CDPH-6000005879/2021 27 AY.119 +England/BRBR-1D03814/2021 25 AY.120 +Japan/SZ-NIG-3-C11829/2021 16 AY.29 +USA/CO-CDPHE-2103125316/2022 24 AY.103 +BRA/SP-NVBS8113GENOV828232321645/2021 1 AY.99.2 +Japan/SZ-NIG-Y211119/2021 16 AY.29 +OV657751 27 AY.122 +NZL/21MV1938/2021 8 AY.39.1.1 +NZL/21CV3349/2021 9 AY.39.1.1 +NZL/21CV2240/2021 8 AY.39.1.1 +LAO/LOMWRU-1656/2021 3 AY.1 +BRA/PR-NVBS3811GENOV827827149497/2021 11 AY.101 +USA/UT-CDC-LC0073752/2021 2 AY.44 +IND/hospital_3_251/2021 27 B.1.617.2 +SGP/SNDE2/2021 13 AY.23 +UZB/UZB-370/2021 27 AY.122 +OV111693 27 B.1.617.2 +LAO/LOMWRU-1220/2021 3 AY.1 +NZL/21MV0515/2021 27 B.1.617.2 +KEN/C108336/2021 27 AY.116 +USA/TN-CDC-ASC210328737/2021 18 AY.3 +NZL/21CH0068/2021 13 AY.23 +NZL/21MV1445/2021 9 AY.39.1.1 +NZL/21CV0565/2021 9 AY.39.1.1 +USA/GA-CDC-LC0241154/2021 23 AY.25.1 +England/BRBR-1C17A09/2021 27 AY.4 +NZL/21MV0581/2021 27 B.1.617.2 +NZL/21CH0040/2021 13 AY.23 +USA/NC-CDC-LC0278617/2021 27 B.1.617.2 +USA/FL-CDC-STM-000726582/2021 27 AY.119 +BHR/21921940348_S54_L001/2021 7 B.1.617.2 +DJI/NAMRU3_E775/2021 -1 AY.127 +BHR/342527227/2021 27 B.1.617.2 +USA/UT-UPHL-210721516375/2021 2 AY.44 +England/HSLL-191640F/2021 27 AY.4 +OU398601 20 AY.91 +SouthAfrica/NHLS-UCT-LA-Z551/2021 4 AY.32 +Denmark/DCGC-124549/2021 -1 B.1.617.2 +USA/FL-CDC-ASC210105985/2021 18 AY.3 +England/ALDP-154FF6A/2021 27 AY.4 +USA/CA-LACPHL-AF04681/2021 9 AY.39 +Northern_Ireland/NIRE-00ce37/2021 27 AY.4 +BRA/ILMD2200059/2021 27 B.1.617.2 +USA/KY-LMDC-21072134/2021 2 AY.44 +NZL/21MV1801/2021 8 AY.39.1.1 +FRA/IHUCOVID-059959_Nova1/2020 21 AY.43 +NZL/21CV0295/2021 9 AY.39.1.1 +OU857887 21 AY.43 +BRA/RJ-NVBS3512GENOV700922220486/2021 1 AY.99.2 +BRA/DF-NVBS3949GENOV827795260514/2021 1 AY.99.2 +SouthAfrica/NHLS-UCT-GS-E799/2021 26 AY.45 +DJI/NAMRU3_H271_2021/2021 17 AY.126 +USA/NMDOH-2021198917/2021 24 AY.103 +USA/NV-CDC-QDX26215481/2021 2 AY.44 +OV103956 27 AY.46.6 +England/ALDP-1543E4B/2021 27 AY.4 +England/RAND-14FD46D/2021 27 AY.122 +USA/CO-CDC-MMB08780436/2021 2 AY.44 +England/ALDP-152D885/2021 27 AY.4 +USA/OKPHL0027294/2022 24 AY.103 +FRA/IHUCOVID-047042-Nova1M/2020 27 B.1.617.2 +BHR/21921841119_S36_L001/2021 7 AY.33 +USA/TX-CDC-FG-020403/2021 27 B.1.617.2 +KAZ/56_02/2021 27 AY.122 +NZL/21MV2810/2021 8 AY.39.1.1 +USA/CA-CDC-FG-050007/2021 18 AY.3 +BHR/342391861/2021 27 B.1.617.2 +USA/NY-CDC-LC0165209/2021 2 AY.44 +England/CAMC-141DB08/2021 27 B.1.617.2 +NZL/21CH0270/2021 8 AY.39.1.1 +KAZ/60_02/2021 27 AY.122 +USA/CA-CDC-FG-191203/2021 -1 AY.39 +BGD/Laila_4/2021 14 AY.122 +USA/OH-CDC-LC0427178/2021 23 AY.25 +NZL/21MV0652/2021 -1 B.1.617.2 +OU858016 21 