Molecular evolution of peste des petits ruminants virus

Cassava brown streak virus evolves with a nucleotide-substitution rate that is typical for the family Potyviridae

The ipomoviruses (family Potyviridae) that cause cassava brown streak disease (cassava brown streak virus [CBSV] and Uganda cassava brown streak virus [UCBSV]) are damaging plant pathogens that affect the sustainability of cassava production in East and Central Africa. However, little is known about the rate at which the viruses evolve and when they emerged in Africa - which inform how easily these viruses can host shift and resist RNAi approaches for control. We present here the rates of evolution determined from the coat protein gene (CP) of CBSV (Temporal signal in a UCBSV dataset was not sufficient for comparable analysis). Our BEAST analysis estimated the CBSV CP evolves at a mean rate of 1.43 × 10-3 nucleotide substitutions per site per year, with the most recent common ancestor of sampled CBSV isolates existing in 1944 (95% HPD, between years 1922 - 1963). We compared the published measured and estimated rates of evolution of CPs from ten families of plant viruses and showed that CBSV is an average-evolving potyvirid, but that members of Potyviridae evolve more quickly than members of Virgaviridae and the single representatives of Betaflexiviridae, Bunyaviridae, Caulimoviridae and Closteroviridae.

Unveiling of the Co-Infection of Peste des Petits Ruminants Virus and Caprine Enterovirus in Goat Herds with Severe Diarrhea in China

Here, we report the discovery of two viruses associated with a disease characterized by severe diarrhea on a large-scale goat farm in Jilin province. Electron Microscopy observations revealed two kinds of virus particles with the sizes of 150-210 nm and 20-30 nm, respectively. Detection of 276 fecal specimens from the diseased herds showed the extensive infection of peste des petits ruminants virus (63.77%, 176/276) and caprine enterovirus (76.81%, 212/276), with a co-infection rate of 57.97% (160/276). These results were partially validated with RT-PCR, where all five PPRV-positive and CEV-positive specimens yielded the expected size of fragments, respectively, while no fragments were amplified from PPRV-negative and CEV-negative specimens. Moreover, corresponding PPRV and CEV fragments were amplified in PPRV and CEV double-positive specimens. Histopathological examinations revealed severe microscopic lesions such as degeneration, necrosis, and detachment of epithelial cells in the bronchioles and intestine. An immunohistochemistry assay detected PPRV antigens in bronchioles, cartilage tissue, intestine, and lymph nodes. Simultaneously, caprine enterovirus antigens were detected in lung, kidney, and intestinal tissues from the goats infected by the peste des petits ruminants virus. These results demonstrated the co-infection of peste des petits ruminants virus with caprine enterovirus in goats, revealing the tissue tropism for these two viruses, thus laying a basis for the future diagnosis, prevention, and epidemiological survey for these two virus infections.

Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages

Peste des petits ruminants virus (PPRV) causes a highly infectious disease affecting mainly goats and sheep in large parts of Africa, Asia, and the Middle East and has an important impact on the global economy and food security. Full genome sequencing of PPRV strains has proved to be critical to increasing our understanding of PPR epidemiology and to inform the ongoing global efforts for its eradication. However, the number of full PPRV genomes published is still limited and with a heavy bias towards recent samples and genetic Lineage IV (LIV), which is only one of the four existing PPRV lineages. Here, we generated genome sequences for twenty-five recent (2010-6) and seven historical (1972-99) PPRV samples, focusing mainly on Lineage II (LII) in West Africa. This provided the first opportunity to compare the evolutionary pressures and history between the globally dominant PPRV genetic LIV and LII, which is endemic in West Africa. Phylogenomic analysis showed that the relationship between PPRV LII strains was complex and supported the extensive transboundary circulation of the virus within West Africa. In contrast, LIV sequences were clearly separated per region, with strains from West and Central Africa branched as a sister clade to all other LIV sequences, suggesting that this lineage also has an African origin. Estimates of the time to the most recent common ancestor place the divergence of modern LII and LIV strains in the 1960s-80s, suggesting that this period was particularly important for the diversification and spread of PPRV globally. Phylogenetic relationships among historical samples from LI, LII, and LIII and with more recent samples point towards a high genetic diversity for all these lineages in Africa until the 1970s-80s and possible bottleneck events shaping PPRV's evolution during this period. Molecular evolution analyses show that strains belonging to LII and LIV have evolved under different selection pressures. Differences in codon usage and adaptative selection pressures were observed in all viral genes between the two lineages. Our results confirm that comparative genomic analyses can provide new insights into PPRV's evolutionary history and molecular epidemiology. However, PPRV genome sequencing efforts must be ramped up to increase the resolution of such studies for their use in the development of efficient PPR control and surveillance strategies.

An Integrated Ecological Niche Modelling Framework for Risk Mapping of Peste des Petits Ruminants Virus Exposure in African Buffalo (Syncerus caffer) in the Greater Serengeti-Mara Ecosystem

Peste des petits ruminants (PPR) is a highly contagious viral disease of small ruminants that threatens livelihoods and food security in developing countries and, in some cases, wild ungulate species conservation. The Greater Serengeti-Mara Ecosystem (GSME) encompasses one of the major wildlife populations of PPR virus (PPRV)-susceptible species left on earth, although no clinical disease has been reported so far. This study aimed to gain further knowledge about PPRV circulation in the GSME by identifying which factors predict PPRV seropositivity in African buffalo (Syncerus caffer). Following an ecological niche modeling framework to map host-pathogen distribution, two models of PPRV exposure and buffalo habitat suitability were performed using serological data and buffalo censuses. Western Maasai Mara National Reserve and Western Serengeti National Park were identified as high-risk areas for PPRV exposure in buffalo. Variables related to wildlife-livestock interaction contributed to the higher risk of PPRV seropositivity in buffalo, providing supportive evidence that buffalo acquire the virus through contact with infected livestock. These findings can guide the design of cost-effective PPRV surveillance using buffalo as a sentinel species at the identified high-risk locations. As more intensive studies have been carried out in Eastern GSME, this study highlights the need for investigating PPRV dynamics in Western GSME.

Morbillivirus: A highly adaptable viral genus

Over the course of human history, numerous diseases have been caused by the transmission of viruses from an animal reservoir into the human population. The viruses of the genus Morbillivirus are human and animal pathogens that emerged from a primordial ancestor a millennia ago and have been transmitting to new hosts, adapting, and evolving ever since. Through interaction with susceptible individuals, as yet undiscovered morbilliviruses or existing morbilliviruses in animal hosts could cause future zoonotic diseases in humans.

Peste Des Petits Ruminants in the Middle East: Epidemiological Situation and Status of Control and Eradication Activities after the First Phase of the PPR Global Eradication Program (2017–2021)

Peste des petits ruminants (PPR) is a burdensome viral disease primarily affecting small ruminants, which is currently targeted for eradication by 2030 through the implementation of a Global Control and Eradication Strategy (PPR GCES). The PPR GCES, launched in 2015, has strongly encouraged countries to participate in Regional PPR Roadmaps, designated according to the Food and Agricultural Organization of the United Nations (FAO) and World Organisation for Animal Health (WOAH) regions and epidemiological considerations, with each targeted by dedicated meetings and activities. Following the conclusion of the first phase of the PPR Global Eradication Program (PPR GEP) (2017–2021), the present work focuses on the disease situation and status of the eradication campaign in the fourteen countries of the PPR GCES Middle Eastern Roadmap as well as Egypt. PPR is endemic to or suspected to be present in most of the region, except for Bahrain, which, as of 2021, is preparing to apply for official recognition as being free of PPR. Some substantial shortcomings are observed in surveillance and disease reporting, as well as in the implemented control strategies, most notably vaccination. Since many of these limitations are shared by many of the investigated countries, the international cooperation and harmonization of control efforts appears crucial to making PPR eradication attainable in the Middle East.

Molecular detection of mixed infection with peste des petits ruminants and retroviruses in Egyptian sheep and goats

Peste des petits ruminants (PPR) is a contagious viral disease causing massive economic loss to animal industries in endemic countries including Egypt. Although a vaccine is available, coinfections can overwhelm the animal immune system and interfere with vaccine protection. Small ruminant retrovirus (SRR), including enzootic nasal tumor virus (ENTV) and Jaagsiekte sheep retrovirus (JSRV), is responsible for coinfections with PPR. Investigation of clinical cases in this study confirmed the presence of PPR virus by RT-PCR among four flocks. Sequence of five PPR amplicons revealed that all strains had 100% aa similarity and belonged to lineage IV. In addition, these strains had 98-99% nt similarity with all previous Egyptian and African strains from Sudan (MK371449) and Ethiopia (MK371449). Illumina sequencing of a representative sample showed a genome of 5753 nt compatible with ENT-2 virus with 98.42% similarity with the Chinese strain (MN564750.1). Four ORFs representing gag, pro, pol, and env genes were identified and annotated. Pro gene was highly stable while gag, pol, and env showed eight, two, and three aa differences with the reference strains. Sanger sequencing revealed that two amplicons were ENT-2 virus, and one was JSRV. ENT-2 sequences had 100% similarity with KU258870 and KU258871 reference strains while JSRV was 100% similar to the EF68031 reference strain. The phylogenetic tree showed a close relationship between the ENT of goats and the JSRV of sheep. This study highlights the complexity of PPR molecular epidemiology, with SRR that was not molecularly characterized previously in Egypt.

