Meta-Transcriptomic Discovery of a Divergent Circovirus and a Chaphamaparvovirus in Captive Reptiles with Proliferative Respiratory Syndrome

Abstract

Viral pathogens are being increasingly described in association with mass morbidity and mortality events in reptiles. However, our knowledge of reptile viruses remains limited. Herein, we describe the meta-transcriptomic investigation of a mass morbidity and mortality event in a colony of central bearded dragons (Pogona vitticeps) in 2014. Severe, extensive proliferation of the respiratory epithelium was consistently found in affected dragons. Similar proliferative lung lesions were identified in bearded dragons from the same colony in 2020 in association with increased intermittent mortality. Total RNA sequencing identified two divergent DNA viruses: a reptile-infecting circovirus, denoted bearded dragon circovirus (BDCV), and the first exogeneous reptilian chaphamaparvovirus—bearded dragon chaphamaparvovirus (BDchPV). Phylogenetic analysis revealed that BDCV was most closely related to bat-associated circoviruses, exhibiting 70% amino acid sequence identity in the Replicase (Rep) protein. In contrast, in the nonstructural (NS) protein, the newly discovered BDchPV showed approximately 31%–35% identity to parvoviruses obtained from tilapia fish and crocodiles in China. Subsequent specific PCR assays revealed BDCV and BDchPV in both diseased and apparently normal captive reptiles, although only BDCV was found in those animals with proliferative pulmonary lesions and respiratory disease. This study expands our understanding of viral diversity in captive reptiles.

Serpentovirus (Nidovirus) and Orthoreovirus Coinfection in Captive Veiled Chameleons (Chamaeleo calyptratus) with Respiratory Disease

“…Coinfection with different virus genotypes appears to be a natural phenomenon for at least some serpentoviruses found in snakes [ 16 ]. A recent study in bearded dragons described proliferative lung lesions observed in bearded dragons associated with co-infection by circovirus and parvovirus [ 3 ]. In this study, one definitive case of coinfection was identified by metagenomic sequencing and two additional cases of suspected coinfection were identified based on double peaks in Sanger sequencing chromatograms.…”

“…A number of viruses cause disease in captive and wild reptiles, and new viral pathogens are continuously being discovered throughout the world [ 1 , 2 , 3 ]. In 2014, a novel group of nidoviruses (order Nidovirales ), currently classified as serpentoviruses, were identified as potential reptile pathogens [ 4 , 5 , 6 , 7 , 8 ].…”

Viromes in Marine Ecosystems Reveal Remarkable Invertebrate RNA Virus Diversity

“…However, pathogenic viruses represent only a minor proportion of the virosphere (Geoghegan and Holmes 2017; Middelboe and Brussaard 2017; Zhang, et al 2018; Salazar, et al 2019; Zhang, et al 2019). Advances in meta-genomics and meta-transcriptomics led to the discovery of an enormous amount of viruses, most of which are distinct from presently well-defined pathogenic viruses (Shi, et al 2016; Shi, Lin, et al 2018; Chang, Eden, et al 2020; Chang, Li, et al 2020; Pettersson, et al 2020; Wu, et al 2020). These findings have filled important gaps in virus evolution and reflected the fact that RNA viruses with relatively small genome size could also have huge diversity in genomic elasticity (Qin, et al 2014; Zhang, et al 2018).…”

Investigating the Diversity and Host Range of Novel Parvoviruses from North American Ducks Using Epidemiology, Phylogenetics, Genome Structure, and Codon Usage Analysis

“…In recent years, several avian parvoviruses have been identified within the subfamily Hamaparvovirinae . All these viruses are included within the recently established genus Chaphamaparvovirus , which takes its name from the host groups in which its members were initially discovered ( ch iropteran, a vian, and p orcine) and so far includes viruses identified in mammals and birds [ 2 , 3 ], although recent studies also report phylogenetically related viruses in fish and reptiles [ 10 , 11 ]. Currently this genus includes 16 species, with six identified in the avian reservoir.…”