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Bats are widely distributed in Brazil, including the Amazon region, and their association with viral pathogens is well-known. This work aimed to evaluate the metavirome in samples of Molossus sp. bats captured in the Brazilian Amazon from 2019 to 2021. Lung samples from 58 bats were divided into 13 pools for RNA isolation and sequencing followed by bioinformatic analysis. The Retroviridae family showed the highest abundance of viral reads. Although no complete genome could be recovered, the Paramyxoviridae and Dicistroviridae families showed the formation of contigs with satisfactory identity and size characteristics for further analysis. One contig of the Paramyxoviridae family was characterized as belonging to the genus Morbillivirus, being grouped most closely phylogenetically to Porcine morbillivirus. The contig related to the Dicistroviridae family was identified within the Cripavirus genus, with 94%, 91%, and 42% amino acid identity with Culex dicistrovirus 2, Rhopalosiphum padi, and Aphid lethal paralysis, respectively. The presence of viruses in bats needs constant updating since the study was able to identify viral sequences related to families or genera still poorly described in the literature in association with bats.

We have identified fifty-eight samples that were positive for Dengue-4 among 119 samples with negative diagnoses for dengue via the Platelia™ dengue NS1 Ag in Aracaju, State of Sergipe, Brazil. We determined that the low sensitivity of the NS1 Ag test could be related to secondary dengue infections in the studied population. Therefore, we concluded that the sensitivity and specificity of the Platelia™ dengue NS1 Ag test as a screening method for monitoring circulating dengue serotypes must be reevaluated. In addition, regional endo-epidemic profiles should also be considered due to the prevalence of secondary responses.

A wide diversity of pathogenic mosquito-borne viruses circulate in the Brazilian Amazon, and the intense deforestation can contribute to the spread of these viruses. In this context, this study aimed to investigate the viral diversity in mosquitoes of the genera Aedes, Culex, Haemagogus, and Sabethes from a transition area between the Amazon, Cerrado, and Caatinga biomes in Brazil. Metagenomic high-throughput sequencing was used to characterize the virome of 20 mosquito pools. A total of 15 virus-like genomes were identified, comprising species genomically close to insect-specific viruses of the families Iflaviridae, Metaviridae, Lispiviridae, Rhabdoviridae, Xinmoviridae, and Parvoviridae and species of plant viruses of the families Solemoviridae, Virgaviridae, and Partitiviridae. However, sequences of viruses associated with human and animal diseases were not detected. Most of the recovered genomes were divergent from those previously described. These findings reveal that there are a large number of unknown viruses to be explored in the middle-north of Brazil.

Dengue virus 2 (DENV-2) seriously contributes to dengue-related mortality. It includes five nonsylvatic genotypes, with cosmopolitan being the most widespread with a significant contribution to the total number of DENV-2 cases globally. In South America, the cosmopolitan genotype was first recorded in 2019 in Madre de Dios, Peru, and then in Goias (Midwest Brazil) in November 2021. In this study, we tested 163 human serum samples from Acre (Northern Brazil) collected during a DENV outbreak between 2020 and 2021 for all DENV genotypes by RT-qPCR. Of the 163 samples, 139 were positive for DENV-2, and 5 were positive for DENV-1. Five DENV-2-positive samples from early 2021 were sequenced, and the sequences clustered with the three other DENV-2 cosmopolitan genotype sequences already recorded on the continent. These results create a geographical link, suggesting the possible route of introduction of the DENV-2 cosmopolitan genotype into Brazil through the border with Peru, from which it may have dispersed to Midwest Brazil.

Advances in diagnostic techniques, along with environmental changes driven by human activity, have intensified the surveillance and monitoring of virus and arbovirus circulation on the Amazon. These efforts have increased the detection of insect-specific viruses in field-collected hematophagous arthropods. This study reports the first isolation of the Aguas Brancas virus from mosquitoes collected in the Brazilian Amazon and in a rural area of Brasília, Federal District, Brazil. Arthropods of the family Culicidae, genus Limatus durhamii, were collected at ground level in forest fragments. Sample BEAR812610 originated from Ananindeua, Pará, within the Evandro Chagas Institute’s grounds, and sample BEAR839941 from a forest fragment in Brasília (Ceilândia—Núcleo Rural Boa Esperança, Site B4). Specimens were identified to the species/genus level, macerated, and the supernatant inoculated into C6/36 and Vero cell cultures for viral isolation. The presence of arboviruses was determined by indirect immunofluorescence using antibodies against major arbovirus groups. Positive samples were sequenced for nucleotide and amino acid identification, and phylogenetic analysis confirmed the virus as belonging to the genus Orthoflavivirus. This represents the first report of the isolation and characterization of the insect-specific Aguas Brancas virus.

