Atypical Prolonged Viral Shedding With Intra-Host SARS-CoV-2 Evolution in a Mildly Affected Symptomatic Patient.

Marielton Dos Passos Cunha,Ana Paula Pessoa Vilela,Luiz Gustavo Bentim Góes,Sabrina Baroni,Vinícius De Morais Barroso,Lilian Gomes De Oliveira,Jean Pierre Schatzmann Peron,Sandra Marcia Muxel,Angélica Cristine De Almeida Campos,Paola Minóprio,Camila Vieira Molina,Stephanie Maia Acuña,Yan De Souza Angelo

doi:10.3389/fmed.2021.760170

Marielton Dos Passos Cunha, Ana Paula Pessoa Vilela + Show 11 more

Open Access

https://doi.org/10.3389/fmed.2021.760170

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Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is caused by a respiratory virus with a wide range of manifestations, varying from asymptomatic to fatal cases, with a generally short outcome. However, some individuals present long-term viral shedding. We monitored 38 individuals who were mildly affected by the SARS-CoV-2 infection. Out of the total studied population, three (7.9%) showed atypical events regarding the duration of positivity for viral RNA detection. In one of these atypical cases, a previously HIV-positive male patient presented a SARS-CoV-2 RNA shedding and subgenomic RNA (sgRNA) detected from the upper respiratory tract, respectively, for 232 and 224 days after the onset of the symptoms. The SARS-CoV-2 B.1.1.28 lineage, one of the most prevalent in Brazil in 2020, was identified in this patient in three serial samples. Interestingly, the genomic analyses performed throughout the infectious process showed an increase in the genetic diversity of the B.1.1.28 lineage within the host itself, with viral clearance occurring naturally, without any intervention measures to control the infection. Contrasting widely spread current knowledge, our results indicate that potentially infectious SARS-CoV-2 virus might be shed by much longer periods by some infected patients. This data call attention to better adapted non-pharmacological measures and clinical discharge of patients aiming at preventing the spread of SARS-CoV-2 to the population.

Highlights

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, Hubei province, China, in late December 2019 [1,2,3] causing highly transmissible respiratory infection and acute disease in humans
This first criterion of inclusion consisted in the presence of cold/flu symptoms, such as fever and/or respiratory symptoms, following criteria recommended by the Brazilian Ministry of Health guidelines for Coronavirus Disease 2019 (COVID-19) diagnosis and treatment
We found a positive correlation by the detection of Envelope and RNAdependent RNA polymerase (RdRp) genes (r = 0.89) in the first sample collected in the molecular assay (Figure 1A)

Summary

Introduction

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, Hubei province, China, in late December 2019 [1,2,3] causing highly transmissible respiratory infection and acute disease in humans. Since the SARS-CoV-2 emergence, hundreds of thousands of viral consensus genomes have been sequenced and quickly made available around the world [9]. The rapid spread of SARS-CoV2, initially with an apparent low diversity, suggested that the ancestor of the virus accumulated a genetic diversity allowing for the emergence of several phylogenetic lineages while spreading geographically across the world [9]. Genetically diverse viral populations that co-circulate within a single host began to be explored in some population groups infected with SARS-CoV2 [10,11,12,13]

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