Vigilância genômica para SARS-CoV-2 como ferramenta para monitorizar entradas de variantes: o município de Apodi-RN como modelo
Data
2022-04-13
Autores
Freire Neto, Francisco Paulo 
Orientadores
Nader, Helena Bonciani
Tipo
Tese de doutorado
Título da Revista
ISSN da Revista
Título de Volume
Resumo
Objetivos: O estudo teve como objetivo geral avaliar os aspectos moleculares do
SARS-CoV-2 e as características clínicas da COVID-19 em Apodi, Rio Grande do
Norte, para entender a dinâmica do vírus, as entradas de variantes e a evolução
clínica pós-infeccção em uma população previamente naive. O município de Apodi
foi utilizado como modelo para avaliar a circulação viral e as implicações da
pandemia por tido sua população monitorizada e testada para Sars-CoV-2.
Métodos: Foram avaliadas pessoas com sintomas gripais que procuraram o Centro
de Combate a COVID-19 no município de Apodi, no período de abril de 2020 a julho
de 2021, os quais tiveram amostras de material nasal coletado para realização de
RT-qPCR para SARS-CoV-2. No período de agosto de 2021 a fevereiro de 2022 a
maioria das pessoas foi avaliada por testes rápidos de antígenos. Dados clínicos
foram analisados. A fim de identificar as linhagens circulantes no município, a cada
mês, 5 amostras de SARS-CoV-2 foram selecionadas e sequenciadas respeitando
dois requisitos básicos: 1) indivíduos geograficamente distantes entre si e 2) Cts
(threshold cycle) menores que 30. Análises filogenéticas e filodinâmicas das
sequências foram avaliadas. Resultados e discussão: Um total de 7840 pessoas
foram testadas por RT-qPCR, das quais 3391 (43%) foram positivas para
SARS-CoV-2, no período de abril de 2020 a julho de 2021 e 7397 testes de rápidos
de antígenos foram realizados no período de agosto de 2021 a 10 de fevereiro de
2022, das quais 2205 foram anti-SARS-CoV-2 reagentes. Os meses de maio de
2021 e de janeiro de 2022 apresentaram o maior número de óbitos e de casos da
COVID-19, respectivamente. Esses dados sugerem fortemente que o progresso da
vacinação proporcionou um declínio acentuado no número de óbitos. Como
observado em janeiro de 2022, o pico da doença não foi acompanhado por um
elevado número de mortes, pois cerca de 85% da população já se encontrava
vacinada, o que não se observava em maio de 2021, quando apenas 10% da
população Apodiense com pelo menos uma dose de vacina. Diferenças na
sintomatologia também foram observadas durante esses dois períodos, sendo os
casos de gravidade evidenciados majoritariamente nos indivíduos antes da vacinação. Análise genômica do vírus mostrou que 14 linhagens foram introduzidas
no município, sendo a linhagem P.1 (VOC gamma) a que apresentou a maior
incidência. Houve um padrão múltiplo na inserção das variantes acompanhando o
comportamento para outras localidades no Brasil e nos demais países do mundo. A
VOC Delta foi identificada no mês de julho, entretanto não houve um aumento no
número de casos nos meses seguintes. A entrada da P.1 está associada ao aumento
no número de casos e de óbitos. Essa variante se mostrou rapidamente a mais
prevalente, ficando em torno de 80% dentre as amostras testadas. Além disso, foi
visto que as amostras positivas para P.1 mostraram uma capacidade de infecção
cerca de 10x maior que as variantes que a precederam, bem como uma capacidade
de causar óbitos em indivíduos mais jovens. Conclusões: A entrada da variante P.1
precedeu o aumento no número de casos e de óbitos no decurso de fevereiro de
2021 a junho de 2021 e sua análise filogenética mostrou que a mesma apresentou
um padrão de inserção múltiplo na cidade. Em seguida, verificou-se também a
entrada das variantes Delta e Ômicron. Apesar de tais variantes apresentarem um
alto índice de transmissibilidade, a variante Ômicron destacou-se por promover um
recorde no número de casos os quais não foram incididos sobre o número de óbitos,
com a maioria dos indivíduos apresentando sintomas leves no trato respiratório
superior. Esses dados refletem o papel relevante da proteção vacinal ao longo do
ano de 2021. A entrada de variantes, bem como as mutações às quais os vírus
estão sujeitos, conforme os estudos realizados em Apodi, mostram a magnitude do
problema para controle da disseminação viral. O entendimento, além da antecipação
desses eventos, pode ajudar nas estratégias de controle da disseminação do
SARS-CoV-2 para ter-se uma chance de evitar a endemização deste vírus. Todos
esses dados reforçam ainda mais a importância da vigilância genômica no combate
e controle de doenças infecto-contagiosas e o seu potencial para compreender a
biologia viral, contribuindo assim para o melhoramento e o desenvolvimento de
vacinas e de novos antivirais
Objectives: The general objective of this study was to evaluate the molecular aspects of SARS-CoV-2 and the clinical characteristics of COVID-19 in Apodi, state of Rio Grande do Norte, to understand the dynamics of the virus, the entry of variants and the clinical evolution in a previously naive population using this municipality as a model for viral circulation. Methods: People with respiratory symptoms who sought the COVID-19 testing center in the municipality of Apodi were evaluated from April 2020 to July 2021 and had samples of nasal material collected to perform RT-qPCR for SARS-CoV-2 as well as rapid antigen tests were performed from August 2021 to February 2022. Clinical data were analyzed. In order to identify the circulating strains in the municipality, each month, 5 samples of SARS-CoV-2 were selected and sequenced regarding two basic requirements: 1) geographical distance between individuals and 2) Cts (threshold cycle) lower than 30. Phylogenetic and phylodynamic analysis of the sequences were evaluated. Results: A total of 7840 people were tested from April 2020 to July 2021 by RT-qPCR, of which 3391 (43%) were positive for SARS-CoV-2 and 7397 rapid antigen tests were performed from August 2021 to February 2022, of which 2205 were anti-SARS-CoV-2 reagents. May 2021 and January 2022 had the highest number of deaths and COVID-19 cases, respectively. This data strongly suggests that the progress of vaccination has led to a sharp decline in the number of deaths. As observed in January 2022, the peak of the disease was not accompanied