SARS-CoV-2 reinfections with BA.1 (Omicron) variant among fully vaccinated individuals in northeastern Brazil

Freire-Neto, Francisco Paulo; Teixeira, Diego Gomes; Cunha, Dayse C S da; Morais, Ingryd C; Tavares, Celisa P M; Gurgel, Genilson P; Medeiros, Sanderson D N; Santos, David C Dos; Sales, Alexandre de O; Jerônimo, Selma M. B.

doi:10.1371/journal.pntd.0010337

Cited by 10 publications

(10 citation statements)

References 32 publications

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“…This increase in the number of cases in the state follows what was observed in the rest of the country in the same period 32 . The high prevalence of the BA.1 lineage in genomes sequenced in the country is explained by the fact that this lineage is strongly associated with cases of infection and reinfection in vaccinated individuals 33 …”

Section: Discussionsupporting

confidence: 71%

“…32 The high prevalence of the BA.1 lineage in genomes sequenced in the country is explained by the fact that this lineage is strongly associated with cases of infection and reinfection in vaccinated individuals. 33 Ai et al 34 June and July from 2022 respectively. Study conducted in South Africa in 2022, demonstrated that the BA.4 and BA.5 lineages emerged approximately 4 months after the onset of the wave of COVID-19 cases caused by the BA.1 strain in the country.…”

Section: Discussionmentioning

confidence: 99%

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Molecular epidemiology of SARS‐CoV‐2 variants in circulation in the state of Maranhão, Brazil

de Sousa,

Ferreira,

Lobato

et al. 2023

Journal of Medical Virology

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Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a coronavirus belonging to the beta CoV genus, responsible for SARS in humans, which became known as COVID‐19. The emergence of variants of this virus is related to the presence of cases of reinfection, reduced vaccine effectiveness and greater transmission of the virus. Objective: In this study, we evaluated the molecular epidemiology of SARS‐CoV‐2 lineages circulating in the state of Maranhão. This is a cross‐sectional and retrospective epidemiological study of genomic surveillance of SARS‐CoV‐2. The study comprised of 338 genomes sequenced by the Next Generation Sequencing technique on Illumina's Miseq equipment, submitted to Global Initiative on Sharing Avian Influenza Data, 190 (56.2%) are from samples of female and 148 (43.8%) from male patients. Sequencing performed covered samples of patients aged between 1 and 108 years, with emphasis on the age groups from 30 to 39 years with 15.0% of sequenced genomes and 20 to 29 years with 12.4%. As for the distribution of sequenced genomes by health macro‐regions, 285 (84.3%) are from cities in the northern macro‐region. We evidenced the circulation of 29 lineages and sub‐lineages, four of which belonging to the Delta variant (AY.43, AY.99.1, AY.99.2 and AY.101 responsible for 4.5% of the genomes) and the others belonging to the Omicron variant, with emphasis on: BA.1 and sub‐lineages (42.8%); BA.4, BA.5 and sub‐lineages (5.3% and 41.1%); the sub‐lineages DL.1 and BQ.1 (5% and 2%). A strong genomic surveillance system allows the study of the natural history of the disease, when there is a resurgence of SARS‐CoV‐2 cases.

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Section: Discussionsupporting

confidence: 71%

Section: Discussionmentioning

confidence: 99%

Molecular epidemiology of SARS‐CoV‐2 variants in circulation in the state of Maranhão, Brazil

de Sousa,

Ferreira,

Lobato

et al. 2023

Journal of Medical Virology

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“…During COVID-19 the first three years of the COVID19 pandemic, the SARS-CoV-2 mutated and evolved with genetic variation in the population of circulating viral strains and after over 48 months of circulation within the human population it continues to mutate. The emergence of more recent SARS-CoV-2 variants, characterized by heightened transmissibility, raises concerns regarding their potential to compromise the protective effects of adaptive immunity elicited through natural infection or vaccination, since apparently immunity to either cases may be short lived (19), as we have observed here previously. Nevertheless, it is important to note that previous immunity, whether acquired through prior infection or vaccination, continues to demonstrate its association with protection against COVID-19 severity (55).…”

Section: Discussionmentioning

confidence: 56%

“…Intriguingly, SARS-CoV-2 variants had a significant impact on the number of cases and deaths in different parts of the globe, as seen when the Gamma variant emerged in South America (13)(14)(15) and the Delta and its sublineages in other parts of the globe (16,17). Those variants had distinct pathogenesis because of immune escaping from prior immunity generated through natural infection and/or vaccination (18,19).…”

Section: Introductionmentioning

confidence: 99%

Understanding SARS-CoV-2 Spike glycoprotein clusters and their impact on immunity of the population from Rio Grande do Norte, Brazil

