key: cord-309512-d8n9711b
authors: Bacus, Michael G.; Dayap, Stephen Adrian H.; Tampon, Nikki Vanesa T.; Udarbe, Marielle M.; Puentespina, Roberto P.; Villanueva, Sharon Yvette Angelina M.; de Cadiz, Aleyla E.; Achondo, Marion John Michael M.; Murao, Lyre Anni E.
title: Global genetic patterns reveal host tropism versus cross-taxon transmission of bat Betacoronaviruses
date: 2020-05-05
journal: bioRxiv
DOI: 10.1101/2020.05.04.076281
sha: 
doc_id: 309512
cord_uid: d8n9711b

Emerging infectious diseases due to coronavirus (CoV) infections have received significant global attention in the past decade and have been linked to bats as the original source. The diversity, distribution, and host associations of bat CoVs were investigated to assess their potential for zoonotic transmission. Phylogenetic, network, and principal coordinate analysis confirmed the classification of betacoronaviruses (BetaCoVs) into five groups (2A to 2E) and a potentially novel group, with further division of 2D into five subgroups. The genetic co-clustering of BetaCoVs among closely related bats reflects host taxon-specificity with each bat family as the host for a specific BetaCoV group, potentially a natural barrier against random transmission. The divergent pathway of BetaCoV and host evolution suggests that the viruses were introduced just prior to bat dispersal and speciation. As such, deviant patterns were observed such as for 2D-IV, wherein cross-taxon transmission due to overlap in bat habitats and geographic range among genetically divergent African bat hosts could have played a strong role on their shared CoV lineages. In fact, a few bat taxa especially the subfamily Pteropodinae were shown to host diverse groups of BetaCoVs. Therefore, ecological imbalances that disturb bat distribution may lead to loss of host specificity through cross-taxon transmission and multi-CoV infection. Hence, initiatives that minimize the destruction of wildlife habitats and limit wildlife-livestock-human interfaces are encouraged to help maintain the natural state of bat BetaCoVs in the wild. Importance Bat Betacoronaviruses (BetaCoVs) pose a significant threat to global public health and have been implicated in several epidemics such as the recent pandemic by severe acute respiratory syndrome coronavirus 2. Here, we show that bat BetaCoVs are predominantly host-specific, which could be a natural barrier against infection of other host types. However, a strong overlap in bat habitat and geographic range may facilitate viral transmission to unrelated hosts, and a few bat families have already been shown to host multi-CoV variants. We predict that continued disturbances on the ecological balance may eventually lead to loss of host specificity. When combined with enhanced wildlife-livestock-human interfaces, spillover to humans may be further facilitated. We should therefore start to define the ecological mechanisms surrounding zoonotic events. Global surveillance should be expanded and strengthened to assess the complete picture of bat coronavirus diversity and distribution and their potential to cause spillover infections.

Emerging and re-emerging infectious diseases greatly affect public health and global economies

(1). These diseases involve pathogenic strains that recently evolved, pathogens that infect human 52 population for the first time, and pathogens that re-occur at higher frequency (2). Majority of these 53 emerging infectious diseases are caused by microorganisms from non-human source or zoonotic 54 pathogens from wild animals (3). In particular, emerging infectious diseases due to coronavirus (CoV) 

However, some deviations were also noted. For example, bat hosts that belong to genetically 212 unrelated taxa were mixed in some BetaCoV groups. The Mollosidae bat Eumops glaucinus was found in World leaf-nosed bat Trianeops persicus in 2D-IV of Epomophorinae bats. Looking at the host, certain bat 217 families were observed to harbor BetaCoVs that belong to various lineages. The Rousettinae bats were 218 found to carry both 2D-I/2D-III and 2D-IV BetaCoVs, and the Old World fruit bats 2B, 2D-IV, and 2E. The 

The divergence of the bats and their BetaCoVs were compared to evaluate common evolutionary 223 pathways (Fig. 5B) . The vesper microbats diverged as a separate group from the rest of the bats. The 

In contrast, our findings support a previously proposed hypothesis that CoVs limit cross-species 

Although bat BetaCoVs are host taxon-specific, their evolutionary pathways are different from evolution with its host. Instead, this is indicative that the currently circulating viruses may have been introduced relatively recently, i.e. to the most recent common ancestors of each bat taxon but prior to 283 global dispersion and speciation, during which the virus acquired adaptation to its host. The recent 284 introduction of BetaCoVs in bats implies that other factors may have had the opportunity to influence 285 virus-host dynamics. In the succeeding discussions, we will present two deviant phenomena that 286 exemplify this: cross-taxon transmission of CoVs and bat hosts with multi-CoV lineages.

We provide genetic evidence for cross-taxon transmission as indicated by genetically unrelated 

Microbial threats to health: taxonomy-history?taxnode_id=20186105

A new virus isolated from the human respiratory 480 tract

Identification of a new human coronavirus

Molecular pathology of emerging coronavirus 485 infections

Dobsonia moluccensis. The IUCN Red List of Threatened Species

Notes on the dry season roosting and foraging behaviour 51

Food availability and annual migration of the 57

Replication and shedding of MERS-CoV in Jamaican fruit bats 597 (Artibeus jamaicensis)

Further evidence for bats as the evolutionary source of Middle East 600 respiratory syndrome coronavirus

Coronaviruses: important emerging human 602 pathogens

Urbanization and disease 604 emergence: dynamics at the wildlife-livestock-human interface

Mechanisms of zoonotic severe acute respiratory syndrome coronavirus host range expansion in 608 human airway epithelium

Wuhan Municipal Commission of Health and Health on 64

Detection and characterization of a novel bat-borne coronavirus in Singapore using multiple 626 molecular approaches

Preliminary assessment of activity 628 pattern and diet of the lesser dog faced fruit bat Cynopterus brachyotis in a Dipterocarp Forest

Development of a one-step RT-632 PCR assay for detection of pancoronaviruses (α-, β-, γ-, and δ-coronaviruses) using newly 633 designed degenerate primers for porcine and avianfecal samples

jModelTest: phylogenetic model averaging. Molecular biology and 639 evolution

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus 642 evolution

Posterior 644 summarization in Bayesian phylogenetics using Tracer 1.7. Systematic biology

PAST: Paleontological statistics software 646 package for education and data analysis