tetano
Editor, Senior Moderator
Genome Biol Evol
. 2021 Jan 29;evab015.
doi: 10.1093/gbe/evab015. Online ahead of print.
Rapid spread of mutant alleles in worldwide SARS-CoV-2 strains revealed by genome-wide single nucleotide polymorphism and variation analysis
Zhenglin Zhu[SUP] 1 [/SUP], Gexin Liu[SUP] 1 [/SUP], Kaiwen Meng[SUP] 2 [/SUP], Liuqing Yang[SUP] 3 [/SUP], Di Liu[SUP] 4 [/SUP], Geng Meng[SUP] 2 [/SUP]
Affiliations
Abstract
The novel coronavirus (SARS-CoV-2) has become a pandemic and is threatening human health globally. Here, we report 9 newly evolved SARS-CoV-2 single nucleotide polymorphism (SNP) alleles those underwent a rapid increase (7 cases) or decrease (2 cases) in their frequency for 30% ∼ 80% in the initial four months, which are further confirmed by intra-host single nucleotide variation (iSNV) analysis using raw sequence data including 8217 samples. The 9 SNPs are mostly (8/9) located in the coding region and are mainly (6/9) nonsynonymous substitutions. The 9 SNPs show a complete linkage in SNP pairs and belong to 3 different linkage groups, named LG_1 to LG_3. Analyses in population genetics show signatures of adaptive selection towards the mutants in LG_1, but no signal of selection for LG_2. Population genetic analysis results on LG_3 show geological differentiation. Analyses on geographic COVID-19 cases and published clinical data provide evidence that the mutants in LG_1 and LG_3 benefit virus replication and those in LG_1 have a positive correlation with the disease severity in COVID-19 infected patients. The mutants in LG_2 show a bias towards mildness of the disease based on available public clinical data. Our findings may be instructive for epidemiological surveys and disease control of COVID-19 in the future.
Keywords: COVID-19; SARS-CoV-2; SNP; iSNV; mutants.
. 2021 Jan 29;evab015.
doi: 10.1093/gbe/evab015. Online ahead of print.
Rapid spread of mutant alleles in worldwide SARS-CoV-2 strains revealed by genome-wide single nucleotide polymorphism and variation analysis
Zhenglin Zhu[SUP] 1 [/SUP], Gexin Liu[SUP] 1 [/SUP], Kaiwen Meng[SUP] 2 [/SUP], Liuqing Yang[SUP] 3 [/SUP], Di Liu[SUP] 4 [/SUP], Geng Meng[SUP] 2 [/SUP]
Affiliations
- PMID: 33512495
- DOI: 10.1093/gbe/evab015
Abstract
The novel coronavirus (SARS-CoV-2) has become a pandemic and is threatening human health globally. Here, we report 9 newly evolved SARS-CoV-2 single nucleotide polymorphism (SNP) alleles those underwent a rapid increase (7 cases) or decrease (2 cases) in their frequency for 30% ∼ 80% in the initial four months, which are further confirmed by intra-host single nucleotide variation (iSNV) analysis using raw sequence data including 8217 samples. The 9 SNPs are mostly (8/9) located in the coding region and are mainly (6/9) nonsynonymous substitutions. The 9 SNPs show a complete linkage in SNP pairs and belong to 3 different linkage groups, named LG_1 to LG_3. Analyses in population genetics show signatures of adaptive selection towards the mutants in LG_1, but no signal of selection for LG_2. Population genetic analysis results on LG_3 show geological differentiation. Analyses on geographic COVID-19 cases and published clinical data provide evidence that the mutants in LG_1 and LG_3 benefit virus replication and those in LG_1 have a positive correlation with the disease severity in COVID-19 infected patients. The mutants in LG_2 show a bias towards mildness of the disease based on available public clinical data. Our findings may be instructive for epidemiological surveys and disease control of COVID-19 in the future.
Keywords: COVID-19; SARS-CoV-2; SNP; iSNV; mutants.