Skip to main content
2024 BMES Annual Meeting Main banner
Icon Legend
This session is not in your schedule.
This session is in your schedule. Click again to remove it.
Back

Technologies for Emerging Infectious Diseases

Technologies for Emerging Infectious Diseases - Poster Session D

Poster AA13 - Rapid Emergence and Adaptive Evolution of Diverse SARS-CoV-2 Variants in Individuals with Advanced HIV Infection

Friday, October 25, 2024
3:30 PM – 4:30 PM EST
Location: Exhibit Hall E, F & G

Introduction: Multiple studies have documented new SARS-CoV-2 mutations in people with HIV (PWH) and suggested that SARS-CoV-2 variants, including variants of concern (VOCs), may preferentially arise in PWH. Nonetheless, the processes of intra-host evolution that produce these variants are incompletely understood due to consensus-based short-read whole genome sequencing which is a standard technology enabling to track SARS-CoV-2 consensus sequence changes and identify some minor variant mutations in genomic surveillance. Alternatively, high-throughput single-genome amplification and sequencing (HT-SGS), which enables detection of unique linked groupings of mutations (i.e. haplotypes) at the level of single genomes, is more suitable for estimates of intra-host population diversity and allows a better understanding of evolutionary relationship among viruses.

Materials and

Methods: We sequenced SARS-CoV-2 spike genes in nasal swabs of longitudinal sample sets from 25 people without HIV (PWOH) and 22 PWH, who were subgrouped on the basis of CD4 T cell counts (CD4 counts). We developed HT-SGS, which used Pacific Biosciences single molecule, real-time technology (SMRT) coupled with unique molecular identifiers (UMIs) of virus genome sequences, to generate up to ~103 single-copy sequences per sample with high accuracy.

Results, Conclusions, and Discussions: Following variant and haplotype calling against a model of residual errors in single-genome sequences, this approach detected mutations that were present in as few as 0.45% of amplifiable virus genomes per sample. In addition, HT-SGS provided minimum estimates of intra-host population diversity and enables downstream analysis of evolutionary relationships among viruses in each person. Intra-host spike gene diversity was significantly higher in PWH with CD4 counts < 200 cells/L than in the other subgroups (Fig. 1). These individuals had a median of 3.5 secondary Pango lineages/person, while PWOH had showed no secondary lineages. Through longitudinal analysis, remarkable features of SARS-CoV-2 dynamics were observed in PWH with CD4 counts < 200 cells/L, including 1) high early diversity, beginning shortly after COVID-19 symptom onset (Fig. 2a), 2) rapid changes in frequency of the most abundant haplotypes, and 3) large changes in population haplotype composition over time (Fig. 2b). Intra-host polymorphisms in PWH with CD4 counts < 200 cells/L included greater numbers of synonymous (reflecting more virus replicative cycles) and nonsynonymous mutations (often overlapping with defining mutations of VOCs) than other subgroups, indicating a high mutational burden. In addition, we found that patterns of gene evolution in PWH with CD4 counts < 200 cells/L resulted from adaptation of the virus to the host by selective forces (positive selection).

Acknowledgements (Optional):