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The phylogenetic relationship within SARS-CoV-2s: An expanding basal clade
Steve Shen1, Zhao Zhang1, Funan He2
1Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
Molecular Phylogenetics and Evolution
|November 26, 2020
Summary
The study identified the earliest SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) sequences, revealing an expanding basal clade that has been spreading for months. This suggests SARS-CoV-2 possesses strong RNA proofreading capabilities.
Area of Science:
- Virology
- Genomics
- Evolutionary Biology
Background:
- The origin of SARS-CoV-2, the virus causing COVID-19, remains unclear.
- Coronaviruses are known for their RNA proofreading mechanisms to maintain genome integrity during replication.
Purpose of the Study:
- To develop a method for identifying the basal clade of SARS-CoV-2 genome sequences.
- To investigate the early evolution and transmission dynamics of SARS-CoV-2.
Main Methods:
- Whole genome sequence alignment of SARS-CoV-2.
- Pairwise comparison of mutation sites to identify the least mutated (basal) clade using the parsimony principle.
- Analysis of viral genome datasets from GISAID and NCBI.
Main Results:
- The basal clade of SARS-CoV-2 was identified and found to be expanding over time in different datasets.
- An expanding basal clade indicates sustained replication and spread of the least mutated SARS-CoV-2 for at least four months.
- SARS-CoV-2 lacking nonstructural proteins 13-16 showed a significantly higher mutation rate, highlighting the virus's robust RNA proofreading capability.
- Selection analyses suggest that the cross-species transmission and human adaptation of SARS-CoV-2 likely occurred before the observed outbreak.
Conclusions:
- SARS-CoV-2 exhibits an exceptional RNA proofreading capability, preserving its genome integrity during prolonged transmission.
- The findings provide insights into the early evolutionary events and transmission patterns of SARS-CoV-2, potentially predating the pandemic's recognized start.
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