Re-Emerged Genotype IV of Japanese Encephalitis Virus Is the Youngest Virus in Evolution

An outbreak of viral encephalitis caused by a Japanese encephalitis virus (JEV) genotype IV infection occurred in Australia between 2021 and 2022. A total of 47 cases and seven deaths were reported as of November 2022. This is the first outbreak of human viral encephalitis caused by JEV GIV since it was first isolated in Indonesia in the late 1970s. Here, a comprehensive phylogenetic analysis based on the whole genome sequences of JEVs revealed it emerged 1037 years ago (95% HPD: 463 to 2100 years). The evolutionary order of JEV genotypes is as follows: GV, GIII, GII, GI, and GIV. The JEV GIV emerged 122 years ago (95% HPD: 57-233) and is the youngest viral lineage. The mean substitution rate of the JEV GIV lineage was 1.145 × 10-3 (95% HPD values, 9.55 × 10-4, 1.35 × 10-3), belonging to rapidly evolving viruses. A series of amino acid mutations with the changes of physico-chemical properties located in the functional important domains within the core and E proteins distinguished emerging GIV isolates from old ones. These results demonstrate the JEV GIV is the youngest JEV genotype at a rapid evolution stage and has good host/vector adaptability for introduction to non-endemic areas. Thus, surveillance of JEVs is highly recommended.

Simultaneous detection and identification of Peste des petits ruminants Virus Lineages II and IV by MCA-Based real-time quantitative RT-PCR assay within single reaction

BACKGROUND

Peste des petits ruminants (PPR) disease is a cross-species infectious disease that severely affects small ruminants and causes great losses to livestock industries in various countries. Distinguishing vaccine-immunized animals from naturally infected animals is an important prerequisite for the eradication of PPR. At present PPRV are classified into lineages I through IV, and only one vaccination strain, Nigeria/75/1, belongs to lineage II, but all of the epidemic strains in China at present are from lineage IV.

RESULTS

To achieve this goal, we developed an SYBR Green I real-time qRT-PCR method for rapid detection and identification of PPRV lineages II and IV by analyzing different melting curve analyses. The negative amplification of other commonly circulating viruses such as orf virus, goat poxvirus, and foot-and-mouth disease virus demonstrated that primers targeting the L gene of PPRV were extremely specific. The sensitivity of the assay was assessed based on plasmid DNA and the detection limit achieved was 100 copies of PPRV lineages II and IV.

CONCLUSION

Since the method has high sensitivity, specificity, and reproducibility, it will be effectively differentiated PPRV lineages II from PPRV lineages IV in PPRV infected animals.

Immunoinformatics Approach for Epitope Mapping of Immunogenic Regions (N, F and H Gene) of Small Ruminant Morbillivirus and Its Comparative Analysis with Standard Vaccinal Strains for Effective Vaccine Development

BACKGROUND

Outbreaks of small ruminant morbillivirus (SRMV) are regularly occurring in Pakistan despite vaccine availability. This study was designed to identify substitutions within the immunogenic structural and functional regions of the nucleocapsid, fusion, and hemagglutinin genes of SRMV and their comparison with vaccinal strains of Nigerian and Indian origin.

METHODS

Swabs and tissue samples were collected from diseased animals. RT-PCR was used to characterize selected genes encoded by viral RNA. The study's N, F, and H protein sequences and vaccinal strains were analyzed for B and T cell epitope prediction using ABCpred, Bipred, and IEDB, respectively.

RESULTS

Significant substitutions were found on the C terminus of the nucleocapsid, within the fusion motif region of the fusion gene and in the immunoreactive region of the hemagglutinin gene.

CONCLUSION

Our results emphasize the need for the development of effective vaccines that match the existing variants of SRMV strains circulating in Pakistan.

Epidemiologic and import risk analysis of Peste des petits ruminants between 2010 and 2018 in India

BACKGROUND

Peste des petits ruminants (PPR) is a serious disease that affects goats, sheep and other small ruminants. As one of the earliest and most serious countries, PPR has seriously threatened India's animal husbandry economy.

RESULTS

In this study, the spatiotemporal characteristics of the PPR in India outbreaks were analyzed. Between 2010 and 2018, the epidemic in India broke out all over the country in a cluster distribution. Epidemic clusters in northern and southern India are at higher risk, and the outbreak time of PPR has significant seasonality. The results of the analysis of the development and transmission of PPR under the natural infection conditions showed that the PPR outbreak in India reached a peak within 15 days. Finally, the quantitative risk analysis results based on scenario tree show showed that the average probability of infecting PPRV in live sheep exported from India was 1.45 × 10^-4.

CONCLUSIONS

This study analyzed the prevalence of PPR in India. The analysis of transmission dynamics on the development of the epidemic provides a reference for the prevention and control of the epidemic. At the same time, it provides risk analysis and suggestions on trade measures for the trading countries of India.

Evolutionary dynamics of codon usages for peste des petits ruminants virus

Peste des petits ruminants virus (PPRV) is an important agent of contagious, acute and febrile viral diseases in small ruminants, while its evolutionary dynamics related to codon usage are still lacking. Herein, we adopted information entropy, the relative synonymous codon usage values and similarity indexes and codon adaptation index to analyze the viral genetic features for 45 available whole genomes of PPRV. Some universal, lineage-specific, and gene-specific genetic features presented by synonymous codon usages of the six genes of PPRV that encode N, P, M, F, H and L proteins reflected evolutionary plasticity and independence. The high adaptation of PPRV to hosts at codon usages reflected high viral gene expression, but some synonymous codons that are rare in the hosts were selected in high frequencies in the viral genes. Another obvious genetic feature was that the synonymous codons containing CpG dinucleotides had weak tendencies to be selected in viral genes. The synonymous codon usage patterns of PPRV isolated during 2007–2008 and 2013–2014 in China displayed independent evolutionary pathway, although the overall codon usage patterns of these PPRV strains matched the universal codon usage patterns of lineage IV. According to the interplay between nucleotide and synonymous codon usages of the six genes of PPRV, the evolutionary dynamics including mutation pressure and natural selection determined the viral survival and fitness to its host.

Expansion in host dynamics of peste des petits ruminants: Potential attribute of outbreaks in disease-endemic settings

Since the first case report in 1942, the peste-des-petits-ruminants virus (PPRV) has been causing infection in a wide range of susceptible hosts, particularly in disease-endemic regions. In the last 40 years, various reports highlighted the evidence of disease and viral genome in around 46 animal species from nine diverse families, including Bovidae, Cervidae, Camelidae, Suidae, Canidae, Felidae, Muridae, and Elephantidae. This evidence of clinical and/ or subclinical infection and the presence of the virus in an extended range of susceptible hosts emphasizes the cross-species transmission that remains a significant obstacle to effective control, particularly in disease-endemic regions. Therefore, a better understanding of virus transmission, host susceptibility, and epidemiological investigation of the disease is crucial to achieving the goals of efficient disease control and eradication programs initiated by OIE and FAO in various diseases-endemic regions. Nevertheless, the propensity of PPRV to inter- and intra-transmission may be a possible constraint in disease control strategies in terms of the new outbreak with the involvement of unusual or novel hosts. Considering this aspect, we tried to summarize the scattered data on PPR in available information about the susceptibility of a wide range of wildlife species, large ruminants, camels, and unusual hosts.

A curated dataset of peste des petits ruminants virus sequences for molecular epidemiological analyses

Peste des petits ruminants (PPR) is a highly contagious and devastating viral disease infecting predominantly sheep and goats. Tracking outbreaks of disease and analysing the movement of the virus often involves sequencing part or all of the genome and comparing the sequence obtained with sequences from other outbreaks, obtained from the public databases. However, there are a very large number (>1800) of PPRV sequences in the databases, a large majority of them relatively short, and not always well-documented. There is also a strong bias in the composition of the dataset, with countries with good sequencing capabilities (e.g. China, India, Turkey) being overrepresented, and most sequences coming from isolates in the last 20 years. In order to facilitate future analyses, we have prepared sets of PPRV sequences, sets which have been filtered for sequencing errors and unnecessary duplicates, and for which date and location information has been obtained, either from the database entry or from other published sources. These sequence datasets are freely available for download, and include smaller datasets which maximise phylogenetic information from the minimum number of sequences, and which will be useful for simple lineage identification. Their utility is illustrated by uploading the data to the MicroReact platform to allow simultaneous viewing of lineage date and geographic information on all the viruses for which we have information. While preparing these datasets, we identified a significant number of public database entries which contain clear errors, and propose guidelines on checking new sequences and completing metadata before submission.

