Discovery of Novel Coronaviruses in Rodents

Viral diversity in wild rodents in the regions of Canaã de Carajás and Curionopólis, State of Pará, Brazil

Wild rodents serve as crucial reservoirs for zoonotic viruses. Anthropogenic and environmental disruptions, particularly those induced by mining activities, can destabilize rodent populations and facilitate the emergence of viral agents. In the Canaã dos Carajás and Curionópolis regions of Brazil, significant environmental changes have occurred due to mining expansion, potentially creating conditions conducive to the emergence of rodent-associated viral diseases. This study aimed to investigate the viral diversity in wild rodents captured in Canaã dos Carajás and Curionópolis, Pará, between 2017 and 2019. A total of 102 rodent samples were taxonomically identified through karyotyping and screened for anti-Orthohantavirus antibodies using the ELISA method. Subsequently, nucleotide sequencing and bioinformatics analyses were conducted on 14 selected samples to characterize the virome. This selection was based on the most commonly associated rodent genera as reservoirs of Orthohantavirus and Mammarenavirus. Of the 102 samples tested via ELISA, 100 were negative, and two showed optical density at the cutoff point. Sequencing of the 14 samples generated approximately 520 million reads, with 409 million retained after quality control. These reads were categorized into 53 viral families, including both DNA and RNA viruses, with Retroviridae, Baculoviridae, and Microviridae being the most abundant. Viral contigs were identified, including one fragment related to Arenaviridae and three to Filoviridae. Metagenomic analysis revealed high viral diversity in the sampled rodents, with the presence of viral families of public health concern, such as Arenaviridae and Filoviridae. The findings suggest that increased human activities associated with mining may contribute to the emergence of these viruses, underscoring the need for ongoing surveillance to prevent potential outbreaks.

Lack of detection of SARS-CoV-2 in wildlife from Kerala, India in 2020-21

Spillover of SARS-CoV-2 into a variety of wild and domestic animals has been an ongoing feature of the human pandemic. The establishment of a new reservoir in white-tailed deer in North America and increasing divergence of the viruses circulating in them from those circulating in the human population has highlighted the ongoing risk this poses for global health. Some parts of the world have seen more intensive monitoring of wildlife species for SARS-CoV-2 and related coronaviruses but there are still very large gaps in geographical and species-specific information. This paper reports negative results for SARS-CoV-2 PCR based testing using a pan coronavirus end point RDRP PCR and a Sarbecovirus specific E gene qPCR on lung and or gut tissue from wildlife from the Indian State of Kerala. These animals included: 121 Rhinolophus rouxii (Rufous Horsehoe Bat), six Rhinolophus bedommei (Lesser Woolly Horseshoe Bat), 15 Rossettus leschenaultii (Fulvous Fruit Bat), 47 Macaca radiata (Bonnet macaques), 35 Paradoxurus hermaphroditus (Common Palm Civet), five Viverricula indica (Small Indian Civet), four Herpestes edwardsii (Common Mongoose), ten Panthera tigris (Bengal Tiger), eight Panthera pardus fusca (Indian Leopard), four Prionailurus bengalensis (Leopard cats), two Felis chaus (Jungle cats), two Cuon alpinus (Wild dogs) and one Melursus ursinus (sloth bear).

Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau

Rodents are natural reservoirs of diverse zoonotic viruses and widely distributed on the Tibetan Plateau. A comprehensive understanding of the virome in local rodent species could provide baseline of viral content and assist in efforts to reduce the risk for future emergence of rodent related zoonotic diseases. A total of 205 tissue and fecal samples from 41 wild Qinghai voles were collected. Metagenomic analyses were performed to outline the characteristics of the viromes, and phylogenetic analyses were used to identify the novel viral genomes. The virome distribution among five tissues (liver, lung, spleen, small intestine with content and feces) was also compared. We identified sequences related to 46 viral families. Novel viral genomes from distinct evolutionary lineages with known viruses were characterized for their genomic and evolutionary characteristics, including Hepatovirus, Hepacivirus, Rotavirus, and Picobirnavirus. Further analyses revealed that the core virome harbored by rodent internal tissues were quite different from the virome found in intestine and fecal samples. These findings provide an overview of the viromes in wild Qinghai voles, which are unique and the most common rodent species in the eastern Tibetan Plateau. A high diversity of viruses is likely present in rodent species in this area.