Patterns of within-host genetic diversity in SARS-CoV-2

Abstract

Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.

Severe acute respiratory disease in American mink (Neovison vison) experimentally infected with SARS-CoV-2

“…One sample for which fewer than 50,000 reads were reads mapped for the sample (Supplemental 8B). These results are consistent with findings in other deep viral genome sequencing efforts (19,20) and the need for tempered conclusions with the detection of low-level variants and small datasets. Therefore, we focus on changes in consensus sequence relative to the inoculum.…”

SARS-CoV-2 infection and persistence throughout the human body and brain

“…Our use of a single-copy sequencing approach for the SARS-CoV-2 spike allowed us to demonstrate homogeneous virus populations in many tissues, while also revealing informative virus variants in others. Low intra-individual diversity of SARS-CoV-2 sequences has been observed frequently in previous studies [18][19][20] , and likely relates to the intrinsic mutation rate of the virus as well as lack of early immune pressure to drive virus evolution in new infections. It is important to note that our HT-SGS approach has both a high accuracy and a high sensitivity for minor variants within each sample, making findings of low virus diversity highly reliable 21 .…”

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

“…2 ). Good concordance was achieved in replicated sequencing for samples with relatively high viral loads (Ct ≤30), while a high proportion of discordant iSNVs was observed in samples with relatively lower viral loads (Ct >30), possibly generated by PCR biases 16 , 17 (Supplementary Fig. 2c–h ).…”