Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

Abstract

Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified a viral load threshold that minimizes false positives. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.

SARS-CoV-2 within-host diversity and transmission

“…Among the 41 individuals, we observed little concordance in minor variant frequencies across time points within individuals. Our observations, consistent with other studies ( 24 – 26 ), suggest a dynamic within-host landscape but also reflect the inherent stochasticity associated with low-viral-load samples.…”

Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant

“…The most distant sequence presented only four nucleotides' difference from the index case sample. This suggests, during an outbreak, the relatively low substitution rate of SARS-CoV-2 presents challenges to infer transmission chains purely base on consensus sequences [11][12][13] . To infer the minor sequence variations along with the viral spreading, we estimated withinhost virus diversity for each sample by mapping polymorphic sites onto the consensus genome of the index case (XG5137_GZ_2021/5/21) to generate a list of intra-host single-nucleotide variants (iSNVs).…”

“…To infer the minor sequence variations along with the viral spreading, we estimated withinhost virus diversity for each sample by mapping polymorphic sites onto the consensus genome of the index case (XG5137_GZ_2021/5/21) to generate a list of intra-host single-nucleotide variants (iSNVs). Minor iSNVs were called by setting 3% as the threshold of minor allele frequency to exclude the potential PCR and sequencing errors 12,14,15 . There were sequences having minor intra-host single nucleotide variants (iSNVs) in 10 of 31 substituted positions which may shed lights on how variants have emerged, grew and finally fixed during the epidemic.…”

Limited within-host diversity and tight transmission bottlenecks limit SARS-CoV-2 evolution in acutely infected individuals

“…While understanding the process of variant generation and transmission is critically important, a clear consensus on how frequently variants are shared and transmitted between individuals has been elusive. Estimates of SARS-CoV-2 diversity within hosts have been highly variable, and comparing results among labs has been complicated by sensitivity to variant-calling thresholds and inconsistent laboratory controls (20)(21)(22)(23). Some data suggest that SARS-CoV-2 genetic diversity within individual hosts during acute infections is limited (20,24) and shaped by genetic drift and purifying selection (21,(25)(26)(27).…”