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Teixeira DG, Rodrigues-Neto JF, da Cunha DCS, Jeronimo SMB. Understanding SARS-CoV-2 spike glycoprotein clusters and their impact on immunity of the population from Rio Grande do Norte, Brazil. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105556. [PMID: 38242186 DOI: 10.1016/j.meegid.2024.105556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
SARS-CoV-2 genome underwent mutations since it started circulating within the human population. The aim of this study was to understand the fluctuation of the spike clusters concomitant to the population immunity either due to natural infection and/or vaccination in a state of Brazil that had both high rate of natural infection and vaccination coverage. A total of 1725 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 to correlate with circulating variants. From March 2020 to June 2022, the state of Rio Grande do Norte reported 579,931 COVID-19 cases with a 1.4% fatality rate across the 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 (AY.*), which circulated in Brazil in the latter half of 2021, featuring fewer unique epitopes. Cluster 1 (Gamma (P.1 + P.1.*)) dominated the first half of 2021. Late 2021 had two new clusters, Cluster 2 (Omicron, (B.1.1.529 + BA.*)), and Cluster 3 (BA.*) with the most unique epitopes, in addition to Cluster 4 (Delta sub lineages) which 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.
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Affiliation(s)
- Diego Gomes Teixeira
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - João Firmino Rodrigues-Neto
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Escola Multicampi de Ciências Médicas do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Caicó, Rio Grande do Norte, Brazil
| | - Dayse Caroline Severiano da Cunha
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Selma Maria Bezerra Jeronimo
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Departmento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande Norte, Natal, Rio Grande do Norte, Brazil; Instituto Nacional de Ciência e Tecnologia de Doenças Tropicais, Natal, Rio Grande do Norte, Brazil.
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Ismail NF, Rahman AE, Kulkarni D, Zhu F, Wang X, del Carmen Morales G, Srivastava A, Allen KE, Spinardi J, Kyaw MH, Nair H. Incidence and outcome of SARS-CoV-2 reinfection in the pre-Omicron era: A global systematic review and meta-analysis. J Glob Health 2023; 13:06051. [PMID: 37994839 PMCID: PMC10667793 DOI: 10.7189/jogh.13.06051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023] Open
Abstract
Background With the emergence of new variants and sub-lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), reinfections can significantly impact herd immunity, vaccination policies, and decisions on other public health measures. We conducted a systematic review and meta-analysis to synthesise the global evidence on SARS-CoV-2 reinfections in the pre-Omicron era. Methods We searched five global databases (MEDLINE, Embase, CINAHL Plus, Global Health, WHO COVID-19) on 12 May 2022 and 28 July 2023 and three Chinese databases (CNKI, Wanfang, CQvip) on 16 October 2022 for articles reporting incidence and outcomes of SARS-CoV-2 reinfection before the period of Omicron (B.1.1.529) predominance. We assessed risk of bias using Joanna Briggs Institute critical appraisal tools and conducted meta-analyses with random effects models to estimate the proportion of SARS-CoV-2 reinfection among initially infected cases and hospitalisation and mortality proportions among reinfected ones. Results We identified 7593 studies and extracted data from 64 included ones representing 21 countries. The proportion of SARS-CoV-2 reinfection was 1.16% (95% confidence interval (CI) = 1.01-1.33) based on 11 639 247 initially infected cases, with ≥45 days between the two infections. Healthcare providers (2.28%; 95% CI = 1.37-3.40) had a significantly higher risk of reinfection than the general population (1.00%; 95% CI = 0.81-1.20), while young adults aged 18 to 35 years (1.01%; 95% CI = 0.8-1.25) had a higher reinfection burden than other age groups (children <18 years old: 0.57%; 95% CI = 0.39-0.79, older adults aged 36-65 years old: 0.53%; 95% CI = 0.41-0.65, elderly >65 years old: 0.37%; 95% CI = 0.15-0.66). Among the reinfected cases, 8.12% (95% CI = 5.30-11.39) were hospitalised, 1.31% (95% CI = 0.29-2.83) were admitted to the intensive care unit, and 0.71% (95% CI = 0.02-2.01) died. Conclusions Our data suggest a relatively low risk of SARS-CoV-2 reinfection in the pre-Omicron era, but the risk of hospitalisation was relatively high among the reinfected cases. Considering the possibility of underdiagnosis, the reinfection burden may be underestimated. Registration PROSPERO: CRD42023449712.
