Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil
Authors: Xavier Joilson , Alcantara Luiz Carlos Junior , Fonseca Vagner , Lima Mauricio , Castro Emerson , Fritsch Hegger , Oliveira Carla , Guimarães Natalia , Adelino Talita , Evaristo Mariane , Rodrigues Evandra S. , Santos Elaine Vieira , de La-Roque Debora , de Moraes Laise , Tosta Stephane , Neto Adelino , Rosewell Alexander , Mendonça Ana Flavia , Leite Anderson , Vasconcelos Andreza , Silva de Mello Arabela L. , Vasconcelos Bergson , Montalbano Camila A. , Zanluca Camila , Freitas Carla , de Albuquerque Carlos F. C. , Duarte dos Santos Claudia Nunes , Santos Cleiton S. , dos Santos Cliomar Alves , Gonçalves Crhistinne C. Maymone , Teixeira Dalane , Neto Daniel F. L. , Cabral Diego , de Oliveira Elaine C. , Noia Maciel Ethel L. , Pereira Felicidade Mota , Iani Felipe , de Carvalho Fernanda P. , Andrade Gabriela , Bezerra Gabriela , de Castro Lichs Gislene G. , Pereira Glauco Carvalho , Barroso Haline , Franz Helena Cristina Ferreira , Ferreira Hivylla , Gomes Iago , Riediger Irina N. , Rodrigues Isabela , de Siqueira Isadora C. , Silva Jacilane , Rico Jairo Mendez , Lima Jaqueline , Abrantes Jayra , do Nascimento Jean Phellipe M. , Wasserheit Judith N. , Pastor Julia , de Magalhães Jurandy J. F. , Luz Kleber Giovanni , Lima Neto Lidio G. , Frutuoso Livia C. V. , da Silva Luana Barbosa , Sena Ludmila , de Sousa Luis Arthur F. , Pereira Luiz Augusto , Demarchi Luiz , Câmara Magaly C. B. , Astete Marcela G. , Almiron Maria , Lima Maricelia , Umaki Zardin Marina C. S. , Presibella Mayra M. , Falcão Melissa B. , Gale Michael , Freire Naishe , Marques Nelson , de Moura Noely F. O. , Almeida Da Silva Pedro E. , Rabinowitz Peter , da Cunha Rivaldo V. , Trinta Karen S. , do Carmo Said Rodrigo F. , Kato Rodrigo , Stabeli Rodrigo , de Jesus Ronaldo , Hans Santos Roselene , Kashima Simone , Slavov Svetoslav N. , Andrade Tamires , Rocha Themis , Carneiro Thiago , Nardy Vanessa , da Silva Vinicius , Carvalho Walterlene G. , Van Voorhis Wesley C. , Araujo Wildo N. , de Filippis Ana M. B. , Giovanetti Marta 
Published: July 2023

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 across the country since its first detection in 2014 in Northeast Brazil. In this work, we carried out on-site training activities in genomic surveillance in partnership with the National Network of Public Health Laboratories that have led to the generation of 422 chikungunya virus 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 genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersal dynamics of the chikungunya virus East-Central-South-African 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 the genetic diversity of the chikungunya virus in Brazil.