TY - JOUR T1 - Emergence of the East-Central-South-African genotype of Chikungunya virus in Brazil and the city of Rio de Janeiro may have occurred years before surveillance detection AU - Souza, Thiago Moreno L. AU - Rangel Vieira, Yasmine AU - Delatorre, Edson AU - Barbosa-Lima, Giselle AU - Luiz, Raul Leal Faria AU - Vizzoni, Alexandre AU - Jain, Komal AU - Mesquita Miranda, Milene AU - Bhuva, Nishit AU - Gogarten, Jan F. AU - Ng, James AU - Thakkar, Riddhi AU - Surrage Calheiros, Andrea AU - Monteiro, Ana Paula Teixeira AU - Bozza, Fernando A. AU - Tschoeke, Diogo A. AU - Leomil, Luciana AU - de Mendonça, Marcos Cesar Lima AU - dos Santos Rodrigues, Cintia Damasceno AU - Torres, Maria C. AU - Bispo de Filippis, Ana Maria AU - Ribeiro Nogueira, Rita Maria AU - Thompson, Fabiano L. AU - Lemos, Christina AU - Durovni, Betina AU - Cerbino-Neto, José AU - Morel, Carlos M. AU - Lipkin, W. Ian AU - Mishra, Nischay AB - Brazil, which is hyperendemic for dengue virus (DENV), has had recent Zika (ZIKV) and (CHIKV) Chikungunya virus outbreaks. Since March 2016, CHIKV is the arbovirus infection most frequently diagnosed in Rio de Janeiro. In the analysis of 1835 syndromic patients, screened by real time RT-PCR, 56.4% of the cases were attributed to CHIKV, 29.6% to ZIKV, and 14.1% to DENV-4. Sequence analyses of CHIKV from sixteen samples revealed that the East-Central-South-African (ECSA) genotype of CHIKV has been circulating in Brazil since 2013 [95% bayesian credible interval (BCI): 03/2012-10/2013], almost a year before it was detected by arbovirus surveillance program. Brazilian cases are related to Central African Republic sequences from 1980’s. To the best of our knowledge, given the available sequence published here and elsewhere, the ECSA genotype was likely introduced to Rio de Janeiro early on 2014 (02/2014; BCI: 07/2013-08/2014) through a single event, after primary circulation in the Bahia state at the Northestern Brazil in the previous year. The observation that the ECSA genotype of CHIKV was circulating undetected underscores the need for improvements in molecular methods for viral surveillance. KW - Bioinformatics KW - Viral epidemiology KW - 610 Medizin und Gesundheit PY - 2019 LA - eng PB - Robert Koch-Institut JO - Scientific Reports VL - 9 IS - 2760 SP - 1 EP - 7 DO - 10.1038/s41598-019-39406-9 ER -