by a high number of deaths, because the vaccination rate was over 85% in the municipality, which was not observed in May 2021, when only 10% of the Apodiense population was vaccinated with at least one dose. Differences in symptoms were also observed during those periods in which severity cases were verified the most in individuals before vaccination. Genomic analysis of the virus showed that 14 strains were introduced in the municipality, with the P.1 strain (VOC gamma) showing the highest incidence. There was a multiple pattern in the insertion of variants, following the behavior for other locations in Brazil and in other countries of the world. Delta VOC was identified in July, however there was no increase in the number of cases in the following months. The entry of P.1 was 10 associated with an increase in the number of cases and deaths. This variant quickly proved to be the most prevalent, reaching around 80% of the samples tested. In addition, P.1 positive samples showed an infection capacity about 10 times greater than the variants that preceded it, as well as an ability to cause death in younger individuals. Conclusions: The entry of the P.1 variant preceded the increase in the number of cases and deaths from February 2021 to June 2021 and its phylogenetic analysis showed a multiple insertion pattern in Apodi. Then, the entry of Delta and Ômicron variants was also verified. Despite these variants having a high rate of transmissibility, the Ômicron variant stood out for promoting a record in the number of cases which were not affected by the number of deaths, with the majority of individuals experiencing mild upper respiratory tract symptoms. These data reflect the relevant role of vaccine protection throughout the year 2021. According to the studies carried out in Apodi, the entry of variants, as well as the mutations to which the viruses are subject, show the magnitude of the problem to control viral dissemination. Understanding these events, could predict and enlighten strategies to control the spread of SARS-CoV-2, thus avoiding the endemicity of this virus. All data further reinforce the importance of genomic surveillance in controlling infectious diseases and its potential to understand viral biology, contributing to the improvement and the development of vaccines and new antivirals.
Objectives: The general objective of this study was to evaluate the molecular aspects of SARS-CoV-2 and the clinical characteristics of COVID-19 in Apodi, state of Rio Grande do Norte, to understand the dynamics of the virus, the entry of variants and the clinical evolution in a previously naive population using this municipality as a model for viral circulation. Methods: People with respiratory symptoms who sought the COVID-19 testing center in the municipality of Apodi were evaluated from April 2020 to July 2021 and had samples of nasal material collected to perform RT-qPCR for SARS-CoV-2 as well as rapid antigen tests were performed from August 2021 to February 2022. Clinical data were analyzed. In order to identify the circulating strains in the municipality, each month, 5 samples of SARS-CoV-2 were selected and sequenced regarding two basic requirements: 1) geographical distance between individuals and 2) Cts (threshold cycle) lower than 30. Phylogenetic and phylodynamic analysis of the sequences were evaluated. Results: A total of 7840 people were tested from April 2020 to July 2021 by RT-qPCR, of which 3391 (43%) were positive for SARS-CoV-2 and 7397 rapid antigen tests were performed from August 2021 to February 2022, of which 2205 were anti-SARS-CoV-2 reagents. May 2021 and January 2022 had the highest number of deaths and COVID-19 cases, respectively. This data strongly suggests that the progress of vaccination has led to a sharp decline in the number of deaths. As observed in January 2022, the peak of the disease was not accompanied by a high number of deaths, because the vaccination rate was over 85% in the municipality, which was not observed in May 2021, when only 10% of the Apodiense population was vaccinated with at least one dose. Differences in symptoms were also observed during those periods in which severity cases were verified the most in individuals before vaccination. Genomic analysis of the virus showed that 14 strains were introduced in the municipality, with the P.1 strain (VOC gamma) showing the highest incidence. There was a multiple pattern in the insertion of variants, following the behavior for other locations in Brazil and in other countries of the world. Delta VOC was identified in July, however there was no increase in the number of cases in the following months. The entry of P.1 was 10 associated with an increase in the number of cases and deaths. This variant quickly proved to be the most prevalent, reaching around 80% of the samples tested. In addition, P.1 positive samples showed an infection capacity about 10 times greater than the variants that preceded it, as well as an ability to cause death in younger individuals. Conclusions: The entry of the P.1 variant preceded the increase in the number of cases and deaths from February 2021 to June 2021 and its phylogenetic analysis showed a multiple insertion pattern in Apodi. Then, the entry of Delta and Ômicron variants was also verified. Despite these variants having a high rate of transmissibility, the Ômicron variant stood out for promoting a record in the number of cases which were not affected by the number of deaths, with the majority of individuals experiencing mild upper respiratory tract symptoms. These data reflect the relevant role of vaccine protection throughout the year 2021. According to the studies carried out in Apodi, the entry of variants, as well as the mutations to which the viruses are subject, show the magnitude of the problem to control viral dissemination. Understanding these events, could predict and enlighten strategies to control the spread of SARS-CoV-2, thus avoiding the endemicity of this virus. All data further reinforce the importance of genomic surveillance in controlling infectious diseases and its potential to understand viral biology, contributing to the improvement and the development of vaccines and new antivirals.