Viral metagenomics of six bat species in close contact with humans in southern China

Abstract

Accumulating studies have shown that bats could harbor various important pathogenic viruses that could be transmitted to humans and other animals. Extensive metagenomic studies of different organs/tissues from bats have revealed a large number of novel or divergent viruses. To elucidate viral diversity and epidemiological and phylogenetic characteristics, six pooled fecal samples from bats were generated (based on bat species and geographic regions characteristic for virome analysis). These contained 500 fecal samples from six bat species, collected in four geographic regions. Metagenomic analysis revealed a plethora of divergent viruses originally found in bats. Multiple contigs from influenza A virus and coronaviruses in bats shared high identity with those from humans, suggesting possible cross-species transmission, whereas a number of contigs, whose sequences were taxonomically classifiable within Alphapapillomavirus, Betaretrovirus, Alpharetrovirus, Varicellovirus, Cyprinivirus, Chlorovirus and Cucumovirus had low identity to viruses in existing databases, which indicated possible evolution of novel viral species. None of the established caliciviruses and picornaviruses were found in the 500 fecal specimens. Papillomaviruses with high amino acid identity were found in Scotophilus kuhlii and Rhinolophus blythi, challenging the hypotheses regarding the strict host specificity and co-evolution of papillomaviruses. Phylogenetic analysis showed that four bat rotavirus A strains might be tentative G3 strains, according to the Rotavirus Classification Working Group classification.

A Preliminary Study of the Virome of the South American Free-Tailed Bats (Tadarida brasiliensis) and Identification of Two Novel Mammalian Viruses

“…Various human and non-human PVs, including bat PVs, have frequently been identified in healthy epithelia and may represent part of the native epithelial microflora [34,57,58]. Several studies have suggested the presence of PVs in Old World bat species using conventional [57,58,93] or NGS aproches [20,41,94,95]. The only PV type (MmoPV1) identified in a New World bat species (Molossus molossus) has recently been described [26], suggesting a crude sampling imbalance and a severe lack of information to elucidate the evolutionary mechanisms driving PV diversification on the global scale.…”

Sensitivity and specificity of metatranscriptomics as an arbovirus surveillance tool

“…It can be used to detect both known and novel viruses while providing whole genome information, making it a powerful surveillance tool. Metatranscriptomics has been used in a range of surveillance situations, including detecting viruses in human sewage 1 , monitoring viruses in invertebrate vectors such as ticks 2 and vertebrate reservoirs such as bats 3 , and tracking virus strains during an outbreak 4 . The successful utilisation of metatranscriptomics in a range of surveillance applications suggests it has potential to enhance current arbovirus (arthropod-borne virus) surveillance programs.…”

Virus Metagenomics in Farm Animals: A Systematic Review

“…Particularly, metagenomic NGS (mNGS) allows unbiased detection of all microbes and viruses in a sample, showing potential for timely detection of rare or novel infectious etiologies, as well as for surveillance of foodborne and waterborne viruses [20][21][22][23][24][25][26]. However, the use of mNGS as a potential surveillance tool requires a deeper understanding of what is "normal" diversity in humans [27], as well as wildlife [28,29] and farm animals [30]. Characterizing species-specific metagenomes could potentially be used to provide a surveillance baseline for early detection and for tracking of movements of pathogens across different hosts, and has been promoted by projects like the global virome project [31].…”