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Affiliation(s)
- Nabihah Farhana Ismail
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
- Communicable Disease Control Unit, Public Health Department, Johor State, Malaysia
| | - Ahmed Ehsanur Rahman
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
- International Centre for Diarrhoeal Diseases Research, Bangladesh
| | - Durga Kulkarni
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
| | - Fuyu Zhu
- School of Public Health, Nanjing Medical University, Jiangsu, China
| | - Xin Wang
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
- School of Public Health, Nanjing Medical University, Jiangsu, China
| | | | - Amit Srivastava
- Pfizer, Vaccines, Emerging Markets
- Orbital Therapeutics, United States of America
| | | | | | | | - Harish Nair
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
- School of Public Health, Nanjing Medical University, Jiangsu, China
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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de Sousa LAF, Ferreira LSDS, Lobato LFL, Ferreira HLDS, Sousa LHDS, Santos VFD, Nunes PRS, Maramaldo CEC, Neto SS, Sampaio HL, Silva FVD, Brito MDC, Lima WKR, Lima CZGPA, Neto LGL. Molecular epidemiology of SARS-CoV-2 variants in circulation in the state of Maranhão, Brazil. J Med Virol 2023; 95:e29092. [PMID: 37724346 DOI: 10.1002/jmv.29092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/20/2023]
Abstract
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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Affiliation(s)
- Luis Artur Ferreira de Sousa
- Virology Laboratory, Postgraduation Program in Microbial Biology, CEUMA University, UniCEUMA, São Luís, Maranhão, Brazil
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
| | | | - Luis Felipe Lima Lobato
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
- Postgraduation Program in Tropical Medicine-IOC/FIOCRUZ-RJ, Rio de Janeiro, Brazil
| | | | | | - Valdenice Ferreira Dos Santos
- Post-graduate Programme in Biodiversity and Biotechnology (BIONORTE), CEUMA University, UniCEUMA, São Luís, Maranhão, Brazil
| | - Paulo Ricardo Silva Nunes
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
| | | | - Sebastião Silveira Neto
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
| | - Hellen Lobato Sampaio
- Virology Laboratory, Postgraduation Program in Microbial Biology, CEUMA University, UniCEUMA, São Luís, Maranhão, Brazil
| | - Fabiano Vieira da Silva
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
- Postgraduation Program in Tropical Medicine-IOC/FIOCRUZ-RJ, Rio de Janeiro, Brazil
| | - Marcelo da Costa Brito
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
| | - Washington Kleber Rodrigues Lima
- Post-graduate Programme in Biodiversity and Biotechnology (BIONORTE), CEUMA University, UniCEUMA, São Luís, Maranhão, Brazil
- UniCEUMA, CEUMA University, São Luís, Maranhão, Brazil
| | | | - Lidio Gonçalves Lima Neto
- Virology Laboratory, Postgraduation Program in Microbial Biology, CEUMA University, UniCEUMA, São Luís, Maranhão, Brazil
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
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Girardi V, Gularte JS, Demoliner M, da Silva MS, Filippi M, de Abreu Góes Pereira VM, Hansen AW, Rosa RB, Fleck JD, Spilki FR. Reinfection by SARS-CoV-2 by divergent Omicron sublineages, 16 days apart. Braz J Microbiol 2023; 54:1847-1851. [PMID: 37269428 PMCID: PMC10239041 DOI: 10.1007/s42770-023-01018-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/09/2023] [Indexed: 06/05/2023] Open
Abstract
Since the beginning of the SARS-CoV-2 pandemic, studies on the variants and sublineages stand out, mainly in the cases of reinfection in a short period. In this study, we describe a case of infection by BA.1.1 sublineage in an individual from Southern Brazil. The same patient acquired reinfection with sublineage BA.2 within 16 days after the first detection. The viral extraction and RT-qPCR were performed on the samples LMM72045 (collected in May 2022) and LMM72044 (collected in June 2022). After the confirmation of SARS-CoV-2 infection, we conducted the sequencing and viral genome analysis. This case of reinfection affected a 52-year-old male patient, without comorbidities, with three doses of vaccines against COVID-19, showing symptoms on May 19. These symptoms lasted for approximately six days. The patient returned to work activities on May 30. However, on June 4, the patient felt a new round of clinical signs that lasted for approximately seven days. Analysis of the viral genomes recovered from patients' clinical samples revealed that the two COVID-19 episodes were related to two divergent VOC Omicron sublineages, namely, BA.1.1 for the first round of symptoms and BA.2 for the second infection. Based on our findings, we can say that the present case of reinfection is the shortest described so far.
