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Since May 2020, we have been conducting a comprehensive study to understand the natural history of SARS-CoV-2 infection in Rio de Janeiro, Brazil. Our focus has been on following families, systematically collecting respiratory tract swabs and blood samples, monitoring symptoms, and gathering data on vaccine status. This paper aims to describe the household cohort across five epidemic waves of SARS-CoV-2, providing an overview of the collected data and a description of the epidemiological, clinical, and immunological characteristics and incidence of SARS-CoV-2 infection. Our cohort includes 691 participants from 189 households. During the five epidemic waves, we detected 606 infections. The incidence density of SARS-CoV-2 infection ranged from 4 (Delta) to 56 (B.1.1.33) per 1,000 person-week, with a peak in wave B.1.1.33 in all age groups. The seroprevalence of SARS-CoV-2 antibodies (IgG anti spike protein) varied from 37%, in the pre-VoC period, to 99%, in the Omicron period, progressively increasing after each wave in a similar manner regardless of age. As we have monitored the cohort continuously since the beginning of the pandemic, we were able to collect data across different scenarios according to the predominant lineage in circulation. Via active monitoring of families, we were able to carry out an epidemiological surveillance on SARS-CoV-2, including its variants, persistence of symptoms, and changes in immunity over time in the population, contributing to knowledge of the natural history of SARS-CoV-2 infection.

The main objective of this study was to investigate the dynamic of SARS-CoV-2 viral excretion in rectal swab (RS), saliva, and nasopharyngeal swab (NS) samples from symptomatic patients and asymptomatic contacts. In addition, in order to evaluate the replication potential of SARS-CoV-2 in the gastrointestinal (GI) tract and the excretion of infectious SARS-CoV-2 from feces, we investigated the presence of subgenomic nucleoprotein gene (N) mRNA (sgN) in RS samples and cytopathic effects in Vero cell culture. A prospective cohort study was performed to collect samples from symptomatic patients and contacts in Rio de Janeiro, Brazil, from May to October 2020. One hundred and seventy-six patients had samples collected at home visits and/or during the follow up, resulting in a total of 1633 RS, saliva, or NS samples. SARS-CoV-2 RNA was detected in 130 (73.9%) patients who had at least one sample that tested positive for SARS-CoV-2. The presence of replicating SARS-CoV-2 in RS samples, measured by the detection of sgN mRNA, was successfully achieved in 19.4% (6/31) of samples, whilst infectious SARS-CoV-2, measured by the generation of cytopathic effects in cell culture, was identified in only one RS sample. Although rare, our results demonstrated the replication capacity of SARS-CoV-2 in the GI tract, and infectious viruses in one RS sample. There is still a gap in the knowledge regarding SARS-CoV-2 fecal-oral transmission. Additional studies are warranted to investigate fecal or wastewater exposure as a risk factor for transmission in human populations.

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.33-derived lineage named N.9 was described recently in Brazil and it's considered a potential variant of interest (VOI) due to the presence of E484K substitution at the receptor-binding domain (RBD) of the Spike (S) protein., Objective: To describe the first detection of variant N.9 in Rio de Janeiro State., Methods: SARS-CoV-2 N.9 was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR), whole-genome sequencing and phylogenetic analysis., Findings: Here, we report two SARS-CoV-2 N.9 lineage strains in Rio de Janeiro. One of them had only the E484K substitution of the six N.9 lineage-defining mutations. Other three strains pre-defined as N.9 have the same genomic profile. These four strains are grouped within the B.1.1.33 lineage and basal to the N.9 lineage in our phylogenetic analysis, and we call them "N.9-like/B.1.1.33 + E484K"., Main Conclusions: The phylogenetic analysis shows four independent introductions of N.9 in the state of Rio de Janeiro in October and December 2020, January and March 2021. SARS-CoV-2 N.9 dissemination in the Rio de Janeiro could have been limited by the emergence and dominance of other variants, mainly by the lineage P.2 VOI Zeta that emerged in the same period and co-circulated with N.9, as observed in the neighboring State of São Paulo.