High genetic diversity of alphacoronaviruses in bat species (Mammalia: Chiroptera) from the Atlantic Forest in Brazil
Larissa Mayumi Bueno, Laís Santos Rizotto, Amanda de Oliveira Viana, Laura Morais Nascimento Silva, Maria Vitória dos Santos de Moraes, Júlia Cristina Benassi, Guilherme Pereira Scagion, Erick Gustavo Dorlass, Bruna Larotonda Telezynski Lopes, Irineu Noberto Cunha, Ramiro Melinski, Igor Ferreira de Alvarenga, Gabriel Lins Leitão, Roberta Costa Rodrigues, Iolanda Maria da Silva Pereira, Lilia D’ark Nunes dos Santos, Fabiane Fisch, Alana Drielle Rocha, Dagoberto Port, Gabriela Stahelin, A. Greatti, Ana Caroline de Souza Barnabé, Junko Tsukamoto, Erika Hingst‐Zaher, Severino Mendes de Azevedo, Wallace Rodrigues Telino Júnior, Joaquim Olinto Branco, Tatiana Ometto, Jansen de Araújo, Clarice Weis Arns, Helena Lage Ferreira, Edison Luíz Durigon
Abstract
Bat coronaviruses (Bat-CoVs) represent around 35% of all virus genomes described in bats. Brazil has one of the highest mammal species diversity, with 181 species of bats described so far. However, few Bat-CoV surveillance programmes were carried out in the country. Thus, our aim was to jevaluate the Bat-CoV diversity in the Atlantic Forest, the second biome with the highest number of bat species in Brazil. We analysed 456 oral and rectal swabs and 22 tissue samples from Atlantic Forest bats, detecting Alphacoronavirus in 44 swab samples (9.6%) targeting the RdRp gene from seven different bat species, three of which have never been described as Bat-CoV hosts. Phylogenetic analysis of the amino acid (aa) sequences coding the RdRp gene grouped the sequences obtained in our study with Bat-CoV previously detected in identical or congeneric bat species, belonging to four subgenera, with high aa identity (over 90%). The RdRp gene was also detected in three tissue samples from Diphylla ecaudata and Sturnira lilium, and the partial S gene was successfully sequenced in five tissues and swab samples of D. ecaudata. The phylogenetic analysis based on the partial S gene obtained here grouped the sequence of D. ecaudata with CoV from Desmodus rotundus previously detected in Peru and Brazil, belonging to the Amalacovirus subgenus, with aa identity ranging from 73.6% to 88.8%. Our data reinforce the wide distribution of Coronaviruses in bats from Brazil and the novelty of three bats species as Bat-CoV hosts and the co-circulation of four Alphacoronavirus subgenera in Brazil.