AY.43 +USA/MD-CDC-ASC210249084/2021 22 AY.103 +BHR/921383172_S272_L001/2021 27 B.1.617.2 +GMB/18367/2021 10 AY.34.1 +SouthAfrica/NHLS-UCT-GS-D040/2021 26 AY.45 +SouthAfrica/NHLS-UCT-AM-Z051/2021 26 AY.45 +USA/IN-CDC-ASC210080742/2021 9 AY.39 +NZL/21MV0743/2021 9 AY.39.1.1 +NZL/21MV3377/2021 8 AY.39.1.1 +England/PHEP-YYDFXQE/2022 27 AY.4 +VNM/OUCRU-NHTD281/2021 13 AY.23 +NZL/21CH0672/2021 8 AY.39.1.1 +BRA/PE-NVBS11106GENOV828537018936/2021 1 AY.99.2 +BRA/SP-NVBS11003GENOV828391823103/2021 1 AY.99.2 +BRA/RJ-NVBS8798GENOV828209752618/2021 1 AY.99.2 +BRA/PR-NVBS8517GENOV045385298482/2021 11 AY.101 +BRA/PR-NVBS8501GENOV828212410864/2021 11 AY.101 +BRA/RJ-NVBS5426GENOV827932075988/2021 1 AY.99.2 +USA/CO-CDC-MMB08948682/2021 23 AY.25 +IND/GBRC808a/2021 -1 AY.122 +England/CAMC-142DAEA/2021 27 B.1.617.2 +England/ALDP-1587670/2021 27 AY.4 +USA/TX-CDC-ASC210119371/2021 27 B.1.617.2 +USA/CO-CDC-MMB09720202/2021 24 AY.103 +OW046753 21 AY.43 +OY470884 27 AY.4 +USA/CA-CDC-FG-056443/2021 24 AY.103 +NZL/21MV0634/2021 14 AY.122 +SYC/SS995/2021 19 AY.122 +Switzerland/GE-HUG-35467598/2021 -1 B.1.617.2 +SouthAfrica/NHLS-UCT-GS-C595/2021 4 AY.32 +IND/INSACOG-GBRC1600/2021 27 B.1.617.2 +NGA/CV2713/2021 0 AY.99 +NGA/CV3792/2021 6 AY.36 +NGA/CV3797/2021 6 AY.36 +KAZ/86_02/2021 27 AY.122 +NZL/21CV0260/2021 9 AY.39.1.1 +SouthAfrica/NHLS-UCT-GS-C025/2021 26 AY.45 +BRA/RJ-NVBS11968GENOV828485614921/2021 21 AY.43 +BRA/PI-NVBS9840GENOV701341187596/2021 21 AY.43 +BRA/PR-NVBS10011GENOV828384609295/2021 11 AY.101 +BRA/DF-NVBS9940GENOV70987484766/2021 1 AY.99.2 +IND/hospital_2_110/2021 27 B.1.617.2 +England/PHEC-31B9E6/2021 27 AY.4 +England/MILK-1B1D7FE/2021 27 AY.4 +USA/CO-CDC-MMB10993310/2021 24 AY.103 +USA/WA-CDC-LC0378381/2021 2 AY.44 +USA/1865100/2021 18 AY.3 +IND/GBRC672a/2021 27 B.1.617.2 +NZL/21MV2499/2021 8 AY.39.1.1 +USA/CA-CDC-QDX25164347/2021 18 AY.3 +IND/GBRC672b/2021 27 B.1.617.2 +England/MILK-1532735/2021 14 AY.122 +USA/KY-CDC-ASC210480990/2021 23 AY.25 +England/LOND-1358AC9/2021 27 AY.4 +England/MILK-1B0299C/2021 27 AY.4 +USA/CO-CDC-MMB08864860/2021 27 B.1.617.2 +THA/CONI-1019/2021 5 AY.85 +OY418363 27 AY.4 +OY486041 27 AY.4 +SouthAfrica/NHLS-UCT-GP-6559/2021 4 AY.32 +SouthAfrica/NHLS-UCT-LA-Z733/2021 4 AY.32 +SouthAfrica/NHLS-UCT-GS-AF17/2021 4 AY.32 +COL/SEC-1541G/2021 23 AY.25.1 +Switzerland/AG-UHB-43144757/2021 27 AY.4 +NGA/CV4799/2021 27 B.1.617.2 +USA/IL-CDC-ASC210035037/2021 27 B.1.617.2 +England/PLYM-18E10BF/2021 27 AY.4 +KEN/SS4263/2021 6 AY.36 +England/MILK-30D934A/2022 27 AY.4.2 +BRA/PI-NVBS9105GENOV701335693775/2021 11 AY.101 +BRA/BA-NVBS5795GENOV828119057056/2021 1 