Chikungunya virus (CHIKV) was first reported in Brazil in 2014 and, after it spread countrywide, an outbreak of febrile illness with reports of arthralgia happened in the municipality of Xinguara, Pará, Brazil in 2017, indicating the virus’ circulation. Here, we aimed to investigate CHIKV in mosquito vectors collected during an active surveillance of virus isolation in cell culture by using molecular detection and viral genome sequencing. A total of 492 Aedes, Culex and Mansonia mosquitoes were collected and separated in 36 pools according to the species and sex, and 22.2% (8/36) were positive. CHIKV was indentified in pools of Ae. aegypti females (n = 5), an Ae. aegypti male (n = 1) and in Culex quinquefasciatus females (n = 2). However, as the mosquitoes’ whole bodies were macerated and used for detection, one cannot suggest the role of the latter in the viral transmission. Despite this, vector competence studies must be carried out in the different species to investigate long-term adaptations. Viral genome sequencing has characterized the East-Central-South-African (ECSA) genotype in all positive pools analyzed, corroborating previous reports for the Amazon region.

Arboviruses transmitted by Aedes aegypti cause high number of cases and deaths annually. The aim was to investigate the presence of the presence of Dengue (DENV), Zika (ZIKV) and Chikungunya (CHIKV) viruses in endemic areas of Maranhão, northeastern Brazil. The study was carried out in Caxias, Codó, Peritoró, and São Mateus do Maranhão in 2019 (Caxias) and 2022. The blood samples were subjected to RNA extraction and then tested by RT-qPCR. Cell culture was used to attempt viral isolation and subsequent sequencing. In total, 171 samples were analyzed (32 from 2019, 18.7%) and 72 (42.1%) were found to have arboviruses: 68 (39.7%) from Caxias; 2 (1.1%) from Codó; 1 (0.6%) from Peritoró; and 1 (0.6%) from São Mateus. Overall, 85.3% (n = 58) of the positive samples were infected with DENV-1, 4 (four) (5.9%) with DENV-2 (Caxias), 1 (one) (1.5%) with DENV-3 (Caxias), and in 6 (six) (7.3%) samples CHIKV was detected, with one co-infection of DENV-1 and CHIKV (Caxias). The DENV-1 genotype V and the ECSA genotype of CHIKV were characterized in samples from Caxias. The detection of DENV-1, DENV-2, DENV-3, and more CHIKV in the interior of Maranhão alerts to the importance of virological studies in these areas.

The municipalities of Peixe-Boi and Santa Bárbara do Pará, both in the Pará State (eastern Amazon), have more than half of their territory deforested. Understanding the viral diversity in wildlife that inhabits the surroundings of human communities contributes to strengthening surveillance. Samples from eleven bats, seven opossums, and eight rodents from the two locations were screened by high-throughput sequencing for virome analysis. Viral reads were assigned into twenty viral families, from which the most abundant was Retroviridae. Host order, tissue type, and season showed a significant effect on viral composition. Five viral genomes of bat ERVs with intact genes were recovered, showing the need to understand their endogenous nature. In addition, a new Buritiense virus (Hantaviridae) strain was also obtained, supporting its circulation in Santa Bárbara do Pará and expanding its genomic information. Together, these findings reinforce the need for continuous surveillance in wild animals, especially in the Amazon region, to anticipate potential threats to public health.

The biting midges Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) is highly relevant to epidemiology and public health, as it includes species that are potential vectors of human and animal arboviruses. The aim of this study was to investigate the presence of RNA viruses in species of the genus Culicoides collected in the Carajás mining complex in the state of Pará. The biting midges were collected in the municipalities of Canaã dos Carajás, Curionópolis and Marabá and morphologically identified. A total of 1139 specimens of seven Culicoides species were grouped into eight pools and subjected to metagenomic analysis. Eight new insect-specific viruses (ISVs) were characterized and assigned to the order Tolivirales, the families Chuviridae, Nodaviridae, Iflaviridae, Mesoniviridae, and Flaviviridae, and the taxon Negevirus. All viruses identified were assigned to clades, families and taxa never reported in Culicoides in Brazil. This study demonstrated that biting midges harbor a significant diversity of RNA viruses, many of which are still unknown, highlighting the importance of studies aiming at virome of these insects.

Dengue virus serotype 2 (DENV-2) is responsible for dengue epidemics on a global scale and is associated with severe cases of the disease. This study conducted a phylogenetic investigation of DENV-2 isolates from 2017 to 2021 originating from the northern states of Brazil. A total of 32 samples from DENV-2 isolates were analyzed, including 12 from Acre, 19 from Roraima, and one from Tocantins. Only one lineage of the Asian-American genotype and one lineage of the cosmopolitan genotype were observed: Lineage 1, Asian-American genotype (connection to Puerto Rico); Lineage 5, cosmopolitan genotype (connection to Peru). Our results provide important data regarding the study of DENV genotypes and lineage distribution and open up possibilities for probable introduction and dissemination routes.