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Increased interregional virus exchange and nucleotide diversity outline the expansion of the chikungunya virus ECSA lineage in Brazil.

ABSTRACT: The emergence and reemergence of mosquito-borne diseases in Brazil such as Yellow Fever, Zika, Chikungunya, and Dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus (CHIKV) across the country since its first detection in 2014 in Northeast Brazil. Faced with this scenario, on-site training activities in genomic surveillance carried out in partnership with the National Network of Public Health Laboratories have led to the generation of 422 CHIKV genomes from 12 Brazilian states over the past two years (2021-2022), a period that has seen more than 312 thousand chikungunya fever cases reported in the country. These new genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersion dynamics of the CHIKV East-Central-South-African (ECSA) lineage in Brazil. Tree branching patterns revealed the emergence and expansion of two distinct subclades. Phylogeographic analysis indicated that the northeast region has been the leading hub of virus spread towards other regions. Increased frequency of C>T transitions among the new genomes suggested that host restriction factors from the immune system such as ADAR and AID/APOBEC deaminases might be driving CHIKV ECSA lineage genetic diversity in Brazil.

SUBMITTER: Xavier J

PROVIDER: S-EPMC10081416 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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Increased interregional virus exchange and nucleotide diversity outline the expansion of the chikungunya virus ECSA lineage in Brazil.

Xavier Joilson J Alcantara Luiz L Fonseca Vagner V Lima Mauricio M Castro Emerson E Fritsch Hegger H Oliveira Carla C Guimarães Natalia N Adelino Talita T Evaristo Mariane M Rodrigues Evandra S ES Santos Elaine Vieira EV de La-Roque Debora D de Moraes Laise L Tosta Stephane S Neto Adelino A Rosewell Alexander A Mendonça Ana Flavia AF Leite Anderson A Vasconcelos Andreza A Silva de Mello Arabela L AL Vasconcelos Bergson B Montalbano Camila A CA Zanluca Camila C Freitas Carla C de Albuquerque Carlos F C CFC Duarte Dos Santos Claudia Nunes CN Santos Cleiton S CS Dos Santos Cliomar Alves CA Maymone Gonçalves Crhistinne C CC Teixeira Dalane D Neto Daniel F L DFL Cabral Diego D de Oliveira Elaine C EC Noia Maciel Ethel L EL Pereira Felicidade Mota FM Iani Felipe F de Carvalho Fernanda P FP Andrade Gabriela G Bezerra Gabriela G de Castro Lichs Gislene G GG Pereira Glauco Carvalho GC Barroso Haline H Ferreira Franz Helena Cristina HC Ferreira Hivylla H Gomes Iago I Riediger Irina N IN Rodrigues Isabela I de Siqueira Isadora C IC Silva Jacilane J Rico Jairo Mendez JM Lima Jaqueline J Abrantes Jayra J do Nascimento Jean Phellipe M JPM Wasserheit Judith N JN Pastor Julia J de Magalhães Jurandy J F JJF Luz Kleber Giovanni KG Lima Neto Lidio G LG Frutuoso Livia C V LCV da Silva Luana Barbosa LB Sena Ludmila L de Sousa Luis Arthur F LAF Pereira Luiz Augusto LA Demarchi Luiz L Câmara Magaly C B MCB Astete Marcela G MG Almiron Maria M Lima Maricelia M Umaki Zardin Marina C S MCS Presibella Mayra M MM Falcão Melissa B MB Gale Michael M Freire Naishe N Marques Nelson N de Moura Noely F O NFO Almeida Da Silva Pedro E PE Rabinowitz Peter P da Cunha Rivaldo V RV Trinta Karen S KS do Carmo Said Rodrigo F RF Kato Rodrigo R Stabeli Rodrigo R de Jesus Ronaldo R Santos Roselene Hans RH Haddad Simone K SK Slavov Svetoslav N SN Andrade Tamires T Rocha Themis T Carneiro Thiago T Nardy Vanessa V da Silva Vinicius V Carvalho Walterlene G WG Van Voorhis Wesley C WC Araujo Wildo N WN de Filippis Ana M B AMB Giovanetti Marta M

medRxiv : the preprint server for health sciences 20230403

The emergence and reemergence of mosquito-borne diseases in Brazil such as Yellow Fever, Zika, Chikungunya, and Dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus (CHIKV) across the country since its first detection in 2014 in Northeast Brazil. Faced with this scenario, on-site training activities in genomic surveillance carried out in partnership with the National Network of Public Health Laboratories have led to t ...[more]

PMID: 37034611

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Project description:BackgroundChikungunya cases was reported to be on the rise in Malaysia from 2019 to 2021. Although potential endemicity was described previously, genotype shift during 2008 outbreak originating from the 2004 Indian Ocean Islands outbreak presents the probability of current CHIKV spread from neighboring countries. This is due to the prevalence of the new IOL sub-lineage which consists of E1-226A wildtype or reverted strains that are circulating in the Indian subcontinent before spreading to neighboring Thailand during 2018-2019 outbreak.MethodIn this study, samples received mostly from the Tangkak, Johor were analyzed. A total 56 CHIKV positive serum samples received in 2021 by Institute of Medical Research Malaysia (IMR), were collected based on sample selection criteria. Selected samples were subjected to total RNA extraction, whole-genome sequencing as well as bioinformatic analysis such as phylogenetic, variant and mutation analysis.ResultsBased on the genomic and phylogenetic analysis, the CHIKV samples from 2021 outbreak were of ECSA-IOL genotype. Genome similarity analysis also revealed that these CHIKVs were highly similar to 2018-2019 outbreak strain from Thailand. In comparison to the 2008 outbreak CHIKV isolate, the current CHIKVs lacked the E1-A226V mutation and harbored the new E1-K211E/E2-V264A sub-linage mutation. Since the E1-K211E/E2-V264A mutation facilitates adaptation to Ae. aegypti as opposed to the E1-A226V mutation which improves adaptation to Ae. albopictus, the emergence 2021 CHIKV outbreak in Malaysia can be postulated due to vector shift. Interestingly, a novel nsP3-T441A/V mutation detected in this study, may also play a role in virus transmission, pathogenicity, fitness and vector adaptation.ConclusionIn summary, the current CHIKV outbreak are strains originated from the Indian subcontinent through Thailand which may have capitalized on vector shifting by adapting to Ae. aegypti. The presence of novel nsP3-T441A/V mutation may also contribute to the spread of this virus across peninsular Malaysia.

Dataset Information

Increased interregional virus exchange and nucleotide diversity outline the expansion of the chikungunya virus ECSA lineage in Brazil.

Publications

Increased interregional virus exchange and nucleotide diversity outline the expansion of the chikungunya virus ECSA lineage in Brazil.

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