Key result
SARS-CoV-2 deep sequencing identifies 158 SNPs revealing intra-host diversity and independent respiratory tissue compartmentalization.
Why the study?
SARS-CoV-2 mutants continuously emerge with enhanced transmission due to high mutation rates, prompting investigation into the single nucleotide polymorphism dynamics of the virus.
Observational
SARS-CoV-2 exhibits intra-host quasispecies diversity and compartmentalization in the respiratory tract during early infection.
SNP surveillance may aid variant tracking; leaves open whether intra-host quasispecies diversity influences transmission or outcomes.
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies’ composition varies with time during the early onset of symptoms, which implicates viral evolution during infection. Network analysis of co-occurring SNPs revealed the most abundant non-synonymous SNP 22,638 in the S glycoprotein RBD region and 28,144 in the ORF8 region. Furthermore, SARS-CoV-2 variations differ in an individual’s respiratory tissue (nose, throat, BALF, or sputum), suggesting independent compartmentalization of SARS-CoV-2 populations in patients. The positive selection analysis of the SARS-CoV-2 genome uncovered the positive selected amino acid G251V on ORF3a. Alternative allele frequency spectrum (AAFS) of all variants revealed that ORF8 could bear alternate alleles with high frequency. Overall, the results show the quasispecies’ profile of SARS-CoV-2 in the respiratory tract in the first two months after the outbreak.
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Gao et al. (2021) conducted an observational in SARS-CoV-2. Deep meta-transcriptomic sequencing was evaluated on Single nucleotide polymorphisms (SNPs) dynamics and intra-host population diversity. Deep meta-transcriptomic sequencing of SARS-CoV-2 identified 158 high-confidence SNPs, revealing intra-host quasispecies diversity and independent compartmentalization in respiratory tissues.
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