Dataset Information

Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status.

ABSTRACT: The emergence and global dissemination of Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) variants of concern (VOCs) have been described as the main factor driving the Coronavirus Disease 2019 pandemic. In Brazil, the Gamma variant dominated the epidemiological scenario during the first period of 2021. Many Brazilian regions detected the Delta variant after its first description and documented its spread. To monitor the introduction and spread of VOC Delta, we performed Polymerase Chain Reaction (PCR) genotyping and genome sequencing in ten regional sentinel units from June to October 2021 in the State of Minas Gerais (MG). We documented the introduction and spread of Delta, comprising 70 per cent of the cases 8 weeks later. Comparing the viral loads of the Gamma and Delta dominance periods, we provide additional evidence that the latter is more transmissible. The spread and dominance of Delta did not culminate in the increase in cases and deaths, suggesting that the vaccination may have restrained the epidemic growth. Analysis of 224 novel Delta genomes revealed that Rio de Janeiro state was the primary source for disseminating this variant in the state of MG. We present the establishment of Delta, providing evidence of its enhanced transmissibility and showing that this variant shift did not aggravate the epidemiological scenario in a high immunity setting.

SUBMITTER: Fonseca PLC

PROVIDER: S-EPMC9384558 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature

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Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status.

Fonseca Paula L C PLC Moreira Filipe R R FRR de Souza Rafael M RM Guimarães Natália R NR Carvalho Nara O NO Adelino Talita E R TER Alves Hugo J HJ Alvim Luige B LB Candido Darlan S DS Coelho Helena P HP Costa Alana V B AVB Costa Walyson C WC de Carvalho Alex F AF de Faria Bruna W F BWF de Lima Aline B AB de Oliveira Eneida S ES de Souza Carolina S A CSA de Souza Fernanda G FG Dias Rillery C RC Geddes Victor E V VEV Godinho Igor P IP Gonçalves Alessandro L AL Lourenço Karine L KL Magalhães Rubens D M RDM Malta Frederico S V FSV Medeiros Eva L A ELA Mendes Fernanda S FS Mendes Pedro H B de P PHBP Mendonça Cristiane P T B CPTB Menezes Andre L AL Menezes Diego D Menezes Mariane T MT Miguita Lucyene L Moreira Rennan G RG Peixoto Renata B RB Queiroz Daniel C DC Ribeiro Adriana A AA Ribeiro Ana Paula de B APB Saliba Juliana W JW Sato Hugo I HI Silva Joice do P JDP Silva Natiely P NP Faria Nuno R NR Teixeira Santuza M R SMR da Fonseca Flávio G FG Fernandes Ana Paula S M APSM Zauli Danielle A G DAG Januario José Nélio JN de Oliveira Jaqueline S JS Iani Felipe C de M FCM de Aguiar Renato S RS de Souza Renan P RP

Virus evolution 20220727 2

The emergence and global dissemination of Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) variants of concern (VOCs) have been described as the main factor driving the Coronavirus Disease 2019 pandemic. In Brazil, the Gamma variant dominated the epidemiological scenario during the first period of 2021. Many Brazilian regions detected the Delta variant after its first description and documented its spread. To monitor the introduction and spread of VOC Delta, we performed Polymerase Chain R ...[more]

PMID: 35996592

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Project description:Human adenovirus species F (HAdV-F) type 40 and 41 are commonly associated with acute diarrheal disease (ADD) across the world. Despite being the largest state in southeastern Brazil and having the second largest number of inhabitants, there is no information in the State of Minas Gerais regarding the role of HAdV-F in the etiology of ADD. This study was performed to determine the prevalence, to verify the epidemiological aspects of infection, and to characterize the strains of human adenoviruses (HAdV) detected. A total of 377 diarrheal fecal samples were obtained between January 2007 and August 2011 from inpatient and outpatient children of age ranging from 0 to 12 years. All samples were previously tested for rotavirus, norovirus, and astrovirus, and 314 of 377 were negative. The viral DNA was extracted, amplified using the polymerase chain reaction and the HAdV-positive samples were sequenced and phylogenetically analyzed. Statistical analyses were performed using the Chi-square test (p<0.05), considering two conditions: the total of samples tested (377) and the total of negative samples for the remaining viruses tested (314). The overall prevalence of HAdV was 12.47% (47/377); and in 76.60% (36/47) of the positive samples, this virus was the only infectious agent detected. The phylogenetic analysis of partial sequences of 32 positive samples revealed that they all clustered with the HAdV-F type 41. The statistical analysis showed that there was no correlation between the onset of the HAdV infection and the origin of the samples (inpatients or outpatients) in the two conditions tested: the total of samples tested (p=0.598) and the total of negative samples for the remaining viruses tested (p=0.614). There was a significant association in the occurrence of infection in children aged 0-12 months for the condition 1 (p=0.030) as well as condition 2 (p=0.019). The occurrence of infections due to HAdV did not coincide with a pattern of seasonal distribution. These data indicate the significant involvement of HAdV-F type 41 in the etiology of ADD in Minas Gerais, which demonstrates the importance of other viral agents in the development of the disease after the introduction of rotavirus vaccine immunization.

Project description:Brazil accounted for a total number of 1,276,194 reported cases of chikungunya fever between 2014 and 2022. Additionally, since 2015, the country has experienced an increasing death toll, in which the Northeast and Southeast regions appear to report the worst scenarios. Although the CHIKV transmission dynamics have been studied in many parts of the country since its introduction in 2014, little is still known about chikungunya virus (CHIKV) transmission and genetic diversity in the state of Minas Gerais, located in southeast Brazil. Moreover, no studies have been published characterizing CHIKV genomic surveillance in this state. Thus, to retrospectively explore the CHIKV epidemic in Minas Gerais, we generated 40 genomes from clinical samples using Nanopore sequencing. Phylogenetic analysis indicated that multiple introductions of CHIKV occurred, likely from the northeastern Brazilian states, with the most recent common ancestral strain dating to early March 2016, which is in agreement with local epidemiological reports. Additionally, epidemiological data reveals a decline in the number of reported cases from 2017 to 2021, indicating that population immunity or changes in vector activity may have contributed to the decreasing waves of CHIKV infection. Together, our results shed light on the dispersion dynamics of CHIKV and show that infections decreased from March 2017 to January 2021 despite multiple introductions into Minas Gerais State. In conclusion, our study highlights the importance of combining genomic and epidemiological data in order to assist public health laboratories in monitoring and understanding the patterns and diversity of mosquito-borne viral epidemics. IMPORTANCE Arbovirus infections in Brazil, including chikungunya, dengue, yellow fever, and Zika, result in considerable morbidity and mortality and are pressing public health concerns. However, our understanding of these outbreaks is hampered by the limited availability of genomic data. In this study, we combine epidemiological analysis and portable genome sequencing to retrospectively describe the CHIKV epidemic in Minas Gerais between 2017 and 2021. Our results indicate that the East/Central/South African (ECSA) CHIKV lineage was introduced into Minas Gerais by three distinct events, likely from the North and Northeast regions of Brazil. Our study provides an understanding of how CHIKV initiates transmission in the region and illustrates that genomics in the field can augment traditional approaches to infectious disease surveillance and control.

Dataset Information

Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status.

Publications

Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status.

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