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Affiliation(s)
- Viviane Girardi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil.
| | - Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Mariana Soares da Silva
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Vyctoria Malayhka de Abreu Góes Pereira
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Alana Witt Hansen
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Raquel Borba Rosa
- Secretaria Municipal de Saúde, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Juliane Deise Fleck
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
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Arabi M, Al-Najjar Y, Sharma O, Kamal I, Javed A, Gohil HS, Paul P, Al-Khalifa AM, Laws S, Zakaria D. Role of previous infection with SARS-CoV-2 in protecting against omicron reinfections and severe complications of COVID-19 compared to pre-omicron variants: a systematic review. BMC Infect Dis 2023; 23:432. [PMID: 37365490 DOI: 10.1186/s12879-023-08328-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/13/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 virus elicited a major public concern worldwide since December 2019 due to the high number of infections and deaths caused by COVID-19. The Omicron variant was detected in October 2021 which evolved from the wild-type SARS-CoV-2 and was found to possess many mutations. Omicron exhibited high transmissibility and immune evasion as well as reduced severity when compared to the earlier variants. Although vaccinated individuals were largely protected against infections in previous waves, the high prevalence of both reinfections and breakthrough infections with Omicron was observed. The aim of this review is to understand the effectiveness of previous infection on subsequent reinfection, given its significance in driving public health policy, including vaccination prioritization and lockdown requirements. METHODS A comprehensive literature search was conducted using several databases to target studies reporting data related to the effectiveness of the previous infection with SARS-CoV-2 in protecting against the Omicron variant. Screening of the studies, quality assessment and data extraction were conducted by two reviewers for each study. RESULTS Only 27 studies met our inclusion criteria. It was observed that previous infection was less effective in preventing reinfections with the Omicron variant compared to the Delta variant irrespective of vaccination status. Furthermore, being fully vaccinated with a booster dose provided additional protection from the Omicron variant. Additionally, most infections caused by Omicron were asymptomatic or mild and rarely resulted in hospitalizations or death in comparison to the Delta wave. CONCLUSION A majority of the studies reached a consensus that although previous infection provides some degree of immunity against Omicron reinfection, it is much lower in comparison to Delta. Full vaccination with two doses was more protective against Delta than Omicron. Receiving a booster dose provided additional protection against Omicron. It is therefore clear that neither vaccination nor previous infection alone provide optimal protection; hybrid immunity has shown the best results in terms of protecting against either Omicron or Delta variants. However, additional research is needed to quantify how long immunity from vaccination versus previous infection lasts and whether individuals will benefit from variant-specific vaccinations to enhance protection from infection.
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Affiliation(s)
- Maryam Arabi
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Yousef Al-Najjar
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Omna Sharma
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Ibtihal Kamal
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Aimen Javed
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Harsh S Gohil
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Pradipta Paul
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Aljazi M Al-Khalifa
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Sa'ad Laws
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Dalia Zakaria
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar.
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SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin's Lymphoma. Viruses 2023; 15:v15020377. [PMID: 36851588 PMCID: PMC9962578 DOI: 10.3390/v15020377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/03/2023] Open
Abstract
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 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis. Viruses 2022; 14:v14122715. [PMID: 36560720 PMCID: PMC9784312 DOI: 10.3390/v14122715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/09/2022] Open
Abstract
Several studies have monitored the SARS-CoV-2 variants in Brazil throughout the pandemic. Here, we systematically reviewed and conducted a scientometric analysis of the SARS-CoV-2 genomic surveillance studies using Brazilian samples. A Pubmed database search on October 2022 returned 492 articles, of which 106 were included. Ninety-six different strains were reported, with variant of concern (VOC) gamma (n = 35,398), VOC delta (n = 15,780), and the variant of interest zeta (n = 1983) being the most common. The top three states with the most samples in the published articles were São Paulo, Rio de Janeiro, and Minas Gerais. Whereas the first year of the pandemic presented primary circulation of B.1.1.28 and B.1.1.33 variants, consecutive replacements were observed between them and VOI zeta, VOC gamma, VOC delta, and VOC omicron. VOI mu, VOI lambda, VOC alpha, and VOC beta were also detected but failed to reach significant circulation. Co-infection, re-infection, and vaccine breakthrough reports were found. Article co-citation differed from the co-authorship structure. Despite the limitations, we expect to give an overview of Brazil's genomic surveillance studies and contribute to future research execution.
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