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Identification of Diverse Full-Length Endogenous Betaretroviruses In Hayward et al. Retrovirology 2013, 10:35 http://www.retrovirology.com/content/10/1/35 RESEARCH Open Access Identification of diverse full-length endogenous betaretroviruses in megabats and microbats Joshua A Hayward1,2, Mary Tachedjian3†, Jie Cui4†, Hume Field5, Edward C Holmes4,6, Lin-Fa Wang3,7,8 and Gilda Tachedjian1,2,9* Abstract Background: Betaretroviruses infect a wide range of species including primates, rodents, ruminants, and marsupials. They exist in both endogenous and exogenous forms and are implicated in animal diseases such as lung cancer in sheep, and in human disease, with members of the human endogenous retrovirus-K (HERV-K) group of endogenous betaretroviruses (βERVs) associated with human cancers and autoimmune diseases. To improve our understanding of betaretroviruses in an evolutionarily distinct host species, we characterized βERVs present in the genomes and transcriptomes of mega- and microbats, which are an important reservoir of emerging viruses. Results: A diverse range of full-length βERVs were discovered in mega- and microbat genomes and transcriptomes including the first identified intact endogenous retrovirus in a bat. Our analysis revealed that the genus Betaretrovirus can be divided into eight distinct sub-groups with evidence of cross-species transmission. Betaretroviruses are revealed to be a complex retrovirus group, within which one sub-group has evolved from complex to simple genomic organization through the acquisition of an env gene from the genus Gammaretrovirus. Molecular dating suggests that bats have contended with betaretroviral infections for over 30 million years. Conclusions: Our study reveals that a diverse range of betaretroviruses have circulated in bats for most of their evolutionary history, and cluster with extant betaretroviruses of divergent mammalian lineages suggesting that their distribution may be largely unrestricted by host species barriers. The presence of βERVs with the ability to transcribe active viral elements in a major animal reservoir for viral pathogens has potential implications for public health. Keywords: Retrovirus, Betaretrovirus, Endogenous, Evolution, Bats, Pteropus, Myotis, Rhinolophus Background integration over the course of multiple generations typic- Retroviruses (family Retroviridae) are a diverse and widely ally leads to the accumulation of mutations that render distributed family of RNA viruses distinguished by their them defective and non-functional [2]. use of a viral RNA-dependent DNA polymerase (reverse The retroviral family is composed of seven gene- transcriptase; RT) and ability to integrate into the ge- ra: Alpharetrovirus, Betaretrovirus, Gammaretrovirus, nomes of their cellular hosts [1]. In addition to the exist- Deltaretrovirus, Epsilonretrovirus, Lentivirus,and ence of infectious viral particles that are horizontally Spumavirus [3]. The genomic organization of retrovi- transmitted between hosts (exogenous retroviruses), the ruses is classified as either ‘simple’ or ‘complex’,with capacity of retroviruses to integrate into the host germline simple retroviruses encoding the structural poly- also generates vertically transmissible endogenous retro- proteins Gag and Env, and the functional polyproteins viruses (ERVs) [1,2]. ERVs may or may not be capable Pro and Pol [4]. Complex retroviruses encode additional of producing infectious viral particles, and germline accessory and regulatory proteins with diverse functions that typically establish and maintain virus replication * Correspondence: [email protected] and pathogenesis [5]. The core elements of all retrovi- †Equal contributors ruses are flanked by a pair of typically untranslated nu- 1Retroviral Biology and Antivirals Laboratory, Centre for Virology, Burnet cleotide regions at their 5′ and 3′ ends. In the provirus, Institute, Melbourne, VIC 3004, Australia 2Department of Microbiology, Monash University, Clayton, VIC 3800, Australia formed by integration of the viral cDNA into the host Full list of author information is available at the end of the article © 2013 Hayward et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Hayward et al. Retrovirology 2013, 10:35 Page 2 of 19 http://www.retrovirology.com/content/10/1/35 cell chromosome, these regions are referred to as ‘long export factor, chromosome region maintenance 1/exportin terminal repeats’ (LTR) [4]. 