Molecular insights into peste des petits ruminants virus identified in Bangladesh between 2008 and 2020

An in-depth knowledge of the molecular evolution of the peste des petits ruminants virus (PPRV) is critical for the success of the current global eradication program. For this reason, a molecular evolutionary analysis of PPRVs circulating in Bangladesh over a decade (2008-2020) was performed. The complete genome sequencing of three PPRV isolates from 2008 (BD2), 2015 (BD12) and 2017 (BD17) as well as full length nucleocapsid (N), matrix (M) and fusion (F) gene sequencing of seven more samples from 2015 to 2020 was performed. Phylogenetic analysis classified all ten PPRVs from Bangladesh as members of lineage IV and showed that they were closely related to PPRV strains detected in China and Tibet during 2007-2008, and India during 2014-2018. Time scale Bayesian Maximum Clade Credibility (MCC) phylogenetic analysis of the three complete genomes revealed a mean Time to Most Recent Common Ancestor (TMRCA) of 2000. Comparative deduced amino acid residue analysis at various functional motifs of PPRVs related to virus structure and function, virulence and host adaptation, receptor binding sites and polymerase activity revealed conserved residues among the PPRVs from Bangladesh. In total sixteen epitopes were predicted from four immunogenic proteins i.e. N, M, F and haemagglutinin (H). Interestingly, the predicted epitopes from the N and M proteins shared conserved epitopes with two vaccine strains currently being used, indicating that the strains from Bangladesh could be potentially used as alternative local vaccines.

Retrospective Characterization of Initial Peste des petits ruminants Outbreaks (2008-2012) in the Democratic Republic of the Congo

Peste des petits ruminants (PPR) is an acute, contagious viral disease of small ruminants, goats and sheep. The Democratic Republic of the Congo (DRC) was a PPR-free country until 2007, although in 2006, scare alerts were received from the east and the southwest of the country, reporting repeated mortalities, specifically in goats. In 2008, PPR outbreaks were seen in several villages in the west, leading to structured veterinary field operations. Blood, swabs and pathological specimens consisting of tissues from lungs, spleens, lymph nodes, kidneys, livers and hearts were ethically collected from clinically infected and/or dead animals, as appropriate, in 35 districts. Epidemiological information relating to major risk factors and socio-economic impact was progressively collected, revealing the deaths of 744,527 goats, which converted to a trade value of USD 35,674,600. Samples from infected and dead animals were routinely analyzed by the Central Veterinary Laboratory at Kinshasa for diagnosis, and after official declaration of PPR outbreaks by the FAO in July 2012, selected tissue samples were sent to The Pirbright Institute, United Kingdom, for genotyping. As a result of surveys undertaken between 2008 and 2012, PPR virus (PPRV)-specific antibodies were detected in 25 locations out of 33 tested (75.7%); PPRV nucleic acid was detected in 25 locations out of 35 (71.4%); and a typical clinical picture of PPR was observed in 23 locations out of 35 (65.7%). Analysis of the partial and full genome sequences of PPR viruses (PPRVs) obtained from lymphoid tissues of dead goats collected in Tshela in the DRC in 2012 confirmed the circulation of lineage IV PPRV, showing the highest homology (99.6-100%) with the viruses circulating in the neighboring countries of Gabon, in the Aboumi outbreak in 2011, and Nigeria (99.3% homology) in 2013, although recent outbreaks in 2016 and 2018 in the western part of the DRC that borders with East Africa demonstrated circulation of lineage II and lineage III PPRV.

Molecular epidemiology of peste des petits ruminants virus emergence in critically endangered Mongolian saiga antelope and other wild ungulates

Peste des petits ruminants virus (PPRV) causes disease in domestic and wild ungulates, is the target of a Global Eradication Programme, and threatens biodiversity. Understanding the epidemiology and evolution of PPRV in wildlife is important but hampered by the paucity of wildlife-origin PPRV genomes. In this study, full PPRV genomes were generated from three Mongolian saiga antelope, one Siberian ibex, and one goitered gazelle from the 2016-2017 PPRV outbreak. Phylogenetic analysis showed that for Mongolian and Chinese PPRV since 2013, the wildlife and livestock-origin genomes were closely related and interspersed. There was strong phylogenetic support for a monophyletic group of PPRV from Mongolian wildlife and livestock, belonging to a clade of lineage IV PPRV from livestock and wildlife from China since 2013. Discrete diffusion analysis found strong support for PPRV spread into Mongolia from China, and phylogeographic analysis indicated Xinjiang Province as the most likely origin, although genomic surveillance for PPRV is poor and lack of sampling from other regions could bias this result. Times of most recent common ancestor (TMRCA) were June 2015 (95 per cent highest posterior density (HPD): August 2014 to March 2016) for all Mongolian PPRV genomes and May 2016 (95 per cent HPD: October 2015 to October 2016) for Mongolian wildlife-origin PPRV. This suggests that PPRV was circulating undetected in Mongolia for at least 6 months before the first reported outbreak in August 2016 and that wildlife were likely infected before livestock vaccination began in October 2016. Finally, genetic variation and positively selected sites were identified that might be related to PPRV emergence in Mongolian wildlife. This study is the first to sequence multiple PPRV genomes from a wildlife outbreak, across several host species. Additional full PPRV genomes and associated metadata from the livestock-wildlife interface are needed to enhance the power of molecular epidemiology, support PPRV eradication, and safeguard the health of the whole ungulate community.

Ongoing Assessment of the Molecular Evolution of Peste Des Petits Ruminants Virus Continues to Question Viral Origins

Understanding the evolution of viral pathogens is critical to being able to define how viruses emerge within different landscapes. Host susceptibility, which is spread between different species and is a contributing factor to the subsequent epidemiology of a disease, is defined by virus detection and subsequent characterization. Peste des petits ruminants virus is a plague of small ruminant species that is a considerable burden to the development of sustainable agriculture across Africa and much of Asia. The virus has also had a significant impact on populations of endangered species in recent years, highlighting its significance as a pathogen of high concern across different regions of the globe. Here, we have re-evaluated the molecular evolution of this virus using novel genetic data to try and further resolve the molecular epidemiology of this disease. Viral isolates are genetically characterized into four lineages (I-IV), and the historic origin of these lineages is of considerable interest to the molecular evolution of the virus. Our re-evaluation of viral emergence using novel genome sequences has demonstrated that lineages I, II and IV likely originated in West Africa, in Senegal (I) and Nigeria (II and IV). Lineage III sequences predicted emergence in either East Africa (Ethiopia) or in the Arabian Peninsula (Oman and/or the United Arab Emirates), with a paucity of data precluding a more refined interpretation. Continual refinements of evolutionary emergence, following the generation of new data, is key to both understanding viral evolution from a historic perspective and informing on the ongoing genetic emergence of this virus.

Complete Genome Sequencing of Field Isolates of Peste des Petits Ruminants Virus from Tanzania Revealed a High Nucleotide Identity with Lineage III PPR Viruses

Peste des petits ruminants virus (PPRV) causes a highly devastating disease of sheep and goats that threatens food security, small ruminant production and susceptible endangered wild ruminants. With policy directed towards achieving global PPR eradication, the establishment of cost-effective genomic surveillance tools is critical where PPR is endemic. Genomic data can provide sufficient in-depth information to identify the pockets of endemicity responsible for PPRV persistence and viral evolution, and direct an appropriate vaccination response. Yet, access to the required sequencing technology is low in resource-limited settings and is compounded by the difficulty of transporting clinical samples from wildlife across international borders due to the Convention on International Trade in Endangered Species (CITES) of Wild Fauna and Flora, and Nagoya Protocol regulations. Oxford nanopore MinION sequencing technology has recently demonstrated an extraordinary performance in the sequencing of PPRV due to its rapidity, utility in endemic countries and comparatively low cost per sample when compared to other whole-genome (WGS) sequencing platforms. In the present study, Oxford nanopore MinION sequencing was utilised to generate complete genomes of PPRV isolates collected from infected goats in Ngorongoro and Momba districts in the northern and southern highlands of Tanzania during 2016 and 2018, respectively. The tiling multiplex polymerase chain reaction (PCR) was carried out with twenty-five pairs of long-read primers. The resulting PCR amplicons were used for nanopore library preparation and sequencing. The analysis of output data was complete genomes of PPRV, produced within four hours of sequencing (accession numbers: MW960272 and MZ322753). Phylogenetic analysis of the complete genomes revealed a high nucleotide identity, between 96.19 and 99.24% with lineage III PPRV currently circulating in East Africa, indicating a common origin. The Oxford nanopore MinION sequencer can be deployed to overcome diagnostic and surveillance challenges in the PPR Global Control and Eradication program. However, the coverage depth was uneven across the genome and amplicon dropout was observed mainly in the GC-rich region between the matrix (M) and fusion (F) genes of PPRV. Thus, larger field studies are needed to allow the collection of sufficient data to assess the robustness of nanopore sequencing technology.

