Bats-associated beta-coronavirus detection and characterization: First report from Pakistan

Molecular identification and genetic diversity of Pteropus giganteus and Pipistrellus javanicus from Pakistan: A non-invasive approach

The scarcity of genetic data hinders bat species identification in Pakistan. Despite more than 1480 bat species worldwide, morphology-based identification remains challenging due to the similarity in physical characteristics and the lack of distinct morphological features among many species. This study addresses this gap by employing DNA barcoding (cytochrome b) to identify bat species non-invasively from fecal samples, collected samples without harming the bats, across various regions of Pakistan and identified two bat species, Pteropus giganteus and Pipistrellus javanicus. Phylogenetic analysis of Pipistrellus javanicus sequences clustered with a sequence previously reported sequences from India and China while Pteropus giganteus was made and clustered with previously reported sequences from Bangladesh indicating possible gene flow. We investigated haplotype diversity and nucleotide diversity that revealed P. giganteus displayed moderate genetic diversity (h = 0.714, π = 0.003 respectively) and P. javanicus showed high genetic diversity (h = 1.000, π = 0.020). Pairwise genetic distances (K2P and matrix analysis) revealed varying levels of differentiation among populations within each species, while the negative value in neutrality tests suggested potential/sudden population expansion for both species. The current study offers important insights into the genetic landscape and population dynamics of bat species in Pakistan. Future studies should incorporate additional genetic markers, morphological examinations, and ecological data to definitively characterize these potential new species and contribute to a more comprehensive understanding of Pakistan's bat fauna.

Computational methods in the analysis of SARS-CoV-2 in mammals: A systematic review of the literature

SARS-CoV-2 is an enveloped RNA virus that causes severe respiratory illness in humans and animals. It infects cells by binding the Spike protein to the host's angiotensin-converting enzyme 2 (ACE2). The bat is considered the natural host of the virus, and zoonotic transmission is a significant risk and can happen when humans come into close contact with infected animals. Therefore, understanding the interconnection between human, animal, and environmental health is important to prevent and control future coronavirus outbreaks. This work aimed to systematically review the literature to identify characteristics that make mammals suitable virus transmitters and raise the main computational methods used to evaluate SARS-CoV-2 in mammals. Based on this review, it was possible to identify the main factors related to transmissions mentioned in the literature, such as the expression of ACE2 and proximity to humans, in addition to identifying the computational methods used for its study, such as Machine Learning, Molecular Modeling, Computational Simulation, between others. The findings of the work contribute to the prevention and control of future outbreaks, provide information on transmission factors, and highlight the importance of advanced computational methods in the study of infectious diseases that allow a deeper understanding of transmission patterns and can help in the development of more effective control and intervention strategies.

Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence

Bats are a major reservoir of zoonotic viruses, including coronaviruses. Since the emergence of SARS-CoV in 2002/2003 in Asia, important efforts have been made to describe the diversity of Coronaviridae circulating in bats worldwide, leading to the discovery of the precursors of epidemic and pandemic sarbecoviruses in horseshoe bats. We investigated the viral communities infecting horseshoe bats living in Northern Vietnam, and report here the first identification of sarbecoviruses in Rhinolophus thomasi and Rhinolophus siamensis bats. Phylogenetic characterization of seven strains of Vietnamese sarbecoviruses identified at least three clusters of viruses. Recombination and cross-species transmission between bats seemed to constitute major drivers of virus evolution. Vietnamese sarbecoviruses were mainly enteric, therefore constituting a risk of spillover for guano collectors or people visiting caves. To evaluate the zoonotic potential of these viruses, we analyzed in silico and in vitro the ability of their RBDs to bind to mammalian ACE2s and concluded that these viruses are likely restricted to their bat hosts. The workflow applied here to characterize the spillover potential of novel sarbecoviruses is of major interest for each time a new virus is discovered, in order to concentrate surveillance efforts on high-risk interfaces.