AY.99.2 +USA/RI-CDCBI-RIDOH_JL76NTVMZTJNMCVQ/2021 24 AY.103 +NZL/21MV1543/2021 21 AY.43 +SouthAfrica/NHLS-UCT-GS-H381/2021 4 AY.32 +USA/TX-CDC-STM-000707005/2021 23 AY.25 +BHR/21921669029_S51_L001/2021 7 AY.33 +USA/FL-CDC-LC0152532/2021 2 AY.44 +BRA/21899979EMB/2021 1 AY.99.2 +JAM/202112020/2021 -1 AY.107 +THA/CONI-1245/2021 27 B.1.617.2 +NZL/21MV3219/2021 8 AY.39.1.1 +NZL/21MV3114/2021 9 AY.39.1.1 +NZL/21CV0700/2021 9 AY.39.1.1 +NZL/21MV1138/2021 9 AY.39.1.1 +NZL/21MV1058/2021 9 AY.39.1.1 +SouthAfrica/NHLS-UCT-GS-C931/2021 20 AY.91 +OY380493 27 AY.4 +NZL/21CH0492/2021 8 AY.39.1.1 +KEN/C107816/2021 27 AY.116 +DEU/C3170/2021 27 AY.4 +LAO/LOMWRU-1064/2021 3 AY.1 +USA/NC-CDC-QDX26400284/2021 27 B.1.617.2 +OY307566 27 B.1.617.2 +BGD/IEDCR-OIS-211/2021 14 AY.122 +KEN/SS8584/2022 21 AY.43 +NZL/21CV2645/2021 8 AY.39.1.1 +BRA/ILMD2200449/2021 1 AY.99.2 +South_Africa/UW21070391275/2021 0 AY.99 +BRA/RJ-NVBS9454GENOV700959068020/2021 1 AY.99.2 +NZL/21MV0615/2021 -1 B.1.617.2 +USA/CA-CDC-FG-146492/2021 27 AY.46 +OU857696 -1 AY.4 +NZL/21CV2378/2021 8 AY.39.1.1 +USA/1857106/2021 -1 AY.103 +NZL/21MV0638/2021 14 AY.122 +NZL/21MV0782/2021 9 AY.39.1.1 +USA/MI-CDC-ATM-ZS8ZZX3JU/2021 23 AY.25.1 +DJI/NAMRU3_E272/2021 25 AY.120 +Denmark/DCGC-124059/2021 21 AY.43 +KEN/SS7349/2021 27 AY.116 +BRA/RJ-NVBS3479GENOV700922152084/2021 1 AY.99.2 +Denmark/DCGC-252785/2021 21 AY.43 +USA/TN-CDC-LC0194823/2021 2 AY.44 +Pakistan/UHS2-Pak-361/2021 27 B.1.617.2 +England/MILK-1806852/2021 27 AY.4 +SouthAfrica/NHLS-UCT-GS-C176/2021 4 AY.32 +SouthAfrica/NHLS-UCT-GS-C920/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-GS-AF04/2021 -1 AY.91 +NZL/21MV0613/2021 -1 B.1.617.2 +NZL/21MV2565/2021 8 AY.39.1.1 +KEN/C106189/2021 27 AY.116 +KEN/SS10913/2021 -1 B.1.617.2 +England/PHEC-Y308Y050/2021 27 AY.4 +BRA/EPI_ISL_8890265/2021 10 AY.34.1 +USA/MI-CDC-STM-89D6X8HH6/2021 24 AY.103 +EGY/CCHE57357_W4_A001/2021 17 AY.126 +Japan/SZ-NIG-Y211225/2021 16 AY.29 +USA/CO-CDC-LC0472092/2022 18 AY.3 +Switzerland/VS-ICH-2211264520/2021 -1 AY.98 +URY/p2271/2021 21 AY.43 +OY586390 27 AY.6 +NZL/21CV0346/2021 9 AY.39.1.1 +OU154749 27 B.1.617.2 +KEN/SS4182/2021 27 AY.46 +OV103967 12 AY.100 +NZL/21MV3015/2021 8 AY.39.1.1 +USA/OKPHL0024712/2022 18 AY.3 +SouthAfrica/NHLS-UCT-GP-M981/2021 27 AY.6 +England/MILK-153D318/2021 27 AY.6 +SYC/SS4653/2021 19 AY.122 +IND/GBRC812a/2021 27 AY.122 +USA/SD-CDC-ASC210518027/2021 23 AY.25 +OV109415 17 AY.126 +England/NORW-30E1D75/2021 27 AY.4 +FRA/IHUCOVID-034454_Nova1/2021 27 B.1.617.2 +SYC/SS3654/2021 19 AY.122 +IND/hospital_2_132/2021 27 B.1.617.2 +OY462753 25 AY.120 +IND/hospital_2_326/2021 