RESUMO
The disease coronavirus COVID-19 has been the cause of millions of deaths worldwide. Among the proteins of SARS-CoV-2, non-structural protein 12 (NSP12) plays a key role during COVID infection and is part of the RNA-dependent RNA polymerase complex. The monitoring of NSP12 polymorphisms is extremely important for the design of new antiviral drugs and monitoring of viral evolution. This study analyzed the NSP12 mutations detected in circulating SARS-CoV-2 during the years 2020 to 2022 in the population of the city of Manaus, Amazonas, Brazil. The most frequent mutations found were P323L and G671S. Reports in the literature indicate that these mutations are related to transmissibility efficiency, which may have contributed to the extremely high numbers of cases in this location. In addition, two mutations described here (E796D and R914K) are close and have RMSD that is similar to the mutations M794V and N911K, which have been described in the literature as influential on the performance of the NSP12 enzyme. These data demonstrate the need to monitor the emergence of new mutations in NSP12 in order to better understand their consequences for the treatments currently used and in the design of new drugs.
Assuntos
COVID-19 , RNA-Polimerase RNA-Dependente de Coronavírus , SARS-CoV-2 , Humanos , Brasil , Simulação por Computador , COVID-19/virologia , COVID-19/transmissão , Mutação/genética , SARS-CoV-2/genética , Proteínas não Estruturais Virais/genética , RNA-Polimerase RNA-Dependente de Coronavírus/genética , RNA-Polimerase RNA-Dependente de Coronavírus/metabolismoRESUMO
The SARS-CoV-2 variants of concern (VOCs) Delta and Omicron spread globally during mid and late 2021, respectively. In this study, we compare the dissemination dynamics of these VOCs in the Amazonas state, one of Brazil's most heavily affected regions. We sequenced the virus genome from 4128 patients collected in Amazonas between July 1st, 2021, and January 31st, 2022, and investigated the viral dynamics using a phylodynamic approach. The VOCs Delta and Omicron BA.1 displayed similar patterns of phylogeographic spread but different epidemic dynamics. The replacement of Gamma by Delta was gradual and occurred without an upsurge of COVID-19 cases, while the rise of Omicron BA.1 was extremely fast and fueled a sharp increase in cases. Thus, the dissemination dynamics and population-level impact of new SARS-CoV-2 variants introduced in the Amazonian population after mid-2021, a setting with high levels of acquired immunity, greatly vary according to their viral phenotype.
Assuntos
COVID-19 , SARS-CoV-2 , Humanos , Brasil , Imunidade AdaptativaRESUMO
The rapid spread of the SARS-CoV-2 Variant of Concern (VOC) Gamma in Amazonas during early 2021 fueled a second large COVID-19 epidemic wave and raised concern about the potential role of reinfections. Very few cases of reinfection associated with the VOC Gamma have been reported to date, and their potential impact on clinical, immunological, and virological parameters remains largely unexplored. Here we describe 25 cases of SARS-CoV-2 reinfection in Brazil. SARS-CoV-2 genomic analysis confirmed that individuals were primo-infected with distinct viral lineages between March and December 2020 (B.1.1, B.1.1.28, B.1.1.33, B.1.195, and P.2) and reinfected with the VOC Gamma between 3 to 12 months after primo-infection. We found a similar mean cycle threshold (Ct) value and limited intra-host viral diversity in both primo-infection and reinfection samples. Sera of 14 patients tested 10-75 days after reinfection displayed detectable neutralizing antibodies (NAb) titers against SARS-CoV-2 variants that circulated before (B.1.*), during (Gamma), and after (Delta and Omicron) the second epidemic wave in Brazil. All individuals had milder or no symptoms after reinfection, and none required hospitalization. These findings demonstrate that individuals reinfected with the VOC Gamma may display relatively high RNA viral loads at the upper respiratory tract after reinfection, thus contributing to onward viral transmissions. Despite this, our study points to a low overall risk of severe Gamma reinfections, supporting that the abrupt increase in hospital admissions and deaths observed in Amazonas and other Brazilian states during the Gamma wave was mostly driven by primary infections. Our findings also indicate that most individuals analyzed developed a high anti-SARS-CoV-2 NAb response after reinfection that may provide some protection against reinfection or disease by different SARS-CoV-2 variants.
