Field-Adapted Full Genome Sequencing of Peste-Des-Petits-Ruminants Virus Using Nanopore Sequencing.

Peste-des-petits-ruminants virus (PPRV) is currently the focus of a control and eradication program. Full genome sequencing has the opportunity to become a powerful tool in the eradication program by improving molecular epidemiology and the study of viral evolution. PPRV is prevalent in many resource-constrained areas, with long distances to laboratory facilities, which can lack the correct equipment for high-throughput sequencing. Here we present a protocol for near full or full genome sequencing of PPRV. The use of a portable miniPCR and MinION brings the laboratory to the field and in addition makes the production of a full genome possible within 24 h of sampling. The protocol has been successfully used on virus isolates from cell cultures and field isolates from tissue samples of naturally infected goats.

Perceptions and practices among Zambian sheep and goat traders concerning small ruminant health and disease.

Trade in animals and animal products is a key factor in the transmission of infectious diseases. Livestock traders play an important role in this process, yet there is little knowledge of traders' perceptions of animal disease or their associated actions. The aim of this study was to investigate perceptions and practices of Zambian small ruminant traders with regard to sheep and goat health and disease. It also analysed how existing perceptions and practices might affect risks of disease transmission through trade. A case study was performed at the two largest small livestock markets in Zambia: the Lusaka market in the capital and the Kasumbalesa market near the border with the Democratic Republic of Congo. Semi-structured interviews with 47 traders performed in April-May and September 2018 represent the core material. Zambian small ruminant traders frequently trade animals that have clinical signs of disease, either because they appear unaware or indifferent to the associated risks, experience financial constraints or assign responsibility for disease prevention to other value chain actors. In their decision about whether or not to sell a visibly sick small ruminant, traders appear to consider whether the clinical sign is perceived as 'natural' or the result of an illness, whether the buyer is aware of the animal's health condition, and whether the animal is sold for consumption or breeding purposes. Traders appear to regard the veterinary certificate required to transport small ruminants in Zambia as proof of health, placing the responsibility for potential disease in traded animals on the veterinary authorities. In their description of a model trader, taking good care of and being sensitive to customer needs was emphasized, indicating that an efficient way to encourage traders to change their behaviour is to influence customer demands. In contrast to the focus in previous studies on identifying and filling knowledge gaps, the present study show that lack of knowledge is not central to why traders engage in disease-transmitting behaviour. Greater awareness of other reasons for certain perceptions and practices could lead to the formulation of risk communication strategies and mitigation measures that are relevant for the local context, as well as alternative strategies for changing trader behaviour.

Bornaviruses in naturally infected Psittacus erithacus in Portugal: insights of molecular epidemiology and ecology.

Background: The genus Orthobornavirus comprises non-segmented, negative-stranded RNA viruses able to infect humans, mammals, reptiles and various birds. Parrot bornavirus 1 to 8 (PaBV-1 to 8) causes neurological and/or gastrointestinal syndromes and death on psittacines. We aimed to identify and to produce epidemiologic knowledge about the etiologic agent associated with a death of two female Psittacus erithacus (grey parrot). Methods and Results: Both parrots were submitted for a complete standardised necropsy. Tissue samples were analysed by PCR. The findings in necropsy were compatible with bornavirus infection. Analysis revealed PaBV-4 related with genotypes detected in captive and in wild birds. The N and X proteins of PaBV-4 were more related to avian bornaviruses, while phosphoprotein was more related to variegated squirrel bornavirus 1 (VSBV-1). Within the P gene/phosphoprotein a highly conserved region between and within bornavirus species was found. Conclusions: Portugal is on the routes of the intensive world trade of psittacines. Broad screening studies are required to help understanding the role of wild birds in the emergence and spread of pathogenic bornaviruses. PaBV-4 phosphoprotein is closer to VSBV-1 associated with lethal encephalitis in humans than with some of the avian bornaviruses. The highly conserved P gene/phosphoprotein region is a good target for molecular diagnostics screenings.

Seroprevalence of pestivirus in Eurasian tundra reindeer in Finland, Sweden, Norway, Iceland and Russian Federation.

Reindeer herding is of great importance for the indigenous people of the Fennoscandia peninsula and northern Russia. There are also free-ranging feral populations of reindeer in Finland, Iceland, Norway and Russian Federation. The genus Pestivirus contains several viral species that infect ungulates and often show capacity to transmit between different host species. Sera from 520 Eurasian tundra reindeer (Rangifer tarandus tarandus) from Finland, Sweden, Norway, Iceland and Russian Federation were analysed and the prevalence of pestivirus-specific antibodies was determined. Seropositivity proportion was 48.5% for Sweden and 41.2% for Norway, but only 1.6% for Iceland and 2.5% for Finland. All Russian reindeer investigated were seronegative. Pan-pestivirus RT-PCR of seronegative animals (n = 156) from seropositive herds confirmed their negative status. These results indicate unexpectedly non-uniform circulation of an as yet uncharacterised pestivirus in Eurasian reindeer populations. The high seroprevalence in some regions warrants further studies of pestivirus infection dynamics, effects on reindeer health and population dynamics.