Inhibiting pyrimidine biosynthesis impairs Peste des Petits Ruminants Virus replication through depletion of nucleoside pools and activation of cellular immunity

Replication of peste des petits ruminants virus (PPRV) strongly depends on the cellular environment and resources of host cells including nucleoside pool. Thus, enzymes involved in nucleoside biosynthesis (such as pyrimidine biosynthesis pathway) are regarded as attractive targets for antiviral drug development. Here, we demonstrate that brequinar (BQR) and leflunomide (LFM) which are two specific inhibitors of DHODH enzyme and 6-azauracil (6-AU) which is an ODase enzyme inhibitor robustly inhibit PPRV replication in HEK293T cell line as well as in peripheral blood mononuclear cells isolated from goat. We further demonstrate that these agents exert anti-PPRV activity via the depletion of purimidine nucleotide. Interestingly, these inhibitors can trigger the transcription of antiviral interferon-stimulated genes (ISGs). However, the induction of ISGs is largely independent of the classical JAK-STAT pathway. Combination of BQR with interferons (IFNs) exerts enhanced ISG induction and anti-PPRV activity. Taken together, this study reveals an unconventional novel mechanism of crosstalk between nucleotide biosynthesis pathways and cellular antiviral immunity in inhibiting PPRV replication. In conclusion, targeting pyrimidine biosynthesis represents a potential strategy for developing antiviral strategies against PPRV.

Review of Peste des Petits Ruminants Occurrence and Spread in Tanzania

Simple Summary

Peste des petits ruminants (PPR), caused by PPR virus (PPRV), is a transboundary animal disease of sheep and goats that has a significant impact on farmer’s livelihoods, food and nutritional security; and threatens susceptible wildlife. This review compiled information on the introduction and spread of PPR in Tanzania, from published and unpublished sources. PPR was first confirmed in Tanzania in 2008, but could have been present earlier, based on antibody detection in archived sera. The virus was probably introduced to northern Tanzania through cross-border movement of sheep and goats, and afterwards spread to eastern, central and southern Tanzania through movement of animals by pastoralists and traders. Genome sequencing shows that there have been several introductions of PPRV and it is now considered to be endemic. PPR has not been observed in cattle, camels or wildlife, but sera collected from these species contain PPRV antibodies, indicating virus exposure, probably through contact with infected sheep and goats. Some challenges for PPR control in Tanzania include the spread of the disease through small ruminants movements for pastoralism and trade, and limited veterinary services for disease surveillance and vaccination. The socio-economic impact of PPR justifies investment in a comprehensive disease eradication programme.

Abstract

Peste des petits ruminants (PPR) is an important transboundary animal disease of domestic small ruminants, camels, and wild artiodactyls. The disease has significant socio-economic impact on communities that depend on livestock for their livelihood and is a threat to endangered susceptible wild species. The aim of this review was to describe the introduction of PPR to Tanzania and its subsequent spread to different parts of the country. On-line databases were searched for peer-reviewed and grey literature, formal and informal reports were obtained from Tanzanian Zonal Veterinary Investigation Centres and Laboratories, and Veterinary Officers involved with PPR surveillance were contacted. PPR virus (PPRV) was confirmed in northern Tanzania in 2008, although serological data from samples collected in the region in 1998 and 2004, and evidence that the virus was already circulating in Uganda in 2003, suggests that PPRV might have been present earlier than this. It is likely that the virus which became established in Tanzania was introduced from Kenya between 2006–7 through the cross-border movement of small ruminants for trade or grazing resources, and then spread to eastern, central, and southern Tanzania from 2008 to 2010 through movement of small ruminants by pastoralists and traders. There was no evidence of PPRV sero-conversion in wildlife based on sera collected up to 2012, suggesting that they did not play a vectoring or bridging role in the establishment of PPRV in Tanzania. PPRV lineages II, III and IV have been detected, indicating that there have been several virus introductions. PPRV is now considered to be endemic in sheep and goats in Tanzania, but there has been no evidence of PPR clinical disease in wildlife species in Tanzania, although serum samples collected in 2014 from several wild ruminant species were PPRV sero-positive. Similarly, no PPR disease has been observed in cattle and camels. In these atypical hosts, serological evidence indicates exposure to PPRV infection, most likely through spillover from infected sheep and goats. Some of the challenges for PPRV eradication in Tanzania include movements of small ruminants, including transboundary movements, and the capacity of veterinary services for disease surveillance and vaccination. Using wildlife and atypical domestic hosts for PPR surveillance is a useful indicator of endemism and the ongoing circulation of PPRV in livestock, especially during the implementation of vaccination to control or eliminate the disease in sheep and goats. PPR disease has a major socio-economic impact in Tanzania, which justifies the investment in a comprehensive PPRV eradication programme.

Isolation and identification of peste des petits ruminants virus from goats in Egyptian governorates

Background and Aim

The peste des petits ruminants (PPR) is a highly contagious disease of small ruminants which negatively affects animal production and the socioeconomic status of farmers. Peste des petits ruminants virus (PPRV) encodes eight proteins, with the viral fusion protein (F) playing a role in virus virulence and stimulating an effective protective immune response. This study aimed to isolate and complete the identification of PPRV circulating in goats in different Egyptian governorates and perform molecular characterization of the PPRV F gene.

Materials and Methods

Samples were collected from unvaccinated animals with clinical signs suggestive of PPR. A total of 256 sera were tested for the detection of PPRV antibodies using a competitive enzyme-linked immunosorbent assay (c-ELISA) kit, while 214 samples of blood buffy coat preparation, animal swabs (nasal, ocular, and saliva), and fecal and tissue samples were tested for the detection of the PPRV antigen using an antigen-capture ELISA kit. Molecular diagnosis, gene cloning, blast analysis, and phylogenetic analysis were performed for the molecular characterization of PPRV.

Results

The seroprevalence results of PPRV antibodies in the tested sera showed a total of 67.9% positive samples. The rates of PPR antigen recorded by the antigen-capture ELISA in the swabs (nasal and ocular) and tissue samples were 44.3%, 46.8%, and 43.5%, respectively, with saliva swabs having the highest rate of PPRV positivity (76.4%) and fecal samples having the lowest (33.3%). Molecular characterization of the PPRV Vero cell culture revealed that the circulating PPRV strain belongs to the IV lineage. Blast analysis of the PPRV F gene showed 96.7% identity with the PPRV strain Egypt-2014 fusion protein (F) gene, KT006589.1, differing by 43 single-nucleotide polymorphisms.

Conclusion

The results of this study indicate that the emerging PPRV belongs to the IV lineage among small ruminant animals. The findings also indicate the need for an innovative strategy to control and eliminate this disease based on a regularly administered and effective vaccine, a test to distinguish between infected and vaccinated animals, and the need for further study on the protein structure and PPRV F gene expression, which should help us to understand the molecular evolution of the virus and control and eliminate PPR disease.

Persistence of the historical lineage I of West Africa against the ongoing spread of the Asian lineage of peste des petits ruminants virus

Peste des petits ruminants (PPR) is a highly contagious disease of small ruminants. The causal agent, PPR virus (PPRV), is classified into four genetically distinct lineages. Lineage IV, originally from Asia, has shown a unique capacity to spread across Asia, the Middle East and Africa. Recent studies have reported its presence in two West African countries: Nigeria and Niger. Animals are frequently exchanged between Mali and Niger, which could allow the virus to enter and progress in Mali and to other West African countries. Here, PPRV samples were collected from sick goats between 2014 and 2017 in both Mali and in Senegal, on the border with Mali. Partial PPRV nucleoprotein gene was sequenced to identify the genetic lineage of the strains. Our results showed that lineage IV was present in south‐eastern Mali in 2017. This is currently the furthest West the lineage has been detected in West Africa. Surprisingly, we identified the persistence at least until 2014 of the supposedly extinct lineage I in two regions of Mali, Segou and Sikasso. Most PPRV sequences obtained in this study belonged to lineage II, which is dominant in West Africa. Phylogenetic analyses showed a close relationship between sequences obtained at the border between Senegal and Mali, supporting the hypothesis of an important movement of the virus between the two countries. Understanding the movement of animals between these countries, where the livestock trade is not fully controlled, is very important in the design of efficient control strategies to combat this devastating disease.

Progress towards Eradication of Peste des Petits Ruminants through Vaccination

Peste des petits ruminants (PPR) is a transboundary viral disease that threatens more than 1.74 billion goats and sheep in approximately 70 countries globally. In 2015, the international community set the goal of eradicating PPR by 2030, and, since then, Food and Agriculture Organization of the United Nations (FAO) and World Organization for Animal Health (OIE) have jointly developed and implemented the Global Control and Eradication Strategy for PPR. Here, data from the United Nations Food and Agriculture Organization Statistical Database (FAOSTAT), the OIE World Animal Health Information System (WAHIS), Regional Roadmap Meetings, and countries' responses to PPR Monitoring and Assessment Tool (PMAT) questionnaires were analyzed to inform on current progress towards PPR eradication. OIE recorded the use of over 333 million doses of vaccine in 12 countries from 2015 to 2018, 41.8% of which were used in Asia and 58.2% in Africa. Between 2015 and 2019, a total of 12,757 PPR outbreaks were reported to OIE: 75.1% in Asia, 24.8% in Africa, and 0.1% in Europe. The number of global outbreaks in 2019 fell to 1218, compared with 3688 in 2015. Analysis of vaccine use and PPR outbreaks in countries indicates that disease control strategies, particularly vaccination campaigns and vaccine distribution strategies, still require scientific evaluation. It is imperative that vaccination is undertaken based on the epidemiology of the disease in a region and is coordinated between neighboring countries to restrict transboundary movements. Strengthening surveillance and post-vaccination sero-monitoring at the national level is also essential. The PPR vaccine stock/bank established by FAO, OIE, and other partners have improved the quality assurance and supply of vaccines. However, to achieve PPR eradication, filling the funding gap for vaccination campaigns and other program activities will be critical.