Assuntos
COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , Brasil/epidemiologia , COVID-19/epidemiologia , Diversidade de Anticorpos , Raios gama , Reinfecção , Gravidade do PacienteRESUMO
The Amazonas was one of the most heavily affected Brazilian states by the COVID-19 epidemic. Despite a large number of infected people, particularly during the second wave associated with the spread of the Variant of Concern (VOC) Gamma (lineage P.1), SARS-CoV-2 continues to circulate in the Amazonas. To understand how SARS-CoV-2 persisted in a human population with a high immunity barrier, we generated 1,188 SARS-CoV-2 whole-genome sequences from individuals diagnosed in the Amazonas state from 1st January to 6th July 2021, of which 38 were vaccine breakthrough infections. Our study reveals a sharp increase in the relative prevalence of Gamma plus (P.1+) variants, designated Pango Lineages P.1.3 to P.1.6, harboring two types of additional Spike changes: deletions in the N-terminal (NTD) domain (particularly Δ144 or Δ141-144) associated with resistance to anti-NTD neutralizing antibodies or mutations at the S1/S2 junction (N679K or P681H) that probably enhance the binding affinity to the furin cleavage site, as suggested by our molecular dynamics simulations. As lineages P.1.4 (S:N679K) and P.1.6 (S:P681H) expanded (Re > 1) from March to July 2021, the lineage P.1 declined (Re < 1) and the median Ct value of SARS-CoV-2 positive cases in Amazonas significantly decreases. Still, we did not find an increased incidence of P.1+ variants among breakthrough cases of fully vaccinated patients (71%) in comparison to unvaccinated individuals (93%). This evidence supports that the ongoing endemic transmission of SARS-CoV-2 in the Amazonas is driven by the spread of new local Gamma/P.1 sublineages that are more transmissible, although not more efficient to evade vaccine-elicited immunity than the parental VOC. Finally, as SARS-CoV-2 continues to spread in human populations with a declining density of susceptible hosts, the risk of selecting more infectious variants or antibody evasion mutations is expected to increase. IMPORTANCE The continuous evolution of SARS-CoV-2 is an expected phenomenon that will continue to happen due to the high number of cases worldwide. The present study analyzed how a Variant of Concern (VOC) could still circulate in a population hardly affected by two COVID-19 waves and with vaccination in progress. Our results showed that the answer behind that was a new generation of Gamma-like viruses, which emerged locally carrying mutations that made it more transmissible and more capable of spreading, partially evading prior immunity triggered by natural infections or vaccines. With thousands of new cases daily, the current pandemics scenario suggests that SARS-CoV-2 will continue to evolve and efforts to reduce the number of infected subjects, including global equitable access to COVID-19 vaccines, are mandatory. Thus, until the end of pandemics, the SARS-CoV-2 genomic surveillance will be an essential tool to better understand the drivers of the viral evolutionary process.
Assuntos
COVID-19/enzimologia , Furina/metabolismo , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/genética , Motivos de Aminoácidos , Brasil/epidemiologia , COVID-19/epidemiologia , COVID-19/transmissão , COVID-19/virologia , Vacinas contra COVID-19/administração & dosagem , Furina/genética , Genômica , Humanos , Mutação , Filogenia , SARS-CoV-2/classificação , SARS-CoV-2/isolamento & purificação , SARS-CoV-2/metabolismo , Glicoproteína da Espícula de Coronavírus/metabolismoRESUMO
The coronavirus disease COVID-19 has been the cause of millions of deaths worldwide. Among the SARS-CoV-2 proteins, the non-structural protein 1 (NSP1) has great importance during the virus infection process and is present in both alpha and beta-CoVs. Therefore, monitoring of NSP1 polymorphisms is crucial in order to understand their role during infection and virus-induced pathogenicity. Herein, we analyzed how mutations detected in the circulating SARS-CoV-2 in the population of the city of Manaus, Amazonas state, Brazil could modify the tertiary structure of the NSP1 protein. Three mutations were detected in the SARS-CoV-2 NSP1 gene: deletion of the amino acids KSF from positions 141 to 143 (delKSF), SARS-CoV-2, lineage B.1.195; and two substitutions, R29H and R43C, SARS-CoV-2 lineage B.1.1.28 and B.1.1.33, respectively. The delKSF was found in 47 samples, whereas R29H and R43C were found in two samples, one for each mutation. The NSP1 structures carrying the mutations R43C and R29H on the N-terminal portion (e.g. residues 10 to 127) showed minor backbone divergence compared to the Wuhan model. However, the NSP1 C-terminal region (residues 145 to 180) was severely affected in the delKSF and R29H mutants. The intermediate variable region (residues 144 to 148) leads to changes in the C-terminal region, particularly in the delKSF structure. New investigations must be carried out to analyze how these changes affect NSP1 activity during the infection. Our results reinforce the need for continuous genomic surveillance of SARS-CoV-2 to better understand virus evolution and assess the potential impact of the viral mutations on the approved vaccines and future therapies.
Assuntos
COVID-19/epidemiologia , SARS-CoV-2/genética , Proteínas não Estruturais Virais/genética , Sequência de Aminoácidos/genética , Substituição de Aminoácidos/genética , Brasil/epidemiologia , Humanos , Polimorfismo Genético/genética , Deleção de Sequência/genéticaRESUMO
The northern state of Amazonas is among the regions in Brazil most heavily affected by the COVID-19 epidemic and has experienced two exponentially growing waves, in early and late 2020. Through a genomic epidemiology study based on 250 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from different Amazonas municipalities sampled between March 2020 and January 2021, we reveal that the first exponential growth phase was driven mostly by the dissemination of lineage B.1.195, which was gradually replaced by lineage B.1.1.28 between May and June 2020. The second wave coincides with the emergence of the variant of concern (VOC) P.1, which evolved from a local B.1.1.28 clade in late November 2020 and replaced the parental lineage in <2 months. Our findings support the conclusion that successive lineage replacements in Amazonas were driven by a complex combination of variable levels of social distancing measures and the emergence of a more transmissible VOC P.1 virus. These data provide insights to understanding the mechanisms underlying the COVID-19 epidemic waves and the risk of dissemination of SARS-CoV-2 VOC P.1 in Brazil and, potentially, worldwide.
