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Shared within-host SARS-CoV-2 variation in households (preprint)
medrxiv; 2022.
Preprint
in English
| medRxiv | ID: ppzbmed-10.1101.2022.05.26.22275279
ABSTRACT
Background:
The limited variation observed among SARS-CoV-2 consensus sequences makes it difficult to reconstruct transmission linkages in outbreak settings. Previous studies have recovered variation within individual SARS-CoV-2 infections but have not yet measured the informativeness of within-host variation for transmission inference.Methods:
We performed tiled amplicon sequencing on 307 SARS-CoV-2 samples from four prospective studies and combined sequence data with household membership data, a proxy for transmission linkage.Results:
Consensus sequences from households had limited diversity (mean pairwise distance, 3.06 SNPs; range, 0-40). Most (83.1%, 255/307) samples harbored at least one intrahost single nucleotide variant (iSNV; median 117; IQR 17-208), when applying a liberal minor allele frequency of 0.5% and prior to filtering. A mean of 15.4% of within-host iSNVs were recovered one day later. Pairs in the same household shared significantly more iSNVs (mean 1.20 iSNVs; 95% CI 1.02-1.39) than did pairs in different households infected with the same viral clade (mean 0.31 iSNVs; 95% CI 0.28-0.34), a signal that increases with increasingly liberal thresholds.Conclusions:
Although only a subset of within-host variation is consistently shared across likely transmission pairs, shared iSNVs may augment the information in consensus sequences for predicting transmission linkages.
Full text:
Available
Collection:
Preprints
Database:
medRxiv
Language:
English
Year:
2022
Document Type:
Preprint
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