Ovine adenoviruses infecting sheep and goats in Türkiye: detection and molecular characterization of three different types.

Adenoviruses (AdVs) have been detected in a wide variety of animals. To date, eight types of AdVs in sheep and two types in goats have been identified, which belong to two distinct genera, Mastadenovirus and Atadenovirus. Typically, the term pneumo-enteritis is used to describe adenovirus-induced disease in small ruminants, which has been associated with both enteric and respiratory symptoms of varying severity. The aim of this study was to detect and identify AdVs of small ruminants belonging to the genera Mastadenovirus and Atadenovirus. For this purpose, diagnostic samples (47 lung, 27 intestine, and two pooled tissue samples including intestine and lung) from 49 small ruminants (39 sheep and 10 goats) were used. Following the viral DNA extraction, PCR was carried out by using the primers targeting the hexon gene in order to detect both mast- and atadenoviruses. Sequencing the amplified fragments revealed the presence of three types of ovine adenovirus (OAdV): OAdV-3, OAdV-4, and OAdV-8. Specifically, OAdV-3 was detected in two sheep and a goat while OAdV-4 and OAdV-8 were found in only one sheep each. There is still limited data on the interaction between the viruses in different adenovirus genera and the detected disease, as well as the genetic diversity of adenoviruses, especially in small ruminants. In conclusion, the detection of AdVs in lung and intestinal tissues of small ruminants in this study suggests that these viruses may have contributed to the disease and/or predisposed to other agents.

Whole-genome analysis of a rare G15P[21] group A rotavirus detected at a dairy cattle farm.

Group A rotaviruses (RVAs) are a major cause of severe enteritis in humans and animals. RVAs have been identified in several animal species and their genetic diversity, the segmented nature of their RNA genome and the ability to spill over from one species to another can generate new RVA strains. In this study, we investigated the genome constellations of an unusual, rare, bovine RVA strain, G15P[21], identified from a farm with neonatal diarrhoea of calves in 2006. In parallel, the genome constellations of other RVA strains with different G/P types identified from the same farm in the same time span (2006-2008) were analysed. The genome constellation of strain K53 was G15-P[21]-I2-R2-C2-M2-A13-N2-T9-E2-H3 and was similar, overall, to that of the other bovine RVA strains (G6/10-P[11]-I2-R2-C2-M2-A13-N2-T6-E2-H3) with the exception of the NSP3 segment (T9 vs T6). This study describes RVA genomes with different genotype combinations isolated at a farm and also contributes to the understanding of the diversity and evaluation of rotavirus in a global context.

Molecular characterization of picobirnaviruses in small ruminants with diarrhea in Turkey.

Picobirnaviruses (PBVs), detected in a wide range of host species, are viruses of which limited information is available about their pathogenic potential, ecology, or evolutionary characteristics. In this study, a molecular analysis of segment 2 encoding the PBV RNA-dependent RNA-polymerase (RdRp) in small ruminants with diarrhea in Turkey was undertaken. A total of 66 fecal samples or gut contents from diarrheic small ruminants including 55 sheep and 11 goats were screened. Four samples (6.06%), obtained from sheep in different farms, yielded the expected amplicon size for the genogroup I RdRp gene fragment, whereas no positivity was detected for genogroup II PBVs. Phylogenetic analysis revealed high levels of genetic diversity among the genogroup I PBVs. Additionally, all PBV infected sheep were also positive for rotavirus A. This study, reporting the presence of the PBVs in sheep Turkey for the first time, contributes to the molecular characterization and epidemiology of PBVs.

Isolation and genetic characterization of bovine ephemeral fever virus from epidemic-2020 in Turkey.

Bovine ephemeral fever virus (BEFV) infection occurs seasonally in many tropical and subtropical regions of Africa, Asia (including the Middle East), and Australia while it is exotic in Europe. In this study, the epidemiology of BEFV infection in Turkey that bridges southeastern Europe and Asia, geographically, was investigated according to the comparison of the nucleotide sequences of the virus caused the last epidemic in 2020 with those of the strains previously detected in Turkey as well as BEFV strains from other countries. In the phylogenetic analysis, based on an alignment of full-length G gene sequences, BEFVs from epidemic-2020 were located in Middle Eastern lineage and appear to represent most closely related BEFVs from India-2018 and 2019. The findings will contribute to a better understanding of BEFV epidemiology in Turkey.

