Cryptic circulation of chikungunya virus in São Jose do Rio Preto, Brazil, 2015–2019
Authors: Zini Nathalia , Ávila Matheus Henrique Tavares , Cezarotti Natalia Morbi , Parra Maisa Carla Pereira , Banho Cecília Artico , Sacchetto Livia , Negri Andreia Francesli , Araújo Emerson , Bittar Cintia , Milhin Bruno Henrique Gonçalves de Aguiar , Miranda Hernandes Victor , Dutra Karina Rocha , Trigo Leonardo Agopian , Cecílio da Rocha Leonardo , Alves da Silva Rafael , Celestino Dutra da Silva Gislaine , Fernanda Pereira dos Santos Tamires , de Carvalho Marques Beatriz , Lopes dos Santos Andresa , Augusto Marcos Tayar , Mistrão Natalia Franco Bueno , Ribeiro Milene Rocha , Pinheiro Tauyne Menegaldo , Maria Izabel Lopes dos Santos Thayza , Avilla Clarita Maria Secco , Bernardi Victoria , Freitas Caroline , Gandolfi Flora de Andrade , Ferraz Júnior Hélio Correa , Perim Gabriela Camilotti , Gomes Mirella Cezare , Garcia Pedro Henrique Carrilho , Rocha Rodrigo Sborghi , Galvão Tayna Manfrin , Fávaro Eliane Aparecida , Scamardi Samuel Noah , Rogovski Karen Sanmartin , Peixoto Renan Luiz , Benfatti Luiza , Cruz Leonardo Teixeira , Chama Paula Patricia de Freitas , Oliveira Mânlio Tasso , Watanabe Aripuanã Sakurada Aranha , Terzian Ana Carolina Bernardes , de Freitas Versiani Alice , Dibo Margareth Regina , Chiaravalotti-Neto Francisco , Weaver Scott Cameron , Estofolete Cassia Fernanda , Vasilakis Nikos , Nogueira Mauricio Lacerda 
Published: March 2024

Background
Chikungunya virus (CHIKV) has spread across Brazil with varying incidence rates depending on the affected areas. Due to cocirculation of arboviruses and overlapping disease symptoms, CHIKV infection may be underdiagnosed. To understand the lack of CHIKV epidemics in São José do Rio Preto (SJdRP), São Paulo (SP), Brazil, we evaluated viral circulation by investigating anti-CHIKV IgG seroconversion in a prospective study of asymptomatic individuals and detecting anti-CHIKV IgM in individuals suspected of dengue infection, as well as CHIKV presence in Aedes mosquitoes. The opportunity to assess two different groups (symptomatic and asymptomatic) exposed at the same geographic region aimed to broaden the possibility of identifying the viral circulation, which had been previously considered absent.

Methodology/principal findings
Based on a prospective population study model and demographic characteristics (sex and age), we analyzed the anti-CHIKV IgG seroconversion rate in 341 subjects by ELISA over four years. The seroprevalence increased from 0.35% in the first year to 2.3% after 3 years of follow-up. Additionally, we investigated 497 samples from a blood panel collected from dengue-suspected individuals during the 2019 dengue outbreak in SJdRP. In total, 4.4% were positive for anti-CHIKV IgM, and 8.6% were positive for IgG. To exclude alphavirus cross-reactivity, we evaluated the presence of anti-Mayaro virus (MAYV) IgG by ELISA, and the positivity rate was 0.3% in the population study and 0.8% in the blood panel samples. In CHIKV and MAYV plaque reduction neutralization tests (PRNTs), the positivity rate for CHIKV-neutralizing antibodies in these ELISA-positive samples was 46.7%, while no MAYV-neutralizing antibodies were detected. Genomic sequencing and phylogenetic analysis revealed CHIKV genotype ECSA in São José do Rio Preto, SP. Finally, mosquitoes collected to complement human surveillance revealed CHIKV positivity of 2.76% of A. aegypti and 9.09% of A. albopictus (although it was far less abundant than A. aegypti) by RT–qPCR.

Conclusions/significance
Our data suggest cryptic CHIKV circulation in SJdRP detected by continual active surveillance. These low levels, but increasing, of viral circulation highlight the possibility of CHIKV outbreaks, as there is a large naïve population. Improved knowledge of the epidemiological situation might aid in outbreaks prevention.