14 AY.122 +BHR/342409857/2021 -1 B.1.617.2 +OY521534 27 AY.4.2 +NZL/21MV0851/2021 9 AY.39.1.1 +NZL/21MV0476/2021 27 AY.122 +USA/VT-CDCBI-CRSP_WHQ6IZSXYCAV542D/2021 23 AY.25.1 +LAO/LOMWRU-1750/2022 3 AY.1 +England/ALDP-154A318/2021 27 AY.4 +USA/2078211_BB1L12/2021 -1 AY.25 +BRA/EPI_ISL_8890282/2021 1 AY.99.2 +IND/hospital_2_144/2021 11 B.1.617.2 +SouthAfrica/NHLS-UCT-GP-M988/2021 4 AY.32 +LAO/LOMWRU-1578/2021 5 AY.85 +DJI/NAMRU3_E190/2021 -1 AY.127 +USA/UT-CDC-LC0067238/2021 2 AY.44 +USA/WA-CDC-UW21051458938/2021 -1 B.1.617.2 +Switzerland/VD-CHUV-GEN9194/2021 -1 AY.98 +Switzerland/SG-CLM-01019003/2022 27 AY.46.6 +England/NEWC-2E161C4/2021 -1 AY.4 +USA/FL-CDC-STM-000062223/2021 -1 B.1.617.2 +OV241508 27 AY.4 +USA/KY-DC-DW084_F10/2020 27 B.1.617.2 +OV115766 21 AY.43 +USA/AR-UNM-ACHV00403/2021 2 AY.44 +England/ALDP-167DC2F/2021 27 AY.4 +England/ALDP-166E6BA/2021 27 AY.4 +USA/AR-UNM-M00427736/2021 2 AY.44 +USA/TX-EPICC_Sieve_267/2021 12 AY.100 +NZL/21MV0653/2021 27 AY.4 +NZL/21MV0630/2021 27 B.1.617.2 +NZL/21MV0491/2021 27 B.1.617.2 +England/BRBR-1F1D842/2021 27 AY.4 +BGD/Laila_159/2021 27 B.1.617.2 +Scotland/CVR12448/2021 27 AY.4 +LBY/86574a-37/2021 -1 AY.127 +BGD/icddrb-CMOSH-CU-0024/2021 -1 B.1.617.2 +IND/CWS_0080_54315840/2021 27 B.1.617.2 +England/MILK-17E2152/2021 27 AY.6 +BRA/GO-NVBS9153GENOV700800151826/2021 11 AY.101 +BRA/PR-NVBS932GENOV827684001556/2021 11 AY.101 +BRA/RJ-NVBS3379GENOV821440219995/2021 1 AY.99.2 +BRA/RJ-NVBS3475GENOV827820642971/2021 1 AY.99.2 +LAO/LOMWRU-1741/2021 5 AY.85 +OY692407 -1 AY.4.2 +OU924059 21 AY.43 +BHR/21342768692/2021 -1 AY.4 +OV103843 21 AY.43 +OV104283 27 B.1.617.2 +NZL/21MV0612/2021 13 AY.23 +KEN/C100802/2021 27 AY.116 +OV649594 -1 B.1.617.2 +NGA/CV2627/2021 6 AY.36 +BRA/SP-NVBS10217GENOV828343635761/2021 21 AY.43 +BRA/RJ-NVBS3705GENOV700922769794/2021 1 AY.99.2 +OW677287 -1 AY.127 +OX115909 -1 AY.122 +Scotland/QEUH-15BEFFD/2021 27 AY.4 +IND/CWS_0064_55744582/2021 27 B.1.617.2 +England/ALDP-17A7274/2021 27 AY.4 +USA/MN-CDC-LC0417578/2021 23 AY.25.1 +OV104183 21 AY.43 +IND/GBRC1231/2021 27 B.1.617.2 +England/ALDP-1A3D0FE/2021 27 AY.4 +KEN/C102060/2021 27 AY.116 +USA/WA-UW-21042320745/2021 27 AY.122 +SouthAfrica/NHLS-UCT-GP-N007/2021 27 AY.127 +FRA/IHUCOVID-056680_Nova2/2021 -1 AY.122 +BHR/21921829475_S80_L001/2021 27 AY.5 +OX115240 21 AY.43 +OX112263 21 AY.43 +BRA/SP-NVBS7199GENOV828088949949/2021 -1 AY.46 +BRA/RJ-NVBS3374GENOV827808626665/2021 1 AY.99.2 +NZL/21MV3327/2021 8 AY.39.1.1 +NZL/21CV0619/2021 9 AY.39.1.1 +England/ALDP-1597F18/2021 27 AY.4 +LAO/LOMWRU-1006/2021 5 AY.85 +England/NORT-1BF72BD/2021 27 AY.4 +England/PLYM-1C697E3/2021 27 AY.4 +England/MILK-1CA156D/2021 27 AY.4 +England/ALDP-1DD9CFD/2021 27 AY.4 +USA/1994155/2022 -1 AY.103 +SouthAfrica/NHLS-UCT-GP-6997/2021 26 AY.45 +IND/GBRC629b/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-LA-Z737/2021 -1 AY.4.2 +USA/MD-CDC-LC0438834/2021 -1 AY.103 +Japan/SZ-NIG-3-C11512/2021 16 AY.29 +England/MILK-15B99F4/2021 27 AY.6 +NZL/21MV2460/2021 8 AY.39.1.1 +NZL/21CH0766/2021 8 AY.39.1.1 +England/ALDP-160AC90/2021 27 AY.4 +OV114072 -1 AY.43 +OV104065 27 AY.46.6 +OX115023 21 AY.43 +GMB/16359/2021 10 AY.34.1 +BRA/SP-NVBS6251GENOV828120013997/2021 1 AY.99.2 +BRA/PR-NVBS951GENOV827691903300/2021 11 AY.101 +USA/MA-CDCBI-CRSP_XTNI25OJ62J6REFL/2022 14 AY.122 +NZL/21CV1433/2021 8 AY.39.1.1 +BRA/EPI_ISL_4273530/2021 1 AY.99.2 +USA/MT-UMGC-04179/2020 12 AY.100 +IND/IITRnCoV72/2021 27 B.1.617.2 +KEN/SS4387/2021 27 AY.4.2 +England/PHWC-PYIHRZ/2021 27 AY.4 +KEN/SS319/2021 27 B.1.617.2 +BRA/SP-NVBS11276GENOV045617201167/2021 21 AY.43 +USA/FL-CDC-STM-000733304/2021 27 AY.122 +England/NEWC-272733A/2021 27 AY.4 +LC654314 16 AY.29 +England/NORW-30146BA/2020 27 AY.5 +BGD/icddrb-CMOSH-CU-2552610/2021 -1 B.1.617.2 +HongKong/HKU-220213-219/2021 27 AY.4 +BRA/MS-NVBS12002GENOV700966652335/2021 1 AY.99.2 +BRA/SC-NVBS11443GENOV045617340798/2021 1 AY.99.2 +Denmark/DCGC-276444/2021 21 AY.43 +KEN/SS4140/2021 27 AY.46 +USA/VT-CDC-LC0421640/2021 12 AY.100 +England/PHEC-33B34C/2021 27 AY.4 +England/NORT-1BF71A1/2021 27 AY.4 +SYC/SS3477/2021 19 AY.122 +USA/PA-CDC-ASC210357542/2021 27 AY.119 +USA/NV-CDC-ASC210360432/2021 23 AY.25.1 +BHR/800111222/2021 27 B.1.617.2 +SYC/SS982/2021 19 AY.122 +IND/518MN908947.3/2021 27 AY.127 +USA/WI-CDC-LC0313260/2021 24 AY.103 +KEN/C100662/2021 27 AY.122 +USA/FL-BPHL-8934/2021 27 B.1.617.2 +USA/CA-CDC-FG-146840/2021 24 AY.103 +OU857848 -1 AY.4 +USA/CO-CDC-MMB11437449/2021 2 AY.44 +USA/WV127906/2021 -1 AY.39 +USA/LA-BIE-LSUH001239/2021 23 AY.25 +USA/NV-CDC-QDX26400824/2021 2 AY.44 +USA/NV-CDC-LC0092345/2021 2 AY.44 +USA/NV-CDC-QDX26075778/2021 2 AY.44 +NZL/21CH0619/2021 -1 AY.39.1.1 +USA/CA-CDC-FG-044891/2021 27 B.1.617.2 +Scotland/QEUH-15D96D9/2021 27 AY.4 +BRA/2068554/2021 1 AY.99.2 +USA/WA-CDC-UW21081538446/2021 2 AY.44 +HongKong/HKPU-00191/2021 27 AY.5 +NZL/21MV2755/2021 9 AY.39.1.1 +CHL/AR-UFRO-0200/2021 21 AY.43 +USA/NE-TESTNE_ABHCHDH/2021 2 AY.44 +IND/GBRC806b/2021 -1 B.1.617.2 +NGA/CV3667/2021 6 AY.36 +NGA/CV3854/2021 6 AY.36 +LAO/LOMWRU-0833/2021 3 AY.1 +England/ALDP-15C8A68/2021 27 AY.4 +BRA/RJ-NVBS3505GENOV827813245639/2021 1 AY.99.2 +NGA/CV2918/2021 6 AY.36 +NGA/CV2821/2021 0 AY.99 +USA/MI-CDC-ASC210482469/2021 