Assuntos
COVID-19/epidemiologia , COVID-19/virologia , Genoma Viral/genética , SARS-CoV-2/genética , Adulto , Brasil/epidemiologia , Teste de Ácido Nucleico para COVID-19 , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Epidemiologia Molecular , Filogenia , Filogeografia , Análise Espaço-TemporalRESUMO
A doença do coronavírus COVID-19 tem sido a causa de milhões de mortes em todo o mundo. Dentre as proteínas do SARS-CoV-2, a proteína não estrutural 1 (NSP1) tem grande importância durante o processo de infecção do vírus e está presente tanto em alfa quanto em beta-CoVs. Portanto, o monitoramento dos polimorfismos de NSP1 é crucial para entender seu papel durante a infecção e a patogenicidade induzida pelo vírus. Aqui, analisamos como mutações detectadas no SARS-CoV-2 circulante na população da cidade de Manaus, estado do Amazonas, Brasil, poderiam modificar a estrutura terciária da proteína NSP1. Três mutações foram detectadas no gene SARS-CoV-2 NSP1: deleção dos aminoácidos KSF das posições 141 a 143 (delKSF), SARS-CoV-2, linhagem B.1.195; e duas substituições, R29H e R43C, linhagem SARSCoV-2 B.1.1.28 e B.1.1.33, respectivamente. O delKSF foi encontrado em 47 amostras, enquanto R29H e R43C foram encontrados em duas amostras, uma para cada mutação. As estruturas NSP1 que carregam as mutações R43C e R29H na porção N-terminal (por exemplo, resíduos 10 a 127) mostraram divergência de espinha dorsal menor em comparação com o modelo Wuhan. No entanto, a região C-terminal de NSP1 (resíduos 145 a 180) foi severamente afetada nos mutantes delKSF e R29H. A região variável intermediária (resíduos 144 a 148) leva a alterações na região C-terminal, particularmente na estrutura delKSF. Novas investigações devem ser realizadas para analisar como essas alterações afetam a atividade da NSP1 durante a infecção. Nossos resultados reforçam a necessidade de vigilância genômica contínua do SARS-CoV-2 para entender melhor a evolução do vírus e avaliar o impacto potencial das mutações virais nas vacinas aprovadas e futuras terapias.
RESUMO
Aponta as causas do crescimento do número de casos de Covid-19 no Amazonas e das sucessivas substituições de linhagens do Sars-CoV-2. O estudo indicou que esses fatores foram impulsionados por uma combinação de diminuições das medidas de distanciamento social e pelo surgimento de uma forma mais transmissível do vírus, a variante P.1, identificada em meados de novembro de 2020. Essa variante causou um aumento exponencial da doença, o que estabeleceu a segunda onda da epidemia no estado.
Assuntos
Infecções por Coronavirus , Coronavirus , SARS-CoV-2 , Ecossistema Amazônico , BrasilRESUMO
Neste relatório (pre-print), são apresentados três casos de reinfecção causados pela Variante de Preocupação (VOC) P.1, também conhecida como "cepa de Manaus". As três pacientes eram mulheres adultas, e tiveram a primeira infecção durante a primeira onda da pandemia na primeira metade de 2020. Nos três casos, a linhagem detectada no primeiro diagnóstico molecular era diferente da encontrada posteriormente, evidência da reinfecção. Dois dos casos de reinfecção tiveram apresentação de sintomas leves, enquanto o terceiro foi assintomático, apesar de a quantidade de material genético viral detectado sugerir cargas virais elevadas. As evidências aqui apresentadas sugerem que a imunidade após infecção primária por linhagens anteriores à circulação daquelas contendo a mutação E484K não impede uma nova infecção pela variante P.1, e nem mesmo que pessoas reinfectadas por esta variante espalhem o vírus, embora seja possível que tenha protegido estas três pacientes do desenvolvimento de sintomas graves.
RESUMO
Neste relatório (pre-print), são apresentados três casos de reinfecção causados pela Variante de Preocupação (VOC) P.1, também conhecida como "cepa de Manaus". As três pacientes eram mulheres adultas, e tiveram a primeira infecção durante a primeira onda da pandemia na primeira metade de 2020. Nos três casos, a linhagem detectada no primeiro diagnóstico molecular era diferente da encontrada posteriormente, evidência da reinfecção. Dois dos casos de reinfecção tiveram apresentação de sintomas leves, enquanto o terceiro foi assintomático, apesar de a quantidade de material genético viral detectado sugerir cargas virais elevadas. As evidências aqui apresentadas sugerem que a imunidade após infecção primária por linhagens anteriores à circulação daquelas contendo a mutação E484K não impede uma nova infecção pela variante P.1, e nem mesmo que pessoas reinfectadas por esta variante espalhem o vírus, embora seja possível que tenha protegido estas três pacientes do desenvolvimento de sintomas graves.