Measles virus and rinderpest virus divergence dated to the sixth century BCE

Many infectious diseases are thought to have emerged in humans after the Neolithic revolution. Although it is broadly accepted that this also applies to measles, the exact date of emergence for this disease is controversial. We sequenced the genome of a 1912 measles virus and used selection-aware molecular clock modeling to determine the divergence date of measles virus and rinderpest virus. This divergence date represents the earliest possible date for the establishment of measles in human populations. Our analyses show that the measles virus potentially arose as early as the sixth century BCE, possibly coinciding with the rise of large cities.

Antiviral responses of ATG13 to the infection of peste des petits ruminants virus through activation of interferon response

Not only are autophagy-related (ATG) proteins the essential orchestrators of the autophagy machinery, but also they regulate many other cellular pathways. Here, we demonstrated that ATG13 exerted an obviously antiviral activity against the infection of peste des petits ruminants virus (PPRV) in cell culture model. We found that PPRV infection or the treatment with interferon (IFN) against PPRV infection significantly induced ATG13 expression. Mechanistically, ATG13 stimulated interferon expression and the subsequent activation of the JAK-STAT cascade. These activations triggered the transcription of interferon-stimulated genes (ISGs) to exert antiviral activity. Conversely, the loss of ATG13 significantly attenuated the potency of RIG-IN in activating IFN responses. In summary, we have demonstrated that basal ATG13 was involved in host antiviral activities against PPRV infection and the over-expression of ATG13 activated IFN production to inhibit PPRV replication in an unconventional fashion.

Sentinel surveillance of selected veterinary and public health pathogens in camel population originating from Southern Punjab province, Pakistan

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Camels are susceptible to a wide range of infectious diseases with varying rate of morbidity and mortality.

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Blutongue, peste des petits ruminants and brucellosis are prevalent among camels in southern part of the Punjab provinvce, Pakistan.

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Genome corresponding to Brucella abortus and multiple serotypes of bluetongue were detected among camels.

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Camels should be included for disease control interventions reltaed to brucellosis, blutongue and PPR from their endemic setting worldwide.

An extended range of host susceptibility including camel has been evidenced for some of the important veterinary and public health pathogens, such as brucellosis, peste des petits ruminants (PPR) and bluetongue (BT). However, in disease endemic settings across many parts of the globe, most of the disease control interventions accounts for small and large ruminants, whereas unusual hosts and/or natural reservoirs, such as camels, remain neglected for disease control measures including routine vaccination. Such a policy drawback not only plays an important role in disease epizootiology particularly in settings where disease is endemic, but also serves an obstacle in disease control and subsequent eradication in future. With this background, using pre-validated ELISA and molecular assays [multiplex PCR, reverse transcriptase (RT)-PCR and real-time (rt)-PCR], we conducted a large-scale pathogen- and antibody-based surveillance for brucellosis, peste des petits ruminants and bluetongue in camel population (n = 992) originating from a wide geographical region in southern part of the Punjab province, Pakistan. Varying in each of the selected districts, the seroprevalence was found to be maximum for bluetongue [n = 697 (70.26%, 95% CI: 67.29–73.07)], followed by PPR [n = 193 (19.46%, 95% CI: 17.07–22.09)] and brucellosis [n = 66 (6.65%, 95% CI: 5.22–8.43)]. Odds of seroprevalence were more significantly associated with pregnancy status (non-pregnant, OR = 2.23, 95% CI: 1.86–5.63, p<0.01), farming system (mixed-animal, OR = 2.59, 95% CI: 1.56–4.29, p<0.01), breed (Desi, OR = 1.97, 95% CI: 1.28–4.03, p<0.01) and farmer education (illiterate, OR = 3.17, 95% CI: 1.45–6.93, p<0.01) for BTV, body condition (normal, OR = 3.54, 95% CI: 1.92–6.54, p<0.01) and breed (Desi, OR = 2.19, 95% CI: 1.09–4.40, p<0.01) for brucellosis, and feeding system for PPR (grazing, OR = 2.75, 95% CI: 1.79–4.22, p<0.01). Among the total herds included (n = 74), genome corresponding to BT virus (BTV) and brucellosis was detected in 14 (18.92%, 95 CI: 11.09–30.04) and 19 herds (25.68%, 95% CI: 16.54–37.38), respectively. None of the herds was detected with genome of PPR virus (PPRV). Among the positive herds, serotype 1, 8 and 11 were detected for BTV while all the herds were exclusively positive to B. abortus. Taken together, the study highlights the role of potential disease reservoirs in the persistence and transmission of selected diseases in their susceptible hosts and, therefore, urges necessary interventions (e.g., inclusion of camels for vaccine etc.) for the control of diseases from their endemic setting worldwide.

A Novel Recombinant Newcastle Disease Virus Vectored DIVA Vaccine against Peste des Petits Ruminants in Goats

Peste des petits ruminants virus (PPRV, species: small ruminant morbillivirus) is the causative agent of the eponymous notifiable disease, the peste des petits ruminants (PPR) in wild and domestic sheep and goats. Mortality rates vary between 50% and 100%, causing significant losses of estimated 1.5 to 2 billion US Dollars per year. Live-attenuated PPRV vaccine strains are used in the field for disease prevention, but the application of a more thermostable vaccine enabling differentiation between infected and vaccinated animals (DIVA) would be highly desirable to achieve the goal of global disease eradication. We generated a recombinant Newcastle disease virus (rNDV) based on the live-attenuated NDV Clone 30 that expresses the surface protein hemagglutinin (H) of PPRV strain Kurdistan/11 (rNDV_H_Kur). In vitro analyses confirmed transgene expression as well as virus replication in avian, caprine, and ovine cells. Two consecutive subcutaneous vaccinations of German domestic goats with rNDV_H_Kur prevented clinical signs and hematogenic dissemination after an intranasal challenge with virulent PPRV Kurdistan/11. Virus shedding by different routes was reduced to a similar extent as after vaccination with the live-attenuated PPRV strain Nigeria 75/1. Goats that were either not vaccinated or inoculated with parental rNDV were used as controls. In summary, we demonstrate in a proof-of-concept study that an NDV vectored vaccine can protect against PPR. Furthermore, it provides DIVA-applicability and a high thermal tolerance.

Peste des Petits Ruminants at the Wildlife-Livestock Interface in the Northern Albertine Rift and Nile Basin, East Africa

In the recent past, peste des petits ruminants (PPR) emerged in East Africa causing outbreaks in small livestock across different countries, with evidences of spillover to wildlife. In order to understand better PPR at the wildlife-livestock interface, we investigated patterns of peste des petits ruminants virus (PPRV) exposure, disease outbreaks, and viral sequences in the northern Albertine Rift. PPRV antibodies indicated a widespread exposure in apparently healthy wildlife from South Sudan (2013) and Uganda (2015, 2017). African buffaloes and Uganda kobs <1-year-old from Queen Elizabeth National Park (2015) had antibodies against PPRV N-antigen and local serosurvey captured a subsequent spread of PPRV in livestock. Outbreaks with PPR-like syndrome in sheep and goats were recorded around the Greater Virunga Landscape in Kasese (2016), Kisoro and Kabale (2017) from western Uganda, and in North Kivu (2017) from eastern Democratic Republic of the Congo (DRC). This landscape would not be considered typical for PPR persistence as it is a mixed forest-savannah ecosystem with mostly sedentary livestock. PPRV sequences from DRC (2017) were identical to strains from Burundi (2018) and confirmed a transboundary spread of PPRV. Our results indicate an epidemiological linkage between epizootic cycles in livestock and exposure in wildlife, denoting the importance of PPR surveillance on wild artiodactyls for both conservation and eradication programs.

Expanding Diversity of Susceptible Hosts in Peste Des Petits Ruminants Virus Infection and Its Potential Mechanism Beyond

Peste des petits ruminants (PPR) is a severe respiratory and digestive tract disease of domestic small ruminants caused by PPR virus (PPRV) of the genus Morbillivirus. Although the primary hosts of PPRV are goats and sheep, the host range of PPRV has been continuously expanding and reported to infect various animal hosts over the last decades, which could bring a potential challenge to effectively control and eradicate PPR globally. In this review, we focused on current knowledge about host expansion and interspecies infection of PPRV and discussed the potential mechanisms involved.

