tetano
Editor, Senior Moderator
Open Forum Infect Dis
. 2023 Jan 7;10(2)
fad001.
doi: 10.1093/ofid/ofad001. eCollection 2023 Feb.
Challenges in Harnessing Shared Within-Host Severe Acute Respiratory Syndrome Coronavirus 2 Variation for Transmission Inference
Katharine S Walter[SUP] 1 [/SUP], Eugene Kim[SUP] 2 [/SUP], Renu Verma[SUP] 2 [/SUP], Jonathan Altamirano[SUP] 3 [/SUP], Sean Leary[SUP] 4 [/SUP], Yuan J Carrington[SUP] 4 [/SUP], Prasanna Jagannathan[SUP] 2 5 [/SUP], Upinder Singh[SUP] 2 5 [/SUP], Marisa Holubar[SUP] 2 [/SUP], Aruna Subramanian[SUP] 2 [/SUP], Chaitan Khosla[SUP] 6 7 [/SUP], Yvonne Maldonado[SUP] 3 4 [/SUP], Jason R Andrews[SUP] 2 [/SUP]
Affiliations
Abstract
Background: The limited variation observed among severe acute respiratory syndrome coronavirus 2 (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, including 130 samples from 32 individuals in 14 households and 47 longitudinally sampled individuals, from 4 prospective studies with household membership data, a proxy for transmission linkage.
Results: Consensus sequences from households had limited diversity (mean pairwise distance, 3.06 single-nucleotide polymorphisms [SNPs]; range, 0-40). Most (83.1%, 255 of 307) samples harbored at least 1 intrahost single-nucleotide variant ([iSNV] median, 117; interquartile range [IQR], 17-208), above a minor allele frequency threshold of 0.2%. Pairs in the same household shared significantly more iSNVs (mean, 1.20 iSNVs; 95% confidence interval [CI], 1.02-1.39) than did pairs in different households infected with the same viral clade (mean, 0.31 iSNVs; 95% CI, .28-.34), a signal that decreases with increasingly stringent minor allele frequency thresholds. The number of shared iSNVs was significantly associated with an increased odds of household membership (adjusted odds ratio, 1.35; 95% CI, 1.23-1.49). However, the poor concordance of iSNVs detected across sequencing replicates (24.8% and 35.0% above a 0.2% and 1% threshold) confirms technical concerns that current sequencing and bioinformatic workflows do not consistently recover low-frequency within-host variants.
Conclusions: Shared within-host variation may augment the information in consensus sequences for predicting transmission linkages. Improving sensitivity and specificity of within-host variant identification will improve the informativeness of within-host variation.
Keywords: SARS-CoV-2; genomics; transmission; viral evolution; within-host diversity.
. 2023 Jan 7;10(2)
fad001.doi: 10.1093/ofid/ofad001. eCollection 2023 Feb.
Challenges in Harnessing Shared Within-Host Severe Acute Respiratory Syndrome Coronavirus 2 Variation for Transmission Inference
Katharine S Walter[SUP] 1 [/SUP], Eugene Kim[SUP] 2 [/SUP], Renu Verma[SUP] 2 [/SUP], Jonathan Altamirano[SUP] 3 [/SUP], Sean Leary[SUP] 4 [/SUP], Yuan J Carrington[SUP] 4 [/SUP], Prasanna Jagannathan[SUP] 2 5 [/SUP], Upinder Singh[SUP] 2 5 [/SUP], Marisa Holubar[SUP] 2 [/SUP], Aruna Subramanian[SUP] 2 [/SUP], Chaitan Khosla[SUP] 6 7 [/SUP], Yvonne Maldonado[SUP] 3 4 [/SUP], Jason R Andrews[SUP] 2 [/SUP]
Affiliations
- PMID: 36751652
- PMCID: PMC9898879
- DOI: 10.1093/ofid/ofad001
Abstract
Background: The limited variation observed among severe acute respiratory syndrome coronavirus 2 (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, including 130 samples from 32 individuals in 14 households and 47 longitudinally sampled individuals, from 4 prospective studies with household membership data, a proxy for transmission linkage.
Results: Consensus sequences from households had limited diversity (mean pairwise distance, 3.06 single-nucleotide polymorphisms [SNPs]; range, 0-40). Most (83.1%, 255 of 307) samples harbored at least 1 intrahost single-nucleotide variant ([iSNV] median, 117; interquartile range [IQR], 17-208), above a minor allele frequency threshold of 0.2%. Pairs in the same household shared significantly more iSNVs (mean, 1.20 iSNVs; 95% confidence interval [CI], 1.02-1.39) than did pairs in different households infected with the same viral clade (mean, 0.31 iSNVs; 95% CI, .28-.34), a signal that decreases with increasingly stringent minor allele frequency thresholds. The number of shared iSNVs was significantly associated with an increased odds of household membership (adjusted odds ratio, 1.35; 95% CI, 1.23-1.49). However, the poor concordance of iSNVs detected across sequencing replicates (24.8% and 35.0% above a 0.2% and 1% threshold) confirms technical concerns that current sequencing and bioinformatic workflows do not consistently recover low-frequency within-host variants.
Conclusions: Shared within-host variation may augment the information in consensus sequences for predicting transmission linkages. Improving sensitivity and specificity of within-host variant identification will improve the informativeness of within-host variation.
Keywords: SARS-CoV-2; genomics; transmission; viral evolution; within-host diversity.