SARS-CoV-2 reinfections with BA.1 (Omicron) variant among fully vaccinated individuals in the northeast of Brazil
Authors: Neto Francisco P. F. , Teixeira Diego G. , Cunha Dayse C. S. da , Morais Ingryd C. , Tavares Celisa P. M. , Gurgel Genilson P. , Nascimento Sanderson D. do , Santos David C. dos , Sales Alexandre de O. , Jerônimo Selma M.B. 
Published: April 2022

Background

The first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Rio Grande do Norte, northeast Brazil, was diagnosed on March 12, 2020; thereafter, the pattern of COVID-19 followed the multiple waves as seen elsewhere. Those waves were mostly due to the SARS-CoV-2 virus mutations leading to emergence of variants of concern (VoC). The introduction of new VoCs in a population context of prior SARS-CoV-2 infections or after vaccination has been a challenge in understanding the kinetics of the protective immune response against SARS-CoV-2. The aim of this study was to investigate the outbreak of SARS-CoV-2 reinfections observed in mid-January 2022 in Rio Grande do Norte state, Brazil when the omicron variant was introduced.

Methodology/Principal findings

From a total of 172,965 individuals with mild to severe respiratory symptoms, 58,097 tested positive for SARS-CoV-2 between March 2020 through mid-February 2022. Of those previously infected, 444 had documented a second SARS-CoV-2 infection and 9 of these reinfection cases were selected for sequencing. Genomic analysis revealed that virus lineages diverged between primary and the reinfection, with the latter caused by the Omicron (BA.1) variant among individuals fully vaccinated against SARS-CoV-2.

Conclusions/Significance

Once all subjects whose samples were sequenced had prior SARS-CoV-2 infection and were also fully vaccinated, our data suggest that the Omicron variant evades natural and vaccine-induced immunities, confirming the continuous need to decrease transmission and to develop effective blocking vaccines.

Author summary

The pattern of the COVID-19 pandemic has been characterized by multiple waves of cases with a variety of outcomes from asymptomatic, to moderate or to severe fatal cases. By December 2021, about 75.3% of Rio Grande do Norte population, northeast Brazil, had already been fully vaccinated against SARS-CoV-2 and a decrease in newer detection cases was seen to about 8% of the suspected ones. Nevertheless, with the introduction of the Omicron variant at the end of 2021, the number of new SARS-CoV-2 infections reached its highest peak since the start of the pandemic with 75% of the suspected cases testing positive. From March 2020 to February 2022, we confirmed 444 reinfection cases among the ones tested, of which 62.3% (n=277) occurred during the Omicron outbreak, from December 2021 to early February 2022. Of the reinfection cases, 9 were sequenced and genetic analysis showed that they belong to a BA.1 lineage, which seems to have been introduced multiple times into the region. The primary isolates varied. Thus, our data suggest that the Omicron variant evades immunity provided from either natural infection from any other SARS-CoV-2 variants or from different types of vaccines.