Molecular evolution of kobuviruses in cats

Development and utilization of a multiplex PCR assay for detecting three feline enteroviruses

BACKGROUND

Feline diarrhea is a common digestive tract disease in clinical practice, with watery feces as the main clinical manifestation. There are numerous pathogenic factors causing feline diarrhea, among which viral infections are prevalent, and feline panleukopenia virus (FPV) is the most common pathogen. In recent years, a variety of novel viruses have been detected in the intestines of cats with diarrhea. For example, feline kobuvirus (FKoV) and feline norovirus (FNoV) have been identified. These viruses may have a direct relationship with feline diarrhea or the connection has yet to be discovered. However, with the continuous emergence of these novel viruses and the frequent contact between pet cats and humans, it is prone to large-scale epidemics and outbreaks of viruses. Therefore, developing an accurate, rapid, and simple method to detect novel enteric viruses is of great significance for the early warning of emerging feline enteric viral infectious diseases.

METHODS AND RESULTS

A detailed comparison of the genome sequences of the three aforementioned feline enteroviruses was conducted. Subsequently, three pairs of specific primers were designed by selecting the conserved gene regions, and the single and multiplex PCR amplification reaction systems as well as reaction conditions were repeatedly optimized. The target fragment sizes detected by the multiplex PCR method were 650 bp for FPV, 500 bp for FKoV, and 340 bp for FNoV. Sensitivity tests demonstrated that the lower detection limit was one-tenth of that of single PCR. Meanwhile, the detection results for feline calicivirus (FCV), feline herpesvirus (FHV), and feline coronavirus (FCoV) were all negative. Testing of a total of 209 clinical samples from various regions in Shandong Province revealed that the detection rates of the three viruses were 13.4%, 4.8%, and 3.8%, respectively, and mixed infections were present.

CONCLUSIONS

In this study, an epidemiological investigation of the three feline enteroviruses was performed, and a sensitive, specific, and reproducible multiplex PCR assay was developed, which can be utilized for the detection of clinical samples.

Development of a TaqMan-based multiplex real-time PCR for simultaneous detection of four feline diarrhea-associated viruses

Since their recent discovery, the prevalence of novel feline enteric viruses, including feline bocavirus 1 (FBoV-1), feline astrovirus (FeAstV), and feline kobuvirus (FeKoV), has been reported in China. Co-infections of these viruses with feline parvovirus (FPV) are common causes of diarrhea in cats. Viral co-infections are difficult to identify because of their non-specific clinical signs. To detect and identify these viruses, a quick and specific pathogen-testing approach is required. Here, we establish a real-time PCR (qPCR) based on multiple TaqMan probes for the simultaneous detection of FBoV-1, FeAstV, FeKoV, and FPV. Specific primers and TaqMan fluorescent probes were designed to ensure specificity. The results showed that the detection limit of single qPCR was up to 10 copies, and the detection limit of multiplex qPCR was up to 100 copies, with correlation coefficients >0.995 in all cases. Clinical sample detection revealed a 25.19% (34/135) total rate of co-infection among the viruses and a 1.48% (2/135) quadruple infection rate. Thus, this multiplex qPCR approach can serve as a quick, sensitive, and specific diagnostic tool for FBoV-1, FeAstV, FeKoV, and FPV identification, and it may be utilized for routine surveillance of these emerging and reemerging feline enteric viruses.

Genetic characterization of a novel picornavirus in Algerian bats: co-evolution analysis of bat-related picornaviruses

Bats are reservoirs of numerous zoonotic viruses. The Picornaviridae family comprises important pathogens which may infect both humans and animals. In this study, a bat-related picornavirus was detected from Algerian Minioptreus schreibersii bats for the first time in the country. Molecular analyses revealed the new virus originates to the Mischivirus genus. In the operational use of the acquired sequence and all available data regarding bat picornaviruses, we performed a co-evolutionary analysis of mischiviruses and their hosts, to authentically reveal evolutionary patterns within this genus. Based on this analysis, we enlarged the dataset, and examined the co-evolutionary history of all bat-related picornaviruses including their hosts, to effectively compile all possible species jumping events during their evolution. Furthermore, we explored the phylogeny association with geographical location, host-genus and host-species in both data sets.

Feline Virome-A Review of Novel Enteric Viruses Detected in Cats

Recent advances in the diagnostic and metagenomic investigations of the feline enteric environment have allowed the identification of several novel viruses that have been associated with gastroenteritis in cats. In the last few years, noroviruses, kobuviruses, and novel parvoviruses have been repetitively detected in diarrheic cats as alone or in mixed infections with other pathogens, raising a number of questions, with particular regards to their pathogenic attitude and clinical impact. In the present article, the current available literature on novel potential feline enteric viruses is reviewed, providing a meaningful update on the etiology, epidemiologic, pathogenetic, clinical, and diagnostic aspects of the infections caused by these pathogens.

First report and genetic characterization of feline kobuvirus in diarrhoeic cats in China

Feline kobuvirus (FeKoV) is a newly discovered organism, classified under the species Aichivirus A of the genus Kobuvirus. Since it was first reported in 2013, molecular evidence for FeKoV in the feline population has been restricted to two countries: Korea and Italy. In this study, we collected faecal samples from cats in southern China and detected the FeKoV RNA in these samples. A prevalence rate of 9.9% (8/81) was identified by RT‐PCR, and all positive samples were obtained from diarrhoeic animals. In addition, FeKoV was shown positive associated with diarrhoea in cats, with a correlation coefficient of 0.25. Next, we designed three primer pairs with degenerate bases, which targeted the conservative overlapping region of the entire published FeKoV genome, and sequenced the near‐complete genome of the first Chinese field FeKoV strain, WHJ‐1, using long‐fragment PCR. Finally, we analysed WHJ‐1's homology and phylogeny using the polyprotein gene. The results indicated that FeKoV has rapidly mutated since it was first discovered. This study will help to better understand FeKoV's epidemiology, evolutionary pattern and genetic diversity.

Evolution and phylogeographic dissemination of endemic porcine picornaviruses in Vietnam

Members of the Picornaviridae are important and often zoonotic viruses responsible for a variety of human and animal diseases. However, the evolution and spatial dissemination of different picornaviruses circulating in domestic animals are not well studied. We examined the rate of evolution and time of origin of porcine enterovirus G (EV-G) and porcine kobuvirus species C lineages (PKV-C) circulating in pig farms in Vietnam and from other countries. We further explored the spatiotemporal spread of EV-G and PKV-C in Southwest Vietnam using phylogeographic models. Multiple types of EV-G are co-circulating in Vietnam. The two dominant EV-G types among isolates from Vietnam (G1 and G6) showed strong phylogenetic clustering. Three clades of PKV-C (PKV-C1-3) represent more recent introductions into Vietnam; PKV-C2 is closely related to PKV-C from Southwest China, indicating possible cross-border dissemination. In addition, high virus lineage migration rates were estimated within four districts in Dong Thap province in Vietnam for both EV-G types (G1, G6) and all PKV-C (C1-3) clades. We found that Chau Thanh district is a primary source of both EV-G and PKV-C clades, consistent with extensive pig trading in and out of the district. Understanding the evolution and spatial dissemination of endemic picornaviruses in pigs may inform future strategies for the surveillance and control of picornaviruses.