1 (Crm1/Xpo1) [17,19]. Simple betaretroviruses such as Exogenous retroviruses of zoonotic origin have been MPMV contain a constitutive transport element (CTE) associated with disease in humans, the most notable be- within the nucleotide sequence at the 3′ end of the retro- ing human immunodeficiency virus (HIV) [6]. Other ret- viral genome that recruits a cellular binding factor, Tap roviruses such as human foamy virus (HFV) and human (nuclear RNA export factor 1; NXF1) which mediates nu- T-cell leukemia virus (HTLV) are known to be capable clear export [22,23]. of infecting humans [7,8]. The retroviruses most recently Importantly, ERVs provide a unique opportunity to associated with human disease are betaretroviruses. The study the evolutionary history of this family of viruses as up-regulation of gene products derived from the human they are essentially genetic ‘fossils’ of past retroviral in- endogenous retrovirus-K (HERV-K) group of betare- fections [2,24]. As such, their existence serves as an indi- troviruses has been linked to a diverse range of cancers cation of the potential host range of a given retroviral such as those of the breast, ovaries, and prostate along- lineage and may be interpreted as evidence for the pos- side other significant human maladies [9,10]. sible existence of exogenous retroviruses that have yet to The genus Betaretrovirus consists of the Type B and be isolated. Indeed, previous studies have reported a Type D groups of exogenous and endogenous retrovi- number of endogenous betaretroviruses (βERVs) in spe- ruses and the HERV-K group of endogenous retrovi- cies for which no exogenous betaretrovirus has yet been ruses. Among the exogenous, infectious members of the identified. These include mammalian species as diverse genus are the Type B Mouse mammary tumour virus as primates, horses, rats, lemurs, and an Australian mar- (MMTV), the Type D Jaagsiekte sheep retrovirus (JSRV), supial, the common brushtail possum [25-27]. which causes pulmonary carcinoma in sheep, and the There are over 1,100 known species of bats (order Type D Mason-Pfizer monkey virus (MPMV) which Chiroptera), accounting for approximately 20% of all mam- causes wasting and immunosuppression in new-born malian species [28]. Bats are relatively divergent from other Rhesus monkeys [11-13]. All betaretroviruses utilize var- mammals, having branched off from the Perissodactyla iants of the lysine tRNA primer binding site (PBS) and (containing horses) approximately 88 million years ago encode a deoxyuridine triphosphatase (dUTPase), within (mya) [29]. They are divided into two major groups: their pro gene which functions as a nucleocapsid- megabats (suborder Megachiroptera) which are mainly dUTPase fusion protein [14-16]. Type B and Type D fruit-eating, and microbats (suborder Microchiroptera), betaretroviruses differ in several respects including their smallinsectivoresthatnavigatebymeansofecholo- complement of accessory factors, virion morphology, cation [30]. Notably, bats harbour over 100 viral strategies for RNA nuclear export, and the length of species from a diverse range of virus families includ- their LTR regions. Type B betaretroviruses contain ing the Paramyxoviridae, Coronaviridae, Herpesviridae, spherical viral cores and have LTRs of ~1,200 nucleo- Rhabdoviridae, Arenaviridae, Togaviridae, Flaviviridae, tides while Type D contain cylindrical viral cores and Orthomyxoviridae, Reoviridae, Bunyaviridae, Filoviridae, have LTRs of ~300 nucleotides. The prototypical Type B and Picornaviridae [31]. Bats, belonging to the mamma- betaretrovirus, MMTV, encodes the accessory proteins lian superorder Laurasiatheria, are a major viral reservoir regulator of export of MMTV mRNA (Rem) and nega- that is evolutionarily distinct from another major viral res- tive acting factor (Naf), which have roles in viral mRNA ervoir, rodents, which together with primates belong to export, protein synthesis and gene expression [17-19], in the superorder Euarchontoglires [29,32]. addition to the virulence factor, superantigen (Sag) [20]. Bats have recently gained attention as they have been The Type D retrovirus JSRV has been shown to encode implicated in numerous newly emerging diseases of the trans-acting factor Rej which has a role in protein humans caused by viruses such as SARS-coronavirus, synthesis and may assist RNA nuclear export [21]. While Hendra virus, Nipah virus, and the Ebola virus [33-35]. no distinct oncogenes or Sag-like virulence-associated This track record of zoonotic transmission of previously proteins are known to be encoded by Type D betare- unknown viral pathogens from bats to humans has troviruses, the Env protein of JSRV is associated with prompted calls for a proactive approach to future emer- oncogenesis [13,14]. ging diseases originating in bats [30]. To this end a nat- There are two major strategies employed by betare- ural history survey of bats has begun, and
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