23 AY.25 +BTN/RCDC0014-SV210152/2021 27 B.1.617.2 +SouthAfrica/NHLS-UCT-LA-Z734/2021 4 AY.32 +BRA/SP-NVBS7108GENOV828104046096/2021 -1 AY.46 +NGA/CV3374/2021 6 AY.36 +BRA/RJ-NVBS2716GENOV701231397876/2021 1 AY.99.2 +England/ALDP-15AC3F6/2021 27 AY.4 +MYS/M_C15438/2021 13 AY.23 +USA/PA-BOL-M22000026/2022 -1 AY.39 +OV104379 -1 AY.5 +England/MILK-2BF46A2/2021 27 AY.4 +USA/IN-GD-110321-61/2021 23 AY.25.1 +BRA/ILMD2101357/2021 1 AY.99.2 +England/MILK-19CC198/2021 27 AY.4 +BRA/ILMD2200212/2021 21 AY.43 +NZL/21CV2126/2021 8 AY.39.1.1 +England/MILK-15C996A/2021 27 AY.5 +USA/FL-BPHL-4446/2021 23 AY.25 +NZL/21MV2112/2021 8 AY.39.1.1 +BTN/RCDC0025-SV210163/2021 27 B.1.617.2 +ZAF/NHLS-UCT-GS-E353/2021 26 AY.45 +BRA/SP-NVBS7890GENOV828265263431/2021 1 AY.99.2 +SouthAfrica/NHLS-UCT-GS-C005/2021 4 AY.32 +SouthAfrica/NHLS-UCT-GS-C102/2021 25 AY.120 +BHR/21280338923_S75_L001/2021 17 AY.126 +OV103961 -1 AY.5 +JPN/HiroC77v1/2021 16 AY.29 +NZL/21CV0478/2021 9 AY.39.1.1 +USA/CA-CDC-FG-139693/2021 12 AY.100 +IND/RGCB-LMMD-26/2021 27 B.1.617.2 +KEN/C102874/2021 27 AY.116 +NZL/21MV1252/2021 9 AY.39.1.1 +England/MILK-20BD45B/2021 27 AY.4.2 +BHR/21922000489/2021 15 AY.3 +OV103636 -1 AY.4 +BHR/21342839417_S80_L001/2021 15 AY.3 +OV377291 27 AY.6 +IND/INSACOG-GBRC1607/2021 27 AY.127 +England/MILK-153D327/2021 27 AY.6 +USA/UT-CDC-QDX27028074/2021 18 AY.3 +IND/GBRC1243/2021 27 B.1.617.2 +OY595556 27 AY.4 +BHR/21922024248_S47_L001/2021 15 AY.3 +OV104511 21 AY.43 +OV103964 21 AY.43 +OV103911 21 AY.43 +Japan/SZ-NIG-Y211981/2021 16 AY.29 +USA/CO-CDPHE-2102508951/2021 27 AY.119 +England/QEUH-2DCB815/2021 27 AY.4.2 +England/PLYM-309FF3D/2022 27 AY.4.2 +England/HSLL-1532C90/2021 -1 AY.122 +USA/NE-TESTNE_A1TKXSL/2021 9 AY.39 +DJI/NAMRU3_E301/2021 -1 AY.127 +DJI/NAMRU3_E271/2021 -1 AY.127 +NGA/BCVL-26692/2021 27 B.1.617.2 +Switzerland/TG-ETHZ-671235/2021 21 AY.43 +NGA/CV2841/2021 6 AY.36 +NGA/CV2743/2021 0 AY.99 +HongKong/HKU-220213-218/2021 27 B.1.617.2 +BRA/PR-NVBS3795GENOV827806596045/2021 11 AY.101 +England/ALDP-15A2536/2021 27 AY.4 +England/ALDP-17AA0A4/2021 27 AY.4 +NZL/21MV0522/2021 27 B.1.617.2 +NZL/21MV0833/2021 9 AY.39.1.1 +NZL/21MV1148/2021 9 AY.39.1.1 +IND/547MN908947.3/2021 -1 B.1.617.2 +BRA/RJ-NVBS5320GENOV827956611926/2021 1 AY.99.2 +BRA/RJ-NVBS3729GENOV827824884537/2021 1 AY.99.2 +OV103689 -1 AY.98 +England/MILK-2943855/2021 27 AY.4 +UGA/MUWRP-KIR210110S/2021 27 AY.46 +UGA/MUWRP-KIR210136S/2021 27 AY.46 +NZL/21MV3034/2021 8 AY.39.1.1 +NZL/21CH0836/2021 8 AY.39.1.1 +USA/CO-CDPHE-22317371/2021 2 AY.44 +USA/CA-CDC-FG-070357/2021 2 AY.44 +USA/OKPHL0025524/2021 24 AY.103 +KEN/SS3733/2021 