Teixeira,

Rodrigues-Neto,

Severiano da Cunha

et al. 2023

Preprint

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SARS-CoV-2 genome underwent mutations since it started circulating intensively within the human populations. The aim of this study was to understand the fluctuation of the spike clusters concomitant to high rate of population immunity either due to natural infection and/or vaccination in a state of Brazil that had high rate of infection and vaccination coverage. A total of 1715 SARS-CoV-2 sequences from the state of Rio Grande do Norte, Brazil, were retrieved from GISAID and subjected to cluster analysis. Immunoinformatics were used to predict T- and B-cell epitopes, followed by simulation to estimate either pro- or anti-inflammatory responses and correlate with circulating variants. From March 2020 to June 2022, Rio Grande do Norte reported 579,931 COVID-19 cases with a 1.4% fatality rate across three major waves: May-Sept 2020, Feb-Aug 2021, and Jan-Mar 2022. Cluster 0 variants (wild type strain, Zeta) were prevalent in the first wave and Delta in the latter half of 2021, featuring fewer unique epitopes. Cluster 1 (Gamma [P1]) dominated the first half of 2021. Late 2021 had Clusters 2 (Omicron) and 3 (Omicron sublineages) with the most unique epitopes, while Cluster 4 (Delta sublineages) emerged in the second half of 2021 with fewer unique epitopes. Cluster 1 epitopes showed a high pro-inflammatory propensity, while others exhibited a balanced cytokine induction. The clustering method effectively identified Spike groups that may contribute to immune evasion and clinical presentation, and explain in part the clinical outcome.IMPORTANCEIdentification of epitopes of emerging or endemic pathogens is of importance to estimate population responses and predict clinical outcomes and contribute to vaccine improvement. In the case of SARS-CoV-2, the virus within 6 months of circulation transitioned from the wild-type to novel variants leading to distinct clinical outcomes. Immunoinformatics analysis of viral epitopes of isolates from the Brazilian state of Rio Grande do Norte was performed using a clustering method. This analysis aimed to clarify how the introduction of novel variants in a population characterized by high infection and/or vaccination rates resulted in immune evasion and distinct clinical disease. Our analysis showed that the epitope profiles of each variant explained the respective potential for cytokine production, including the variants that were more likely to cause cytokine storms. Finally, it serves as a mean to explain the multi-wave patterns observed during SARS-CoV-2 pandemics.

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“…A second scenario could be the introduction of new viral quasi-species by a second and independent infection event which could explain the burst of mutations from day 1 to day 37. Previous studies have shown that reinfections occurred mostly by viruses from different genomic lineages, although reinfection can occasionally occur by viruses from the same genomic lineage [ 23 , 24 ].…”

Section: Case Presentationmentioning

confidence: 99%

SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin’s Lymphoma

Villaseñor-Echavarri

Gómez-Romero

Martin-Onraët

et al. 2023

Viruses

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Background. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) is the most transmissible ß-coronavirus in history, affecting all population groups. Immunocompromised patients, particularly cancer patients, have been highlighted as a reservoir to promote accumulation of viral mutations throughout persistent infection. Case presentation. We aimed to describe the clinical course and SARS-CoV-2 mutation profile for 102 days in an immunocompromised patient with non-Hodgkin’s lymphoma and COVID-19. We used RT-qPCR to quantify SARS-CoV-2 viral load over time and whole-virus genome sequencing to identify viral lineage and mutation profile. The patient presented with a persistent infection through 102 days while being treated with cytotoxic chemotherapy for non-Hodgkin’s lymphoma and received targeted therapy for COVID-19 with remdesivir and hyperimmune plasma. All sequenced samples belonged to the BA.1.1 lineage. We detected nine amino acid substitutions in five viral genes (Nucleocapsid, ORF1a, ORF1b, ORF13a, and ORF9b), grouped in two clusters: the first cluster with amino acid substitutions only detected on days 39 and 87 of sample collection, and the second cluster with amino acid substitutions only detected on day 95 of sample collection. The Spike gene remained unchanged in all samples. Viral load was dynamic but consistent with the disease flares. Conclusions. This report shows that the multiple mutations that occur in an immunocompromised patient with persistent COVID-19 could provide information regarding viral evolution and emergence of new SARS-CoV-2 variants.

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SARS-CoV-2 reinfections with BA.1 (Omicron) variant among fully vaccinated individuals in northeastern Brazil

Cited by 10 publications

References 32 publications

Molecular epidemiology of SARS‐CoV‐2 variants in circulation in the state of Maranhão, Brazil

Molecular epidemiology of SARS‐CoV‐2 variants in circulation in the state of Maranhão, Brazil

Understanding SARS-CoV-2 Spike glycoprotein clusters and their impact on immunity of the population from Rio Grande do Norte, Brazil

SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin’s Lymphoma

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