SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution

Abstract

Numerous factors have been identified to influence susceptibility to SARS-CoV-2 infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (HCW; non-cancer controls) by deep sequencing and investigated the within-host viral quasispecies of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2+ swabs from 57 cancer patients and 14 healthcare workers (HCW) from the Brazilian Cancer Institute were collected in April–May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants (iSNVs) were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4-19.7%). Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to HCW (p = 0.009). Intrahost genetic diversity in cancer patients was independent of SARS-CoV-2 Ct values, and was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Such a feature may explain, at least in part, the more adverse outcomes to which cancer/COVID-19 patients experience.Author SummaryCancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. In this study, phylogenetic and variation analysis of SARS-CoV-2 genomes from cancer patients and non-cancer healthcare workers at the Brazilian National Cancer Institute were characterized by deep sequencing. Viral genomes showed signatures characteristic of Brazilian viruses, consistent with the hypothesis of local, community transmission rather than virus importation from abroad. Despite most genomes in patients and healthcare workers belonging to the same lineage, intrahost variability was higher in cancer patients when compared to non-cancer counterparts. The intrahost genomic diversity analysis presented in our study highlights the relaxed evolution of SARS-CoV-2 in a vulnerable population of cancer patients. The high number of minor variations can result in the selection of immune escape variants, resistance to potential drugs, and/or increased pathogenicity. The impact of this higher intrahost variability over time warrants further investigation.

SARS-CoV-2 Genome Sequencing Methods Differ in Their Abilities To Detect Variants from Low-Viral-Load Samples

“…Detecting and locating genomic positions of low-frequency variants from culture-derived specimens can provide insight into the reliability of intrahost single nucleotide variants (iSNVs) called from clinical specimens. The role of intrahost genomic variability in SARS-CoV-2 may be important in inferring transmission events ( 39 ) and may be responsible for significant complications in patients with malignancies ( 40 , 41 ). Thus, such low-frequency variants require ongoing detection and surveillance.…”

One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages

“…Thus, diversity remains low and viral evolution is mainly shaped by purifying selection ( Abu-Raddad et al, 2020 ; Valesano et al, 2021 ; Popa et al, 2020 ; Tonkin-Hill et al, 2020 ; Lythgoe et al, 2021 ). Nonetheless, variability in the number of detectable viral variants was observed among patients with short-term infections ( Popa et al, 2020 ), and still limited data indicate that SARS-CoV-2 intra-host diversity might increase with age ( Al Khatib et al, 2020 ) and in cancer patients ( Al Khatib et al, 2020 ; Siqueira et al, 2020 ). Intense monitoring of viruses transmitted by these (and other) patient categories will thus be required to assess whether they can transmit genetically diverse viral genomes.…”

High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity

“…Indeed, several studies have already revealed the existence of large numbers of withinhost viral populations in SARS-CoV-2 (Wolfel et al, 2020, Shen et al, 2020, Lythgoe et al, 2020, Butler et al, 2020). Genomic and quasispecies analyses showed large numbers intra-host nonsynonymous mutations in nasopharyngeal and oropharyngeal swabs of SARS-CoV-2 positive cases (Zhou et al, 2020a, Siqueira et al, 2020). Intrahost single nucleotide variants (iSNVs) were were also observed in bronchoal-veolar lavage fluid samples of of 8 SARS-CoV-2 patients(Shen et al, 2020).…”