Detection and phylogenetic analysis of parrot bornavirus 4 identified from a Swedish Blue-winged macaw (Primolius maracana) with unusual nonsuppurative myositis.

Background: The genus Orthobornavirus comprises RNA viruses infecting humans, mammals, birds and reptiles, where parrot bornavirus 1 to 8 causes fatal neurological and/or gastrointestinal syndromes in psittacines. There is, to the best of our knowledge, no publication describing avian bornaviruses in pet parrots in Sweden. We aimed to identify and to produce epidemiologic knowledge about the etiologic agent associated with a history of severe weight loss and death of a Primolius maracana.Methods and results: The results of histopathology, immunohistochemistry and real-time RT-PCR were compatible with avian bornavirus infection. Sequencing indicated infection by parrot bornavirus 4 (PaBV-4). The genotype reported shared high identity with PaBV-4 identified from pet psittacines and from wild birds in several countries. The N gene and X protein showed genotype clusters formation. P protein revealed to be more conserved within and between species of bornaviruses. Findings suggest horizontal transmission within and between avian orders and species.Conclusion: There seems to be a worldwide trading without biosafety measures, hence, further disease transmission could be avoided. For screening purposes, the P gene is a good candidate as a universal target in molecular diagnostics. Wild birds may be key pieces in the puzzle of bornavirus epidemiology.

Pestivirus Infections in Semi-Domesticated Eurasian Tundra Reindeer (Rangifer tarandus tarandus): A Retrospective Cross-Sectional Serological Study in Finnmark County, Norway.

Members of the Pestivirus genus (family Flaviviridae) cause severe and economically important diseases in livestock. Serological studies have revealed the presence of pestiviruses in different cervid species, including wild and semi-domesticated Eurasian tundra reindeer. In this retrospective study, serum samples collected between 2006 and 2008 from 3339 semi-domesticated Eurasian reindeer from Finnmark County, Norway, were tested for anti-pestivirus antibodies using an enzyme linked immunosorbent assay (ELISA) and a subset of these by virus neutralization test (VNT). A seroprevalence of 12.5% was found, varying from 0% to 45% among different herding districts, and 20% in western Finnmark, as compared to 1.7% in eastern Finnmark. Seroprevalence increased with age. Pestivirus-specific RNA was not detected in any of the 225 serum samples tested by real-time RT-PCR. Based on VNT results, using a panel of one bovine viral diarrhea virus (BVDV) strain and two border disease virus (BDV) strains, the virus is most likely a reindeer-specific pestivirus closely related to BDV. A characterization of the causative virus and its pathogenic impact on reindeer populations, as well as its potential to infect other domestic and wild ruminants, should be further investigated.

Seroprevalence and risk factors for peste des petits ruminants and selected differential diagnosis in sheep and goats in Tanzania.

Introduction: Livestock husbandry is critical for food security and poverty reduction in a low-income country like Tanzania. Infectious disease is one of the major constraints reducing the productivity in this sector. Peste des petits ruminants (PPR) is one of the most important diseases affecting small ruminants, but other infectious diseases may also be present. Objective: The objective of this study was to determine the seroprevalence and risk factors for exposure to PPR, contagious caprine pleuropneumonia (CCPP), foot-and-mouth disease (FMD), bluetongue (BT), and bovine viral diarrhoea (BVD) in sheep and goats in Tanzania. Methods: Serum samples were collected in 2014 and 2015, and analysed using enzyme-linked immunosorbent assays to detect antibodies to the five pathogens. Results and discussion: This is the first description of seroprevalence of FMD and BT among small ruminants in Tanzania. Risk factor analysis identified sex (female) (OR for 2014: PPR: 2.49, CCPP: 3.11, FMD: 2.98, BT: 12.4, OR for 2015: PPR: 14.1, CCPP: 1.10, FMD: 2.67, BT: 1.90, BVD: 4.73) and increasing age (>2 years) (OR for 2014: PPR: 14.9, CCPP: 2.34, FMD: 7.52, BT: 126, OR for 2015: PPR: 8.13, CCPP: 1.11, FMD: 2.98, BT: 7.83, BVD: 4.74) as risk factors for exposure to these diseases.