Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary

Sánchez-Pacheco, Santiago J.; Kong, Sungsik; Pulido‐Santacruz, Paola; Murphy, Robert W.; Kubatko, Laura

doi:10.1073/pnas.2007062117

Cited by 47 publications

(60 citation statements)

References 5 publications

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“…Yet another notable point is a high mutability in the SR stretch of nucleoprotein, which along with the frequent ORF8 mutations justify their role in host immune evasion 62,66 (Figure 4). Several phylogenetic analyses have been carried out to understand the evolution of SARS-COV-2 16,[69][70][71][72] . A phylogram generated here using the 965 unique sequences having at least one of the significant mutations (LS, MS and HS) by considering the reference sequence (NC_045512.2) as the root indicates the evolution of 4 major clades (Figure 4(B)).…”

Section: Discussionmentioning

confidence: 99%

Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates

Patro

Sathyaseelan

Uttamrao

et al. 2020

Preprint

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To accelerate the drug and vaccine development against the severe acute respiratory syndrome virus 2 (SARS-CoV-2), a comparative analysis of SARS-CoV-2 proteome has been performed in two phases by considering manually curated 31389 whole genome sequences from 84 countries. Among the 9 mutations that occur at a high significance (T85I-NPS2, L37F-NSP6, P323L-NSP12, D614G-spike, Q57H-ORF3a, G251V-ORF3a, L84S-ORF8, R203K-nucleocapsid and G204R-nucleocapsid), R203K-nucleocapsid and G204R-nucleocapsid are co-occurring mutations and P323L-NSP12 and D614G-spike often appear simultaneously. Other notable variations that appear with a moderate to low significance are, M85-NSP1 deletion, D268-NSP2 deletion, 112 amino acids deletion in ORF8, a phenylalanine insertion amidst F34-F36 (NSP6) and several co-existing substitution/deletion (I559V & P585S in NSP2, P504L & Y541C in NSP13, G82 & H83 deletions in NSP1 and K141, S142 & F143 deletions in NSP2) mutations. P323L-NSP12, D614G-spike, L37F-NSP6, L84S-ORF8 and the sequences deficient of the high significant mutations has led to 4 major SARS-CoV-2 clades. The top 5 countries bearing all the high significant and majority of the moderate significant mutations are: USA, England, Wales, Australia and Scotland. Further, the majority of the significant mutations has evolved in the first phase and has already transmitted around the globe indicating the positive selection pressure. Among the 26 SARS-CoV-2 proteins, nucleocapsid protein, ORF3a, ORF8, RNA dependent RNA polymerase and spike exhibit a higher heterogeneity compared with the rest of the proteins. However, NSP9, NSP10, NSP8, the envelope protein and NSP4 are highly resistant to mutations and can be exploited for drug/vaccine development.

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Section: Discussionmentioning

confidence: 99%

Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates

Patro

Sathyaseelan

Uttamrao

et al. 2020

Preprint

View full text Add to dashboard Cite

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“…Such information will be of important value for the development of vaccine, transmission monitoring and ultimately the control of the pandemic. However, most of these studies were based on limited numbers of SARS-CoV-2 genomes collected during early pandemic time, which might lead to debating conclusions [10,[13][14][15][16][17]. To date, more than 40,000 SARS-CoV-2 whole genome sequences have been uploaded to the online platform The Global Initiative on Sharing Avian Influenza Data (GISAID) database (https://www.gisaid.org/) [18,19].…”

Section: Introductionmentioning

confidence: 99%

Genetic spectrum and distinct evolution patterns of SARS-CoV-2

Liu

Shen

Fang

et al. 2020

Preprint

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Four signature groups of single-nucleotide variants (SNVs) were identified using two-way clustering method in about twenty thousand high quality and high coverage SARS-CoV-2 complete genome sequences. Some frequently occurred SNVs predominate but are mutually exclusively presented in patients from different countries and areas. These major SNV signatures exhibited distinguished evolution patterns over time. Although it was rare, our data indicated possible cross-infections with multiple groups of SNVs existed simultaneously in some patients, suggesting infections from different SARS-CoV-2 clades or potential re-combination of SARS-CoV-2 sequences. Interestingly nucleotide substitutions among SARS-CoV-2 genomes tend to occur at the sites where one bat RaTG13 coronavirus sequences differ from Wuhan-Hu-1 genome, indicating the tolerance of mutations on those sites or suggesting that major viral strains might exist between Wuhan-Hu-1 and RaTG13 coronavirus.

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“…Evolutionary analyses suggested S clade appeared to be more related to coronaviruses in animals. Most recently, three major clusters of SNVs involved in the pandemic were found by comparing 160 SARS-CoV-2 genomes (Sanchez-Pacheco et al, 2020) with RaTG13 (Forster et al, 2020a). Researchers also employed standard phylogenomic approaches and compared consensus sequences representing the dominant virus lineage within each infected host (Forster et al, 2020a;Lai et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Such information will be of important value for the development of vaccine, transmission monitoring and ultimately the control of the pandemic. However, most of these studies were based on limited numbers of SARS-CoV-2 genomes collected during early pandemic time, which might lead to debating conclusions (Chookajorn, 2020;Forster et al, 2020b;Kupferschmidt, 2020;Mavian et al, 2020;Rambaut et al, 2020;Sanchez-Pacheco et al, 2020). To date, more than 40,000 SARS-CoV-2 whole genome sequences have been uploaded to the online platform The Global Initiative on Sharing Avian Influenza Data (GISAID) database 1 (Elbe and Buckland-Merrett, 2017;Shu and McCauley, 2017).…”

Section: Introductionmentioning

confidence: 99%

Genetic Spectrum and Distinct Evolution Patterns of SARS-CoV-2

et al. 2020

View full text Add to dashboard Cite

Four signature groups of frequently occurred single-nucleotide variants (SNVs) were identified in over twenty-eight thousand high-quality and high-coverage SARS-CoV-2 complete genome sequences, representing different viral strains. Some SNVs predominated but were mutually exclusively presented in patients from different countries and areas. These major SNV signatures exhibited distinguishable evolution patterns over time. A few hundred patients were detected with multiple viral strainrepresenting mutations simultaneously, which may stand for possible co-infection or potential homogenous recombination of SARS-CoV-2 in environment or within the viral host. Interestingly nucleotide substitutions among SARS-CoV-2 genomes tended to switch between bat RaTG13 coronavirus sequence and Wuhan-Hu-1 genome, indicating the higher genetic instability or tolerance of mutations on those sites or suggesting that major viral strains might exist between Wuhan-Hu-1 and RaTG13 coronavirus.

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Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary

Cited by 47 publications

References 5 publications

Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates

Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates

Genetic spectrum and distinct evolution patterns of SARS-CoV-2

Genetic Spectrum and Distinct Evolution Patterns of SARS-CoV-2

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