Paradigm shift in the diagnosis of peste des petits ruminants: scoping review

Peste des petits ruminants virus causes a highly contagious disease, which poses enormous economic losses in domestic animals and threatens the conservation of wild herbivores. Diagnosis remains a cornerstone to the Peste des petits ruminants Global Control and Eradication Strategy, an initiative of the World Organisation for Animal Health and the Food and Agriculture Organisation. The present review presents the peste des petits ruminants diagnostic landscape, including the practicality of commercially available diagnostic tools, prototype tests and opportunities for new technologies. The most common peste des petits ruminants diagnostic tools include; agar gel immunodiffusion, counter-immunoelectrophoresis, enzyme-linked immunosorbent assays, reverse transcription polymerase chain reaction either gel-based or real-time, reverse transcription loop-mediated isothermal amplification, reverse transcription recombinase polymerase amplification assays, immunochromatographic lateral flow devices, luciferase immunoprecipitation system and pseudotype-based assays. These tests vary in their technical demands, but all require a laboratory with exception of immunochromatographic lateral flow and possibly reverse transcription loop-mediated isothermal amplification and reverse transcription recombinase polymerase amplification assays. Thus, we are proposing an efficient integration of diagnostic tests for rapid and correct identification of peste des petits ruminants in endemic zones and to rapidly confirm outbreaks. Deployment of pen-side tests will improve diagnostic capacity in extremely remote settings and susceptible wildlife ecosystems, where transportation of clinical samples in the optimum cold chain is unreliable.

A comprehensive global perspective on phylogenomics and evolutionary dynamics of Small ruminant morbillivirus

A string of complete genome sequences of Small ruminant morbillivirus (SRMV) have been reported from different parts of the globe including Asia, Africa and the Middle East. Despite individual genome sequence-based analysis, there is a paucity of comparative genomic and evolutionary analysis to provide overarching and comprehensive evolutionary insights. Therefore, we first enriched the existing database of complete genome sequences of SRMVs with Pakistan-originated strains and then explored overall nucleotide diversity, genomic and residue characteristics, and deduced an evolutionary relationship among strains representing a diverse geographical region worldwide. The average number of pairwise nucleotide differences among the whole genomes was found to be 788.690 with a diversity in nucleotide sequences (0.04889 ± S.D. 0.00468) and haplotype variance (0.00001). The RNA-dependent-RNA polymerase (L) gene revealed phylogenetic relationship among SRMVs in a pattern similar to those of complete genome and the nucleoprotein (N) gene. Therefore, we propose another useful molecular marker that may be employed for future epidemiological investigations. Based on evolutionary analysis, the mean evolution rate for the complete genome, N, P, M, F, H and L genes of SRMV was estimated to be 9.953 × 10^–4, 1.1 × 10^–3, 1.23 × 10^–3, 2.56 × 10^–3, 2.01 × 10^–3, 1.47 × 10^–3 and 9.75 × 10^–4 substitutions per site per year, respectively. A recombinant event was observed in a Pakistan-originated strain (KY967608) revealing Indian strains as major (98.1%, KR140086) and minor parents (99.8%, KT860064). Taken together, outcomes of the study augment our knowledge and current understanding towards ongoing phylogenomic and evolutionary dynamics for better comprehensions of SRMVs and effective disease control interventions.

Transcriptional Profiles of Murine Bone Marrow-Derived Dendritic Cells in Response to Peste des Petits Ruminants Virus

Background: Peste des petits ruminants virus (PPRV) is the causative agent of PPR, which can cause an acute, highly contagious and fatal disease of sheep and goats, resulting in significant economic losses for commercial animal husbandry due to its high mortality and morbidity. As professional antigen-presenting cells, dendritic cells (DCs) play a unique role in innate immunity. This study aimed to gain a deeper understanding of the transcriptional response of bone marrow-derived dendritic cells (BMDCs) stimulated with PPRV. Results: Transcriptional profiling was performed using RNA sequencing. Herein, we reported that compared to untreatedBMDCs, 4492 differentially expressed genes (DEGs) were identified following PPRV stimulation, out of these DEGs 2311 were upregulated and 2181 were downregulated, respectively. A total of three gene ontology (GO) term clusters of biological process, cell component and molecular function were significantly enriched in 963 GO terms in the PPRV-stimulated BMDCs. These GO clusters were related to inflammatory response, cell division and vacuole, anchoring junction, positive regulation of cellular component and nucleoside binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of DEGs were enriched in a chemokine signaling pathway, protein processing in endoplasmic reticulum, cell cycle and mTOR signaling pathway. Additionally, identified DEGs of BMDCs were further validated by qRT-PCR and the results were in accordance with the change of the genes. This study suggested the effects of PPRV stimulation on the maturation and function of BMDCs. Conclusion: We found that the dramatic BMDCs transcriptome changes triggered were predominantly related to an inflammatory response and chemokine signaling pathway.

Evidence of Peste des petits Ruminants' Virus in Dromedary Camels in the Kingdom of Saudi Arabia between 2014 and 2016

Infection with the Peste des petits ruminants virus (PPRV) is a highly devastating viral infection of small ruminants. Dromedary camels live in close proximity of small ruminants in Arabian Peninsula (AP) and many other regions in the world. Little is known about the reasons behind continuous PPRV emergence in Saudi Arabia (KSA). Our objective was to test some dromedary camel population across the kingdom for the presence of specific PPRV antibodies. Our results show detection of specific PPRV antibodies (2.92%) in sera of tested dromedary camels from the eastern and south regions of the KSA. Our results suggest the exposure of dromedary camels to PPRV infection. Thus, dromedary camels may play some important roles in the sustainability of PPRV in the small ruminants across the AP. This is the first study examined the nationwide prevalence of the PPRV in dromedary camels in the KSA.

Toward peste des petits virus (PPRV) eradication: Diagnostic approaches, novel vaccines, and control strategies

Peste des petits ruminants (PPR) is an acute transboundary infectious viral disease affecting domestic and wild small ruminants' species besides camels reared in Africa, Asia and the Middle East. The virus is a serious paramount challenge to the sustainable agriculture advancement in the developing world. The disease outbreak was also detected for the first time in the European Union namely in Bulgaria at 2018. Therefore, the disease has lately been aimed for eradication with the purpose of worldwide clearance by 2030. Radically, the vaccines needed for effectively accomplishing this aim are presently convenient; however, the availableness of innovative modern vaccines to fulfill the desideratum for Differentiating between Infected and Vaccinated Animals (DIVA) may mitigate time spent and financial disbursement of serological monitoring and surveillance in the advanced levels for any disease obliteration campaign. We here highlight what is at the present time well-known about the virus and the different available diagnostic tools. Further, we interject on current updates and insights on several novel vaccines and on the possible current and prospective strategies to be applied for disease control.

Epidemic and evolutionary characteristics of peste des petits ruminants virus infecting Procapra przewalskii in Western China

Due to the migration or transboundary spread of domestic and wild animals, peste des petits ruminants virus posed a high potential threat to them. In this study, we initially detected that a class of animal named Procapra przewalskii was infected with peste des petits ruminants virus (PPRV ChinaGS2018) in Gansu province. According to phylogenetic relationships analysis, we found that ChinaGS2018 comprised of 15,954 nucleotides and was classified into IV genotypes. In addition, indirect immunofluorescence assay (IFA) showed that ChinaGS2018 could infect isolated primary goat tracheal epithelium cells (GTC). Comparing with full-length genome sequences revealed that ChinaGS2018 strain has high identity to the reference complete genomes (87.16-99.55%) at the nucleotide level. Multiple sequence alignment showed that F protein has the highest identity of 99.8%, and H protein has the highest nucleotide substitution ratio. Our study also suggested this strain may be transmitted from Xinjiang, China. Along with the migratory of Procapraprzewalskii, this wild ruminant infected with PPRV can pose a huge threat to other wild ruminants and domestic ones. This is the first report describing infected with PPRV which will provide insights into the epidemiology and pathogenesis of this important virus.

A comparative phylogenomic analysis of peste des petits ruminants virus isolated from wild and unusual hosts

Peste des petits ruminants virus (PPRV) infects a wide range of domestic and wild ruminants, and occasionally unusual hosts such as camel, cattle and pig. Given their broad host-spectrum and disease endemicity in several developing countries, it is imperative to elucidate the viral evolutionary insights for their dynamic pathobiology and differential host-selection. For this purpose, a dataset of all available (n = 37) PPRV sequences originating from wild and unusual hosts was composed and in silico analysed. Compared to domestic small ruminant strains of same geographical region, phylogenomic and residue analysis of PPRV sequences originating from wild and unusual hosts revealed a close relationship between strains. A lack of obvious difference among the studied sequences and deduced residues suggests that these are the host factors that may play a role in their susceptibility to PPRV infection, immune response, pathogenesis, excretion patterns and potential clinical signs or resistance to clinical disease. Summarizing together, the comparative analysis enhances our understanding towards molecular epidemiology of the PPRV in wild and unusual hosts for appropriate intervention strategies particularly at livestock-wildlife interface.

