Infectious Disease
HIV and the detectability of within-host minor variants in Mycobacterium tuberculosis whole-genome sequencing data Marie Nancy Séraphin* Marie Nancy Séraphin Séraphin Séraphin Séraphin Séraphin Séraphin Séraphin Séraphin University of Florida, Florida, USA
Background: Within-host minor variants in Mycobacterium tuberculosis (intra-host single nucleotide variants; iSNVs) may improve transmission inference, but detectability depends on sequencing quality. Human immunodeficiency virus (HIV) can alter tuberculosis (TB) biology and specimen characteristics, providing a setting to study when iSNVs are observed.
Methods: We analyzed culture-confirmed TB isolates sequenced by whole-genome sequencing (WGS) from Florida statewide surveillance (n = 342) and a hospital-based cohort in Ghana (n = 97). Using biological replicates from Ghana, we calibrated iSNV-calling thresholds and defined iSNV detectability as ³ 1 iSNV outside repetitive regions. We compared detectability by HIV status overall and in a high-quality subset defined by high read depth and high callable genome. We tested robustness to alternative thresholds and to analyses restricted by sequencing run and quality metrics (read depth and callable genome).
Results: In Florida, iSNV detectability was higher among HIV-positive than HIV-negative isolates [Prevalence Ratio (PR) = 1.43(95% CI:1.25 – 1.63)]. In Ghana, detectability was also higher among HIV-positive isolates [PR = 1.63 (95% CI:0.78 – 3.38)], with greater imprecision due to smaller numbers. Restricting to high-quality samples produced similar or slightly stronger contrasts in both settings. Sensitivity analyses varying thresholds, filters, and outcome definitions did not eliminate the association.
Conclusions: HIV coinfection was associated with higher iSNV detectability in two settings and persisted after restricting to high-quality sequencing. Studies that assume equal minor-variant detectability across host groups may have differential sensitivity by HIV status. Calibrated thresholds, standardized quality criteria, and host-stratified reporting can improve interpretation of iSNV-based within-host diversity measures from M. tuberculosis WGS.