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The phylogenetic relationship within SARS-CoV-2s: An expanding basal clade.

ABSTRACT: The COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whose origin is still shed in mystery. In this study, we developed a method to search the basal SARS-CoV-2 clade among collected SARS-CoV-2 genome sequences. We first identified the mutation sites in the SARS-CoV-2 whole genome sequence alignment. Then by the pairwise comparison of the numbers of mutation sites among all SARS-CoV-2s, the least mutated clade was identified, which is the basal clade under parsimony principle. In our first analysis, we used 168 SARS-CoV-2 sequences (GISAID dataset till 2020/03/04) to identify the basal clade which contains 33 identical viral sequences from seven countries. To our surprise, in our second analysis with 367 SARS-CoV-2 sequences (GISAID dataset till 2020/03/17), the basal clade has 51 viral sequences, 18 more sequences added. The much larger NCBI dataset shows that this clade has expanded with 85 unique sequences by 2020/04/04. The expanding basal clade tells a chilling fact that the least mutated SARS-CoV-2 sequence was replicating and spreading for at least four months. It is known that coronaviruses have the RNA proofreading capability to ensure their genome replication fidelity. Interestingly, we found that the SARS-CoV-2 without its nonstructural proteins 13 to 16 (Nsp13-Nsp16) exhibits an unusually high mutation rate. Our result suggests that SARS-CoV-2 has an unprecedented RNA proofreading capability which can intactly preserve its genome even after a long period of transmission. Our selection analyses also indicate that the positive selection event enabling SARS-CoV-2 to cross species and adapt to human hosts might have been achieved before its outbreak.

SUBMITTER: Shen S

PROVIDER: S-EPMC7684012 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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The phylogenetic relationship within SARS-CoV-2s: An expanding basal clade.

Shen Steve S Zhang Zhao Z He Funan F

Molecular phylogenetics and evolution 20201124

The COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whose origin is still shed in mystery. In this study, we developed a method to search the basal SARS-CoV-2 clade among collected SARS-CoV-2 genome sequences. We first identified the mutation sites in the SARS-CoV-2 whole genome sequence alignment. Then by the pairwise comparison of the numbers of mutation sites among all SARS-CoV-2s, the least mutated clade was identified, which is the basal clade und ...[more]

PMID: 33242581

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Project description:BackgroundThe vertebrate brain is composed of several interconnected, functionally distinct structures and much debate has surrounded the basic question of how these structures evolve. On the one hand, according to the 'mosaic evolution hypothesis', because of the elevated metabolic cost of brain tissue, selection is expected to target specific structures mediating the cognitive abilities which are being favored. On the other hand, the 'concerted evolution hypothesis' argues that developmental constraints limit such mosaic evolution and instead the size of the entire brain varies in response to selection on any of its constituent parts. To date, analyses of these hypotheses of brain evolution have been limited to mammals and birds; excluding Actinopterygii, the basal and most diverse class of vertebrates. Using a combination of recently developed phylogenetic multivariate allometry analyses and comparative methods that can identify distinct rates of evolution, even in highly correlated traits, we studied brain structure evolution in a highly variable clade of ray-finned fishes; the Tanganyikan cichlids.ResultsTotal brain size explained 86% of the variance in brain structure volume in cichlids, a lower proportion than what has previously been reported for mammals. Brain structures showed variation in pair-wise allometry suggesting some degree of independence in evolutionary changes in size. This result is supported by variation among structures on the strength of their loadings on the principal size axis of the allometric analysis. The rate of evolution analyses generally supported the results of the multivariate allometry analyses, showing variation among several structures in their evolutionary patterns. The olfactory bulbs and hypothalamus were found to evolve faster than other structures while the dorsal medulla presented the slowest evolutionary rate.ConclusionOur results favor a mosaic model of brain evolution, as certain structures are evolving in a modular fashion, with a small but non-negligible influence of concerted evolution in cichlid fishes. Interestingly, one of the structures presenting distinct evolutionary patterns within cichlids, the olfactory bulbs, has also been shown to evolve differently from other structures in mammals. Hence, our results for a basal vertebrate clade also point towards a conserved developmental plan for all vertebrates.

Dataset Information

The phylogenetic relationship within SARS-CoV-2s: An expanding basal clade.

Publications

The phylogenetic relationship within SARS-CoV-2s: An expanding basal clade.

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