Discovery and Characterization of Novel Bat Coronavirus Lineages from Kazakhstan

Abstract

Coronaviruses are positive-stranded RNA viruses that infect a variety of hosts, resulting in a range of symptoms from gastrointestinal illness to respiratory distress. Bats are reservoirs for a high diversity of coronaviruses, and focused surveillance detected several strains genetically similar to MERS-coronavirus, SARS-coronavirus, and the human coronaviruses 229E and NL63. The bat fauna of central Asia, which link China to eastern Europe, are relatively less studied than other regions of the world. Kazakhstan is the world's ninth largest country; however, little is understood about the prevalence and diversity of bat-borne viruses. In this study, bat guano was collected from bat caves in three different sites of southern Kazakhstan that tested positive for coronaviruses. Our phylogenetic reconstruction indicates these are novel bat coronaviruses that belong to the genus Alphacoronavirus. In addition, two distinct lineages of Kazakhstan bat coronaviruses were detected. Both lineages are closely related to bat coronaviruses from China, France, Spain, and South Africa, suggesting that co-circulation of coronaviruses is common in multiple bat species with overlapping geographical distributions. Our study highlights the need for collaborative efforts in understudied countries to increase integrated surveillance capabilities toward better monitoring and detection of infectious diseases.

Keywords: Hypsugo savii; Kazakhstan; Myotis blythii; coronavirus; phylogeny; virus discovery.

Figure 1

Geographical map of Kazakhstan showing the global positioning system (GPS) locations of three collection sites in this study. The green figures correspond to the sampling sites and are referenced next to the sequence name in Figure 2.

Figure 2

Phylogenetic relationships of the RNA-dependent reverse polymerase (RdRp) gene sequences of coronavirus, inferred using the maximum-likelihood method with the GTR + GAMMA model in RAxML. Representative virus isolates from Alpha-, Beta-, and Gamma-coronavirus (CoV) were included in the analysis. Colored branches and symbols denote viruses collected from different hosts. New CoV sequences generated from this study are marked by red branches. The dotted box indicates Kazakhstan coronavirus lineages (KZ3 and KZ43) described in this study and their closely related viruses isolated worldwide. The inset displays detailed strain names of the Kazakhstan coronaviruses and their closely related viruses. Cave locations are denoted by different shapes in green. Bootstrap support values greater than 50% are displayed at major nodes. The scale bar indicates the number of nucleotide substitutions per site.

Figure 3

A map of the geographic distribution of Myotis blytii and Hypsugo savii species and where their ranges overlap (created in QGIS). The locations of the KZ3 bat coronavirus monophyletic clade (bootstrap (BS) = 76%) are presented on the map (yellow star), including Kazakhstan bat coronaviruses (KZ-3a and KZ-3b: MK603150–MK603157 and MK603159–MK603161), bat coronaviruses from China (KX285128, KX285140, KX285154, KX285183, KX285201), and bat coronaviruses from Spain (HQ184049, HQ184050). The locations of the KZ43 monophyletic clade (BS = 91%) are also listed on the map (purple star), including the Kazakhstan bat coronavirus (KZ43: MK603158) and bat coronaviruses from France (KT345294–KT345294).