Deep sequencing SARS-CoV-2 samples from New Mexico to interrogate immunological selection on genetic variants

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Although vaccination has blunted the impact of the SARS-CoV-2 pandemic in several countries, the future impact of this virus will depend on its transmissibility, virulence, and ability to evade naturally-acquired and vaccine- mediated immunity. All three phenotypes are currently in flux due to the evolution and spread of novel SARS- CoV-2 variants of concern. Importantly, all of these variants rose to prominence prior to widespread vaccination. Thus, while some may be the product of immune-mediated selection, they did not evolve in response to vaccination per se, and we know next to nothing about whether and how vaccination imposes selection on SARS-CoV-2. To close this knowledge gap, the proposed research will address the question: Do vaccinated study participants still acquire the SARS-CoV-2 virus, and if so, what variants do they carry? We hypothesize that vaccine-mediated immunity may impose selection on variants in one of three ways: (i) between- host selection in which vaccinees are more likely to be infected by variants pre-adapted for immune escape, (ii) within-host selection in which novel variants with capacity for immune escape first evolve in individual vaccinees, and may then be transmitted to vaccinated or unvaccinated individuals, or (iii) a combination of within- and between host selection. Furthermore, we hypothesize that vaccine-mediated immunity will impose stronger selection on SARS-CoV-2 than naturally-induced immunity or mAb therapy. Inferring patterns of within-host selection requires data on within-host population variation, but to date, studies of within-host populations of SARS-CoV-2 have been largely neglected in favor of consensus sequences. Thus, we will obtain residual material from SARS-CoV-2 positive samples from the following groups: (1) ≥ 100 individuals infected at least 5 days and any interval thereafter following vaccination, (2) ≥50 individuals being treated with mAbs, (3) 200 to 400 persistently infected individuals testing positive at least 5 days following an initial positive test, and (4) the first positive test from 100 individuals testing positive early in the pandemic, to represent a control group that is likely at an early point in their first infection. These samples will be provided by Tricore labs from individuals tested in New Mexico. RNA extracted from samples will be subject to both Illumina and PacBio sequencing; data from both approaches will be used to detect consensus variants, indels, and intra-host single-nucleotide variants (iSNVs) at frequencies >2%, and the longer-read Pac Bio data will be used to assess linkage between mutations, facilitating detection of recombination, e.g. (20), and mixed-variant infections (co-infection). These data will be used to quantify intra-host diversity and selection, frequency of common, sub-consensus mutations, convergent evolution of high-risk mutations present in VOC. Phylogenetic association of iSNVs will also be analyzed. Novel mutations that fall within documented antibody binding sites or T cell epitopes will be flagged and scrutinized for spread.