Genomic evidence of SARS-CoV-2 reinfection case with the emerging B.1.2 variant in Brazil

Fonseca, Vagner; Jesus, Ronaldo de; Adelino, Talita; Reis, Alexandre Barbosa; Souza, Breno Bernardes de; Ribeiro, Adriana Aparecida; Guimarães, Natália Rocha; Livorati, Miriam Teresinha Furlam Prado; Neto, Daniel Ferreira de Lima; Kato, Rodrigo Bentes; Portela, Layssa Miranda de Oliveira; Dutra, Leonardo Hermes; Freitas, Carla; Abreu, André Luiz de; Filizzola, Eduardo Regis Melo; Medeiros, Arnaldo Correia de; Iani, Felipe Campos de Melo; Carvalho, Glauco Rodrigues; Lourenço, José; Oliveira, Túlio de; Alcântara, Luiz Carlos Júnior; Giovanetti, Marta

doi:10.1016/j.jinf.2021.05.014

Cited by 13 publications

(7 citation statements)

References 8 publications

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“…These variants have a common mutation N501Y in the S protein receptor-binding domain (RBD), except the Delta variant, which results in the greater affinity of their S protein for ACE2, enhancing viral attachment and subsequent entry into host cells ( Kemp et al, 2020 ; Barton and MacGowan, 2021 ). The emergence of the novel variants has been particularly of great concern ( Rahman et al, 2021 ) since recently published data suggest that previous infections with SARS-CoV-2 may not protect an individual from new variants of SARS-CoV-2 giving rise to reinfection cases in the community ( Fonseca et al, 2021 ). Therefore, it is important to elucidate the genetic information of SARS-CoV-2 cases for clinical and therapeutic management.…”

Section: Introductionmentioning

confidence: 99%

A Case Report: Genetically Distinct Severe Acute Respiratory Syndrome Coronavirus-2 Variant Causing Reinfection

et al. 2021

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Background: The emergence of novel variants has been a great deal of international concern since the recently published data suggest that previous infections with SARS-CoV-2 may not protect an individual from new variants. We report a patient had two distinct episodes of COVID-19 with different variants of SARS-CoV-2.Methods: The nasopharyngeal samples collected from the two episodes were subjected to whole-genome sequencing and comparative genome analysis.Results: The first infection presented with mild symptoms, while the second infection presented with severe outcomes which occurred 74 days after the patient recovered from the first episode. He had elevated C-reactive protein, ferritin, and bilateral consolidation as a sign of acute infection. Genome analysis revealed that the strains from the first and second episodes belonged to two distinct Nexstrain clades 20B and 20I and Pangolin lineages B.1.1.25 and B.1.1.7, respectively. A total of 36 mutations were observed in the episode-2 strain when compared with the reference strain Wuhan-Hu-1. Among them, eight mutations were identified in the receptor-binding domain (RBD).Conclusion: Our findings concern whether the immunity acquired by natural infection or mass vaccination could confer adequate protection against the constantly evolving SARS-CoV-2. Therefore, continuous monitoring of genetic variations of SARS-CoV-2 strains is crucial for interventions such as vaccine and drug designs, treatment using monoclonal antibodies, and patient management.

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Section: Introductionmentioning

confidence: 99%

A Case Report: Genetically Distinct Severe Acute Respiratory Syndrome Coronavirus-2 Variant Causing Reinfection

et al. 2021

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“…The alpha variant carries E474K and L452R mutations in the spike protein, as well as D3L, R203K, S235F, and G204R in NP [27]. Lineage B.1.2 contains a Q667P mutation in the spike protein and P199L and P67S mutations in NP [28]. Both authentic virus variants could be recognized by NP-mAb-40/7 LFIA strips (Figure 3C).…”

Section: Screening Of Antibody Pairs In Lateral Flow Immunoassays (Lfias) To Detect Np Antigenmentioning

confidence: 97%

Monoclonal Antibodies against Nucleocapsid Protein of SARS-CoV-2 Variants for Detection of COVID-19

