Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon

TL;DR

This study shows that SARS-CoV-2 infection, specifically the P.1 variant, alters the nasal bacterial community, increasing harmful bacteria and reducing helpful ones.

Contribution

The study identifies specific bacterial shifts in the nasopharyngeal microbiome associated with SARS-CoV-2 P.1 variant infection in the Brazilian Amazon.

Findings

SARS-CoV-2 infection is linked to decreased commensal bacteria and increased opportunistic bacteria in the nasopharynx.

Opportunistic bacteria like Klebsiella pneumoniae and Staphylococcus spp. are more abundant in infected individuals.

Microbial diversity differs significantly between infected and uninfected individuals.

Abstract

It is important to understand which bacterial taxa are most abundant during SARS-CoV-2 infection and to promote mitigation strategies for conditions subsequent to infection. Nasopharyngeal swab samples were collected from patients infected with SARS-CoV-2 and their family contacts (uninfected and asymptomatic) during the outbreak of the P.1 variant of SARS-CoV-2 in Parintins, Amazonas–Brazil, in March 2021. The samples were investigated by a shotgun sequencing metagenomic approach using the NextSeq 500 Illumina® system. The samples were stratified according to the presence or absence of SARS-CoV-2, household group, sex, and age. Of the total of 63 individuals, 37 (58.73%) were positive for SARS-CoV-2 and 26 (41.27%) were negative for SARS-CoV-2 and other respiratory viruses (FLU, AdV, HBoV, HCoV, HMPV, RSV, PIV, HRV). The alpha diversity indexes Chao1, species observed, Simpson, and Inv Simpson demonstrated a significant difference (p < 0.05) in both the diversity of observed species and the abundance of some taxa between positive and negative individuals. We also observed an abundance of opportunists such as Klebsiella pneumoniae, Staphylococcus spp, and Shigella sonnei, previously associated with the severity of COVID-19. Our results suggest that SARS-CoV-2 infection causes changes in the microenvironment of the nasopharyngeal region, allowing greater proliferation of opportunistic bacteria and decreased abundance of commensal bacteria.

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