Molecular epidemiological update of Peste des Petits Ruminants virus (PPRV) in Ethiopia

Peste des Petits ruminants (PPR) is a devastating disease of small ruminants with high morbidity and mortality rates among susceptible animals. The disease is endemic in much of Africa, the Middle East and Asia and constitutes one of the major hurdles to the improvement of small-ruminant production in these countries. The causal agent of PPR, the Small Ruminant Morbillivirus (SRMV), previously known as PPR virus (PPRV) belongs to the genus Morbillivirus within the family Paramyxoviridae. SRMV can be categorized into four genetically distinct lineages (I to IV). Suspicion of PPR was first reported in Ethiopia in 1977 and since then genetic characterization of circulating viruses has identified lineages III and IV in the country. This study was undertaken to provide an update on the molecular epidemiology of PPR in Ethiopia by analysing animal tissue samples collected between 2011 and 2017. PPR positive samples were identified in four regions of the country. Sequence and phylogenetic analysis of fourteen RT-PCR positive amplicons revealed that all of the SRMV in the samples from 2010 to 2017 belong to sub-clade II of clade I of lineage IV. No lineage III viruses were identified.

Proteomic analysis of murine bone marrow derived dendritic cells in response to peste des petits ruminants virus

Peste des petits ruminants virus (PPRV) poses a great threat to livestock husbandry, especially goat farming due to its high mortality and morbidity. Dendritic cells (DCs), as the principal stimulators of naive Th cells were widely used in antigen processing and presenting. In the previous study, we tested the effects of PPRV on murine bone marrow derived dendritic cells (BMDCs) including surface markers and cytokines. While the aim of this study is to detect the proteomic profile of BMDCs stimulated with PPRV towards key proteins involved in. Following PPRV stimulation, 110 differentially expressed proteins (DEPs) were identified through iTRAQ labelling with LC-MS/MS approach, of which 94 DEPs were up-regulated and 16 DEPs were down-regulated, respectively. Among them 15 out of 110 DGPs were related to innate immune system, three were involved in cell apoptosis, RPS15a and Smox were related to translation of viral mRNA. Additionally, western blot analysis showed identical results to iTRAQ analysis. There will be profound significance for understanding antigen-presenting of BMDCs after stimulation with PPRV.

Pathological and molecular characterisation of peste des petits ruminants in Nubian ibex (Capra nubiana) in Israel

Peste des petits ruminants (PPR) is a devastating disease that generally affects sheep and goats, mostly in Asia, the Middle East and Africa. The disease has been declared a target for global eradication. Despite its high prevalence in domestic flocks and its high seroprevalence among wildlife, it is rarely reported as a fulminant disease in wild ruminant species (with the exception of Central Asia). In this report, we describe a severe PPR outbreak in a zoo herd of Nubian ibex (Capra nubiana), causing the deaths of 2/3 of the herd. The clinical onset was acute with morbid animals exhibiting lethargy and watery-to-bloody diarrhea and death usually within 48 h. The most consistent gross pathologic findings were hemorrhagic abomasitis and enteritis. Oral lesions and pulmonary lesions were rare. Histology revealed necrohemorrhagic enteritis and abomasitis with myriad nuclear and cytoplasmic viral inclusion bodies. Molecular examinations confirmed the diagnosis of PPR and determined that the causative agent belongs to lineage IV. Further molecular examination showed that the virus belongs to the Asian clade of lineage IV and is closely related to a virus described in Turkey.

Peste des petits ruminants in Africa: Meta-analysis of the virus isolation in molecular epidemiology studies

Peste des petits ruminant (PPR) is a highly contagious, infectious viral disease of small ruminant species which is caused by the peste des petits ruminants virus (PPRV), the prototype member of the Morbillivirus genus in the Paramyxoviridae family. Peste des petits ruminant was first described in West Africa, where it has probably been endemic in sheep and goats since the emergence of the rinderpest pandemic and was always misdiagnosed with rinderpest in sheep and goats. Since its discovery PPR has had a major impact on sheep and goat breeders in Africa and has therefore been a key focus of research at the veterinary research institutes and university faculties of veterinary medicine in Africa. Several key discoveries were made at these institutions, including the isolation and propagation of African PPR virus isolates, notable amongst which was the Nigerian PPRV 75/1 that was used in the scientific study to understand the taxonomy, molecular dynamics, lineage differentiation of PPRV and the development of vaccine seeds for immunisation against PPR. African sheep and goat breeds including camels and wild ruminants are frequently infected, manifesting clinical signs of the disease, whereas cattle and pigs are asymptomatic but can seroconvert for PPR. The immunisation of susceptible sheep and goats remains the most effective and practical control measure against PPR. To carry out PPR vaccination in tropical African countries with a very high temperature, a thermostable vaccine using the rinderpest lyophilisation method to the attenuated Nigeria 75/1 PPR vaccine strain has been developed, which will greatly facilitate the delivery of vaccination in the control, prevention and global eradication of PPR. Apart from vaccination, other important questions that will contribute towards the control and prevention of PPR need to be answered, for example, to identify the period when a susceptible naïve animal becomes infectious when in contact with an infected animal and when an infectious animal becomes contagious.

Molecular detection, isolation and characterization of Peste-des-petits ruminants virus from goat milk from outbreaks in Bangladesh and its implication for eradication strategy

Peste-des-petits ruminants (PPR) is a highly contagious transboundary viral disease of small ruminants, which is endemic in much of Africa, the Middle East and Asia. In South Asia, PPR is of significant concern to the Indian subcontinent including Bangladesh as more than 30% of the world's sheep and goats are farmed in this region, predominantly by small, poor and marginal farmers. PPR virus was detected and isolated from goat milk from field samples from PPR outbreaks (2012-2015) in Bangladesh and its full-length sequences obtained. Sequence analysis of the partial N gene of Bangladesh isolates showed 99.3%-100% identity whereas 98.2%-99.6% identity was observed when compared with neighbouring Indian viruses. Further analysis of the full-length genomes indicated that the Bangladesh isolates were 99.3%-99.99% identical among themselves and 98.3%-98.4% identical to neighbouring Indian viruses. These findings further support the transboundary transmission of PPR virus across the Indian and Bangladesh border. In additional, the establishment of a cross-border strategy between India and Bangladesh will be of paramount importance for the eradication of PPR in this region. Molecular detection and isolation of PPR virus from milk is of significant potential concern for spread of the disease to free areas as the major producers of goat milk globally are PPR endemic countries in particular India and Bangladesh, as well as Sudan. Milk is a noninvasive sample type and bulk goat milk sampling for the detection of PPRV would be of practical significance for regional surveillance of PPRV as progress is made towards the targeted 2030 eradication.

Genetic characterization of small ruminant morbillivirus from recently emerging wave of outbreaks in Pakistan

Peste des petits ruminants (PPR) is an endemic and highly infectious disease of several tropical countries, including Pakistan. Despite exhaustive vaccination, outbreaks are on the rise annually across different parts of the country. Clinical outcomes are largely employed to diagnose disease, while comprehensive genomic features of prevailing field strains of SRMV largely remain elusive. Here, we present comparative sequence-based phylogenomics of field strains from three districts representing different agro-livestock production systems during an emerging wave of outbreaks in 2015, together with the first complete genome sequencing of a strain from Pakistan. The analysis revealed clustering of study strain (SRMV/Lahore/UVAS/Pak/2015) to lineage IV, close to isolates characterized previously from India and China. Investigations of inter- and intralineage genetic distances showed a higher genetic distance between SRMV/Lahore/UVAS/Pak/2015 to lineage III viruses than lineages I and II. The characterized Pakistani strain also showed a high percentage of genetic distance from isolates originated from Nigerian and other African small ruminants. Based on these observations, an integrated cross-protection investigation is warranted in the future, not only to define the protective efficacy of currently applied vaccines, but also to continuously elucidate the genomic and evolutionary nature of circulating viruses in the country to achieve disease eradication by 2030.

An overview of process intensification and thermo stabilization for upscaling of Peste des petits ruminants vaccines in view of global control and eradication

Peste des petits ruminants (PPR) has been recognized as a globally distributed disease affecting the small ruminant population. The disease results in severe economic losses mainly to small land holders and low input farming systems. The control of PPR is mainly achieved through vaccination with available live attenuated vaccines. The thermo labile nature of PPR virus poses a major constraint in production of quality vaccines which often results in vaccine failures. The lack of quality vaccine production jeopardize the wide vaccination coverage especially in countries with poor infrastructure due to which PPR persists endemically. The vaccine production system may require augmentation to attain consistent and quality vaccines through efforts of process intensification integrated with suitable stabilizer formulations with appropriate freeze drying cycles for improved thermo tolerance. Manufacturing of live attenuated PPR vaccines during batch cultures might introduce defective interfering particles (DIPs) as a result of high multiplicity of infection (MOI) of inoculums, which has a huge impact on virus dynamics and yield. Accumulation of DIPs adversely affects the quality of the manufactured vaccines which can be avoided through use of appropriate MOI of virus inoculums and quality control of working seed viruses. Therefore, adherence to critical manufacturing standard operating procedures in vaccine production and ongoing efforts on development of thermo tolerant vaccine will help a long way in PPR control and eradication programme globally. The present review focuses on the way forward to achieve the objectives of quality vaccine production and easy upscaling to help the global PPR control and eradication by mass vaccination as an important tool.