6 AY.36 +NGA/CV2493/2021 27 B.1.617.2 +BRA/SP-NVBS11298GENOV130640983453/2021 1 AY.99.2 +BRA/SP-NVBS8021GENOV821445597647/2021 21 AY.43 +NZL/21MV2088/2021 9 AY.39.1.1 +NZL/21CH0719/2021 8 AY.39.1.1 +KEN/SS9152/2021 27 AY.127 +KEN/SS4410/2021 -1 AY.46 +USA/CO-CDPHE-2101947252/2021 2 AY.44 +USA/WA-CDC-UW21050631997/2021 27 B.1.617.2 +NZL/21MV0574/2021 27 AY.122 +NZL/21MV0806/2021 9 AY.39.1.1 +OU858073 27 AY.46.6 +BRA/SP-NVBS11901GENOV828506856026/2021 21 AY.43 +BRA/RJ-NVBS6473GENOV828072025826/2021 1 AY.99.2 +BRA/RJ-NVBS3706GENOV827829238311/2021 1 AY.99.2 +USA/UT-UPHL-210612260296/2021 2 AY.44 +OU515408 -1 B.1.617.2 +BHR/21342661387_S85_L001/2021 7 AY.33 +KEN/C98737/2021 27 AY.116 +KEN/SS4910/2021 27 AY.46 +Japan/SZ-NIG-4-C3/2022 16 AY.29 +NZL/21CV0444/2021 27 AY.4 +USA/WV123341/2021 18 AY.3 +USA/MO-CDC-LC0441741/2021 27 AY.103 +IMS-10215-CVDP-D23B5CBB-4E64-4768-8687-C9D0EBD4638C 27 AY.4 +IMS-10004-CVDP-86117353-C8E6-42F5-88B8-D9ADF9B4EDCD 21 AY.43 +IMS-10587-CVDP-578FBD6F-BBF2-414F-99A3-B56074DC13F4 27 AY.122 +IMS-10150-CVDP-AA19F40F-B602-475F-8808-A6DE6D531B61 -1 AY.98 +IMS-10146-CVDP-1782F70F-36EB-4A3E-B273-7A0ADFC03D00 27 AY.46.6 +IMS-10087-CVDP-92581D79-C43E-436F-B628-06176EBB2BEF -1 B.1.617.2 +IMS-10116-CVDP-DCAFFE99-D611-4D6E-AEBB-95169F29D51E 27 AY.6 +IMS-10302-CVDP-5FAF0324-E761-4C7E-8ECB-201A5B63DCCE 21 AY.43 +IMS-10302-CVDP-99E53E9E-44A4-4D5E-A567-48962AE31748 -1 AY.98 +IMS-10302-CVDP-54C3463B-AB2F-433F-89C7-7C425B32F608 -1 B.1.617.2 +IMS-10036-CVDP-F41D69F6-DC0D-4D14-B730-D9C3C4C3D4B0 17 AY.126 diff --git a/sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters_counts.tsv b/sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters_counts.tsv new file mode 100644 index 00000000..a65102bb --- /dev/null +++ b/sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters_counts.tsv @@ -0,0 +1,70 @@ +Nextclade_pango_collapsed t-sne_label_for_Nextclade_pango_collapsed count +AY.99.2 1 139 +B.1.617.2 27 241 +AY.4.2 27 29 +AY.29 16 41 +AY.4 27 241 +AY.3 18 44 +AY.3 15 13 +AY.101 11 32 +AY.45 26 26 +AY.43 21 98 +AY.33 27 1 +AY.39.1.1 9 82 +AY.44 2 80 +AY.98 -1 11 +AY.1 3 32 +AY.85 5 35 +AY.103 22 10 +AY.127 -1 11 +AY.6 27 22 +AY.25 23 40 +AY.39.1.1 8 58 +AY.100 12 21 +AY.122 14 27 +AY.46 -1 17 +AY.46 27 38 +AY.46.6 27 11 +B.1.617.2 -1 58 +AY.39 9 15 +AY.32 4 41 +AY.103 24 60 +AY.126 17 18 +AY.33 7 12 +AY.91 20 11 +AY.107 27 1 +AY.4 -1 19 +AY.34.1 10 14 +AY.39.1.1 -1 3 +AY.5 27 12 +AY.36 6 48 +AY.20 27 11 +AY.122 27 51 +B.1.617.2 10 5 +AY.23 13 18 +AY.25.1 23 18 +AY.98 27 7 +AY.103 -1 11 +AY.122 19 25 +AY.116 27 27 +AY.103 27 2 +AY.39 -1 14 +AY.120 25 15 +AY.122 -1 12 +AY.43 -1 4 +AY.46 10 1 +AY.119 27 11 +AY.99 0 11 +AY.107 -1 9 +AY.3 27 1 +B.1.617.2 12 2 +AY.25 -1 3 +AY.120 -1 3 +AY.91 -1 2 +AY.119 -1 2 +AY.4.2 -1 5 +AY.1 27 1 +AY.127 27 5 +B.1.617.2 7 1 +B.1.617.2 11 1 +AY.5 -1 2 diff --git a/sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters_counts_without_unclustered.tsv b/sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters_counts_without_unclustered.tsv new file mode 100644 index 00000000..7412e6b6 --- /dev/null +++ b/sars-cov-2-nextstrain/results/single_clade/lineages_and_clusters_counts_without_unclustered.tsv @@ -0,0 +1,53 @@ +Nextclade_pango_collapsed t-sne_label_for_Nextclade_pango_collapsed count +AY.99.2 1 139 +B.1.617.2 27 241 +AY.4.2 27 29 +AY.29 16 41 +AY.4 27 241 +AY.3 18 44 +AY.3 15 13 +AY.101 11 32 +AY.45 26 26 +AY.43 21 98 +AY.33 27 1 +AY.39.1.1 9 82 +AY.44 2 80 +AY.1 3 32 +AY.85 5 35 +AY.103 22 10 +AY.6 27 22 +AY.25 23 40 +AY.39.1.1 8 58 +AY.100 12 21 +AY.122 14 27 +AY.46 27 38 +AY.46.6 27 11 +AY.39 9 15 +AY.32 4 41 +AY.103 24 60 +AY.126 17 18 +AY.33 7 12 +AY.91 20 11 +AY.107 27 1 +AY.34.1 10 14 +AY.5 27 12 +AY.36 6 48 +AY.20 27 11 +AY.122 27 51 +B.1.617.2 10 5 +AY.23 13 18 +AY.25.1 23 18 +AY.98 27 7 +AY.122 19 25 +AY.116 27 27 +AY.103 27 2 +AY.120 25 15 +AY.46 10 1 +AY.119 27 11 +AY.99 0 11 +AY.3 27 1 +B.1.617.2 12 2 +AY.1 27 1 +AY.127 27 5 +B.1.617.2 7 1 +B.1.617.2 11 1 diff --git a/sars-cov-2-nextstrain/scripts/plot-single-clade-lineage-and-cluster-counts.py b/sars-cov-2-nextstrain/scripts/plot-single-clade-lineage-and-cluster-counts.py new file mode 100644 index 00000000..9108e2ca --- /dev/null +++ b/sars-cov-2-nextstrain/scripts/plot-single-clade-lineage-and-cluster-counts.py @@ -0,0 +1,28 @@ +import argparse +import altair as alt +import pandas as pd + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--counts", required=True, help="path to TSV of counts by lineage and cluster") + parser.add_argument("--lineage-column", required=True, help="name of column in counts file for lineages") + parser.add_argument("--cluster-column", required=True, help="name of column in counts file for clusters") + parser.add_argument("--output", required=True, help="PNG dot plot of counts by lineage and cluster") + + args = parser.parse_args() + + df = pd.read_csv( + args.counts, + sep="\t", + ) + + chart = alt.Chart(df).mark_circle().encode( + x=alt.X(f"{args.lineage_column}:N", title="Pango lineage"), + y=alt.Y(f"{args.cluster_column}:N", title="Cluster from t-SNE"), + size="count:Q", + ).properties( + width=400, + height=400, + ) + chart.save(args.output, format="png", scale_factor=2.0)