Molecular characterization of bovine noroviruses and neboviruses in Turkey: detection of recombinant strains.

To investigate the molecular epidemiology and genetic diversity of bovine enteric caliciviruses, a total of 167 fecal samples from diarrheic calves were screened. Bovine noroviruses (BoNoVs) and neboviruses were detected in 56 (33.5%) and 37 (22.1%) fecal samples, respectively. Sequences of the RdRp and capsid gene of selected BoNoVs showed that the GIII.1 and GIII.2 genotypes were in circulation in Turkey. Two of the BoNoV strains were identified as recombinant strains (GIII.P1/GIII.2). All examined neboviruses possessed a Nebraska-like RdRp gene. The two nebovirus strains were classified into lineage 4 based on phylogenetic analysis of VP1 amino acid sequences. One of them showed evidence of a recombination event within the S domain. This study is thus the first to reveal the presence of the BoNoV GIII.1 genotype and recombinant strains of BoNoV and neboviruses in Turkey.

External quality assessment of Rift Valley fever diagnosis in 17 veterinary laboratories of the Mediterranean and Black Sea regions.

Rift Valley fever (RVF) is an arboviral zoonosis that primarily affects ruminants but can also cause illness in humans. The increasing impact of RVF in Africa and Middle East and the risk of expansion to other areas such as Europe, where competent mosquitos are already established, require the implementation of efficient surveillance programs in animal populations. For that, it is pivotal to regularly assess the performance of existing diagnostic tests and to evaluate the capacity of veterinary labs of endemic and non-endemic countries to detect the infection in an accurate and timely manner. In this context, the animal virology network of the MediLabSecure project organized between October 2016 and March 2017 an external quality assessment (EQA) to evaluate the RVF diagnostic capacities of beneficiary veterinary labs. This EQA was conceived as the last step of a training curriculum that included 2 diagnostic workshops that were organized by INIA-CISA (Spain) in 2015 and 2016. Seventeen veterinary diagnostic labs from 17 countries in the Mediterranean and Black Sea regions participated in this EQA. The exercise consisted of two panels of samples for molecular and serological detection of the virus. The laboratories were also provided with positive controls and all the kits and reagents necessary to perform the recommended diagnostic techniques. All the labs were able to apply the different protocols and to provide the results on time. The performance was good in the molecular panel with 70.6% of participants reporting 100% correct results, and excellent in the serological panel with 100% correct results reported by 94.1% of the labs. This EQA provided a good overview of the RVFV diagnostic capacities of the involved labs and demonstrated that most of them were able to correctly identify the virus genome and antibodies in different animal samples.

Evaluation of West Nile Virus Diagnostic Capacities in Veterinary Laboratories of the Mediterranean and Black Sea Regions.

The increasing incidence of West Nile virus (WNV) in the Euro-Mediterranean area warrants the implementation of effective surveillance programs in animals. A crucial step in the fight against the disease is the evaluation of the capacity of the veterinary labs to accurately detect the infection in animal populations. In this context, the animal virology network of the MediLabSecure project organized an external quality assessment (EQA) to evaluate the WNV molecular and serological diagnostic capacities of beneficiary veterinary labs. Laboratories from 17 Mediterranean and Black Sea countries participated. The results of the triplex real time RT-PCR for simultaneous detection and differentiation of WNV lineage 1 (L1), lineage 2 (L2) and Usutu virus (USUV) were highly satisfactory, especially for L1 and L2, with detection rates of 97.9% and 100%, respectively. For USUV, 75% of the labs reported correct results. More limitations were observed for the generic detection of flaviviruses using conventional reverse-transcription polymerase chain reaction (RT-PCR), since only 46.1% reported correct results in the whole panel. As regards the serological panel, the results were excellent for the generic detection of WNV antibodies. More variability was observed for the specific detection of IgM antibodies with a higher percentage of incorrect results mainly in samples with low titers. This EQA provides a good overview of the WNV (and USUV) diagnostic performance of the involved veterinary labs and demonstrates that the implemented training program was successful in upgrading their diagnostic capacities.