Efficient isolation on Vero.DogSLAMtag cells and full genome characterization of Dolphin Morbillivirus (DMV) by next generation sequencing

The Dolphin Morbillivirus (DMV) genome from the first Mediterranean epidemic (1990-’92) is the only cetacean Morbillivirus that has been completely sequenced. Here, we report the first application of next generation sequencing (NGS) to morbillivirus infection of aquatic mammals. A viral isolate, representative of the 2006-’08 Mediterranean epidemic (DMV_IZSPLV_2008), efficiently grew on Vero.DogSLAMtag cells and was submitted to whole genome characterization by NGS. The final genome length was 15,673 nucleotides, covering 99.82% of the DMV reference genome. Comparison of DMV_IZSPLV_2008 and 1990-’92 DMV strain sequences revealed 157 nucleotide mutations and 47 amino acid changes. The sequence similarity was 98.7% at the full genome level. Whole-genome phylogeny suggested that the DMV strain circulating during the 2006-’08 epidemics emerged from the 1990-’92 DMV strain. Viral isolation is considered the “gold standard” for morbillivirus diagnostics but efficient propagation of infectious virus is difficult to achieve. The successful cell replication of this strain allowed performing NGS directly from the viral RNA, without prior PCR amplification. We therefore provide to the scientific community a second DMV genome, representative of another major outbreak. Interestingly, genome comparison revealed that the neglected L gene encompasses 74% of the genetic diversity and might serve as “hypervariable” target for strain characterization.

Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013-2014

Peste des petits ruminants virus (PPRV) causes a highly contagious disease, peste des petits ruminants (PPR), in sheep and goats which has been considered as a serious threat to the local economy in Africa and Asia. However, the in-depth evolutionary dynamics of PPRV during an epidemic is not well understood. We conducted phylogenetic analysis on genomic sequences of 25 PPRV strains from China 2013-2014 outbreaks. All these strains clustered into a novel clade in lineage 4. An evolutionary rate of 2.61 × 10-6 nucleotide substitutions per site per day was estimated, dating the most recent common ancestor of PPRV China 2013-2014 strains to early August 2013. Transmission network analysis revealed that all the virus sequences could be grouped into five clusters of infection, suggesting long-distance animal transmission play an important role in the spread of PPRV in China. These results expanded our knowledge for PPRV evolution to achieve effective control measures.

Analyses of nucleotide, codon and amino acids usages between peste des petits ruminants virus and rinderpest virus

Peste des petits ruminants virus (PPRV) and rinderpest virus (RPV) are two causative agents of an economically important disease for ruminants (i.e., sheep, cattle and goat). In this study, the nucleotide, codon and amino acid usages for PPRV and RPV have been analyzed by multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis represents that ACG for Thr and GCG for Ala are selected with under-representation in both PPRV and RPV, and AGA for Arg in PPRV and AGG for Arg in RPV are used with over-representation. The usage of nucleotide pair (CpG) tends to be removed from viral genes of the two viruses, suggesting that other evolutionary forces take part in evolutionary processes for viral genes in addition to mutation pressure from nucleotide usage at the third codon position. The overall nucleotide usage of viral gene is not major factor in shaping synonymous codon usage patterns, while the nucleotide usages at the third codon position and the nucleotide pairs play important roles in shaping synonymous codon usage patterns. Although PPRV and RPV are closely related antigenically, the codon and amino acid usage patterns for viral genes represent a significant genetic diversity between PPRV and RPV. Moreover, the overall codon usage trends for viral genes between PPRV and RPV are mainly influenced by mutation pressure from nucleotide usage at the third codon position and translation selection from hosts. Taken together, this is first comprehensive analyses for nucleotide, codon and amino acid usages of viral genes of PPRV and RPV and the findings are expected to increase our understanding of evolutionary forces influencing viral evolutionary pathway and adaptation toward hosts.

Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014

Nasopharyngeal swabs were collected from patients through the influenza surveillance network of the CDC of Guangdong. All specimens between 2009 and 2014 were checked for influenza virus using MDCK cells and further subtyped. Of those collected, 542 H1N1pdm09, 230 A(H3N2)and 448 B viruses selected at random were subjected to fluorescence-based NAI assays. Viral RNA was extracted from resistant isolates, and their NA genes were amplified by RT-PCR. Alignment of nucleotides and amino acids was performed. We performed structural modelling and simulations of mutants using Modeller 9.x and AutoDock and analyzed conformations and binding affinities. All tested seasonal type B and H3N2 viruses from 2009 to 2014 remained sensitive to oseltamivir. However, there were five strains (out of 198 tested isolates acquired between June and September 2013) that were resistant to oseltamivir. Another three resistant strains were identified among isolates from March to April 2014. We found that 2013/2014 oseltamivir-resistant strains and 2012/2013/2014 oseltamivir-sensitive strains had all or some of the following mutations: N44S, N200S,V241I, I321V,N369K, N386 K and K432E. MutationsV241I, N369K, N386K and K432E, alone or in conjunction with H275Y, had a significant impact on the binding pattern and affinity of oseltamivir for neuraminidase, rendering neuraminidase less susceptible.

Genome sequencing of an Indian peste des petits ruminants virus isolate, Izatnagar/94, and its implications for virus diversity, divergence and phylogeography

Peste des petits ruminants is an important transboundary disease infecting small ruminants. Genome or gene sequence analysis enriches our knowledge about the evolution and transboundary nature of the causative agent of this disease, peste des petits ruminants virus (PPRV). Although analysis using whole genome sequences of pathogens leads to more precise phylogenetic relationships, when compared to individual genes or partial sequences, there is still a need to identify specific genes/genomic regions that can provide evolutionary assessments consistent with those predicted with full-length genome sequences. Here the virulent Izatnagar/94 PPRV isolate was assembled and compared to all available complete genome sequences (currently in the NCBI database) to estimate nucleotide diversity and to deduce evolutionary relationships between genes/genomic regions and the full length genomes. Our aim was to identify the preferred candidate gene for use as a phylogenetic marker, as well as to predict divergence time and explore PPRV phylogeography. Among all the PPRV genes, the H gene was identified to be the most diverse with the highest evolutionary relationship with the full genome sequences. Hence it is considered as the most preferred candidate gene for phylogenetic study with 93% identity set as a nucleotide cutoff. A whole genome nucleotide sequence cutoff value of 94% permitted specific differentiation of PPRV lineages. All the isolates examined in the study were found to have a most recent common ancestor in the late 19th or in the early 20th century with high posterior probability values. The Bayesian skyline plot revealed a decrease in genetic diversity among lineage IV isolates since the start of the vaccination program and the network analysis localized the ancestry of PPRV to Africa.

Peste des petits ruminants (PPR): A neglected tropical disease in Maghreb region of North Africa and its threat to Europe

BACKGROUND

Peste des petits ruminants (PPR) is a contagious disease listed by the World Organisation for Animal health (OIE) as being a specific hazard. It affects sheep, goats, and wild ungulates, and is prevalent throughout the developing world particularly Asia, the Middle East, and Africa. PPR has been targeted for eradication by 2030 by the Food and Agriculture Organization of the United Nations (FAO) and the OIE, after the successful eradication of the related disease, rinderpest in cattle. PPR was first reported in 1942 in the Ivory Coast in Western Africa and has since extended its range in Asia, the Middle East, and Africa posing an immediate threat of incursion into Europe, South East Asia and South Africa. Although robust vaccines are available, the use of these vaccines in a systematic and rational manner is not widespread, resulting in this devastating disease becoming an important neglected tropical disease in the developing world.

METHODOLOGY

We isolated and characterized the PPR virus from an outbreak in Cheraga, northern Algeria, during October 2015 by analyzing the partial N-gene sequence in comparison with other viruses from the Maghreb region. As well as sequencing the full length viral genome and performing real-time RT-PCR on clinical samples. Maximum-likelihood and Bayesian temporal and phylogeographic analyses were performed to assess the persistence and spread of PPRV circulation from Eastern Africa in the Maghreb region of North Africa.

CONCLUSIONS

Recent PPR outbreaks in Cheraga, in the northern part of Algiers (October 2015) and North-West Morocco (June, 2015) highlight that PPRV has spread to the northern border of North Africa and may pose a threat of introduction to Europe. Phylogeographic analysis suggests that lineage IV PPRV has spread from Eastern Africa, most likely from the Sudan 2000 outbreak, into Northern Africa resulting in the 2008 Moroccan outbreak. Maximum-likelihood and Bayesian analysis shows that these North African viruses cluster closely together suggesting the existence of continual regional circulation. Considering the same virus is circulating in Algeria, Morocco and Tunisia, implementation of a common Maghreb PPR eradication strategy would be beneficial for the region.