Chen

et al. 2021

IJMS

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Mitigation strategies of the coronavirus disease 2019 (COVID-19) pandemic have been greatly hindered by the continuous emergence of SARS-CoV-2 variants. New sensitive, rapid diagnostic tests for the wide-spectrum detection of viral variants are needed. We generated a panel of 41 monoclonal antibodies against the SARS-CoV-2 nucleocapsid protein (NP) by using mice hybridoma techniques. Of these mAbs, nine exhibited high binding activities and were applied in latex-based lateral flow immunoassays (LFIAs). The LFIAs utilizing NP-mAb-7 and -40 had the best sensitivity and lowest limit of detection: 8 pg for purified NP and 625 TCID50/mL for the authentic virus (hCoV-19/Taiwan/4/2020). The specificity tests showed that the NP-mAb-40/7 LFIA strips did not cross-react with five human coronavirus strains or 20 other common respiratory pathogens. Importantly, we found that 10 NP mutants, including alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2) variants, could be detected by NP-mAb-40/7 LFIA strips. A clinical study (n = 60) of the NP-mAb-40/7 LFIA strips demonstrated a specificity of 100% and sensitivity of 90% in infected individuals with cycle threshold (Ct) values < 29.5. These anti-NP mAbs have strong potential for use in the clinical detection of SARS-CoV-2 infection, whether the virus is wild-type or a variant of concern.

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“…A study conducted in the United Kingdom (UK) identified possible reinfections in 0.7% (95% CI 0.6-0·8%) of individuals infected during September-December 2020 and found no evidence that the frequency of reinfections was higher for the VOC Alpha than for pre-existing non-VOCs 19 . In Brazil, previous studies documented a few cases of reinfection with lineages B.1.1.28, B.1.1.33 and B.1.2 20-22 , with lineage P.2 that harbors the mutation S: E484K 23,24 and with the VOC Gamma 17,18 . However, there is no evidence that reinfections with Gamma were more frequent than with non-VOCs.…”

Section: Introductionmentioning

confidence: 97%

A case series of SARS-CoV-2 reinfections caused by the variant of concern Gamma in Brazil

Naveca

Nascimento

et al. 2021

Preprint

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SummaryThe rapid spread of the SARS-CoV-2 Variant of Concern (VOC) Gamma during late 2020 and early 2021 in Brazilian settings with high seroprevalence raised some concern about the potential role of reinfections in driving the epidemic. Very few cases of reinfection associated with the VOC Gamma, however, have been reported. Here we describe 25 cases of SARS-CoV-2 reinfection confirmed by real-time RT-PCR twice within months apart in Brazil. SARS-CoV-2 genomic analysis confirmed that individuals were primo-infected between March and December 2020 with distinct viral lineages, including B.1.1, B.1.1.28, B.1.1.33, B.1.195 and P.2, and then reinfected with the VOC Gamma between 3 to 12 months after primo-infection. The overall mean cycle threshold (Ct) value of the first (25.7) and second (24.5) episodes were roughly similar for the whole group and 14 individuals displayed mean Ct values < 25.0 at reinfection. Sera of 14 patients tested by plaque reduction neutralization test after reinfection displayed detectable neutralizing antibodies against Gamma and other SARS-CoV-2 variants (B.1.33, B.1.1.28 and Delta). All individuals have milder or no symptoms after reinfection and none required hospitalization. The present study demonstrates that the VOC Gamma was associated with reinfections during the second Brazilian epidemic wave in 2021 and raised concern about the potential infectiousness of reinfected subjects. Although individuals here analyzed failed to mount a long-term sterilizing immunity, they developed a high anti-Gamma neutralizing antibody response after reinfection that may provide some protection against severe disease.

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Genomic evidence of SARS-CoV-2 reinfection case with the emerging B.1.2 variant in Brazil

Cited by 13 publications

References 8 publications

A Case Report: Genetically Distinct Severe Acute Respiratory Syndrome Coronavirus-2 Variant Causing Reinfection

A Case Report: Genetically Distinct Severe Acute Respiratory Syndrome Coronavirus-2 Variant Causing Reinfection

Monoclonal Antibodies against Nucleocapsid Protein of SARS-CoV-2 Variants for Detection of COVID-19

A case series of SARS-CoV-2 reinfections caused by the variant of concern Gamma in Brazil

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