Molecular detection and phylogenetic analysis of Peste des petits ruminants virus circulating in small ruminants in eastern Amhara region, Ethiopia

Modeling the Peste des Petits Ruminants (PPR) disease transmission dynamics with impacts of vaccination and restocking in small ruminant population in Amhara region, Ethiopia

Peste des Petits Ruminants (PPR) is a highly contagious transboundary viral disease of small ruminants with significant economic implications caused by the Peste des Petits Ruminants virus. This study employs mathematical modeling to investigate the impact of imperfect PPR vaccines and restocked small ruminants on the transmission dynamics of PPR. A deterministic mathematical model is developed by incorporating vaccinated and restocked subpopulations into the classical SEIR model. The influence of infected animals introduced through restocking on vaccination efficacy in preventing PPR spread is examined. The global dynamics of equilibrium points in the model are analyzed using the Lyapunov-LaSalle invariance principle. Parameter values for numerical simulations are estimated based on monthly PPR data from the Amhara regional state in Ethiopia, obtained from the Ministry of Agriculture. The basic reproduction number (R v ) is calculated to assess the level of PPR in the small ruminant population, and sensitivity analysis of parameters is performed onR v . The analytical and numerical results reveal that infected restocked small ruminants significantly facilitate the spread of PPR in the population. Moreover, even with high efficacy vaccination, the system exhibits a unique asymptotically stable endemic equilibrium. These findings emphasize that appropriate vaccination alone is insufficient to control and eradicate PPR in the region. Implementing strict movement restrictions and biosecurity measures are necessary. These findings provide valuable insights for national policymakers in achieving the regional and national targets for PPR eradication by 2027.

Seroprevalence and associated risk factors of peste des petits ruminants in sheep and goats in three districts of the Central Oromia Region, Ethiopia

Background

Peste des petits ruminants (PPR) is a viral disease that affects domestic and wild small ruminants and camels in Africa, the Middle East, and Asia. Following the successful eradication of rinderpest, the World Organization for Animal Health (WOAH) and the Food and Agriculture Organization (FAO) have undertaken to eradicate PPR by 2030. Regular surveillance and monitoring of the disease in various regions of Ethiopia are crucial to achieving this goal. This study aimed to estimate the prevalence of PPR, assess community awareness of PPR infection, and examine the associated risk factors of the disease in selected districts of the Central Oromia Region, Ethiopia.

Method

The study collected 384 serum samples from 73 flocks containing 217 sheep and 167 goats using a multi-stage sampling technique. A competitive enzyme-linked immunosorbent assay (c-ELISA) was used to detect antibodies against the PPR virus. Additionally, a pre-tested questionnaire was used to gather information on community awareness and potential risk factors for PPRV infection in the study area.

Results

The study found that the overall prevalence of PPR in flocks was 71.2% [95% confidence interval (CI): 59.4%-81.2%]. The prevalence of PPR at the animal level was 50% (95% CI: 44.9%-55.1%), with sheep having a prevalence of 54.4% (95% CI: 47.0%-60.6%) and goats having a prevalence of 44.3% (95% CI: 36.6%-52.2%). The study also found that districts, flock size, and agroecology were independent predictors of PPRV seropositivity in sheep, whereas districts, origin, and mixed species were independent predictors of PPRV seropositivity in goats.

Conclusion

The study revealed a high prevalence of PPR in sheep and goats in the study area. To prevent the spread of the disease, the study suggests quarantining animals before introducing them to districts, regular PPR vaccination, and isolation and molecular characterization of the PPR virus circulating in the study area.

Molecular characterization of Peste des petits ruminants virus (PPRV) in sheep and goats and risk factors associated with it in selected districts of Khyber Pakhtunkhwa-Pakistan

BACKGROUND

Peste des Petits Ruminants (PPR) is an economically significant transboundary viral disease of sheep and goats caused by the PPRV virus, affecting annual losses of 1.45-2.10 billion US dollars globally. We designed the current study to evaluate the positive cases, molecular characterization, phylogenetic analysis, and risk factors correlated with the disease in various districts of Khyber Pakhtunkhwa, Pakistan, with the aim of contributing to these strategies.

METHODS AND RESULTS

A total of 384 samples from three selected districts, i.e., Peshawar, Charsadda and Chitral (n = 128 each), were collected, and the virus was investigated by using the sandwich ELISA, while the N gene of the virus was used as a target for molecular detection via RT-PCR. The confirmed samples were then sequenced, and phylogenetic analysis was performed. According to our findings, the highest positive cases was found in district Peshawar (50.87%), followed by Charsadda and Chitral (24.56%), respectively, while risk factor analysis showed that certain categories, such as species, sex, and age less than two years, have higher risk (P < 0.05) in contrast to their respective categories. Furthermore, sequencing and phylogenetic analysis of representative samples showed that the PPRV strains in the current study clustered in lineage IV, which is circulating in the small ruminant population of Asia, the Middle East, and African countries. Comparative residue analysis highlighted the mutation by representing 242 variable sites out of 371 locations.

CONCLUSIONS

PPRV has foremost importance in Pakistan because the virus was detected in a considerable number of samples, and most of which were sourced from subsidiary areas where veterinary services are not prioritized.

Empirical and model-based evidence for a negligible role of cattle in peste des petits ruminants virus transmission and eradication

Peste des petits ruminants virus (PPRV) is a multi-host pathogen with sheep and goats as main hosts. To investigate the role of cattle in the epidemiology of PPR, we simulated conditions similar to East African zero-grazing husbandry practices in a series of trials with local Zebu cattle (Bos taurus indicus) co-housed with goats (Capra aegagrus hircus). Furthermore, we developed a mathematical model to assess the impact of PPRV-transmission from cattle to goats. Of the 32 cattle intranasally infected with the locally endemic lineage IV strain PPRV/Ethiopia/Habru/2014 none transmitted PPRV to 32 co-housed goats. However, these cattle or cattle co-housed with PPRV-infected goats seroconverted. The results confirm previous studies that cattle currently play a negligible role in PPRV-transmission and small ruminant vaccination is sufficient for eradication. However, the possible emergence of PPRV strains more virulent for cattle may impact eradication. Therefore, continued monitoring of PPRV circulation and evolution is recommended.

Recapitulation of Peste des Petits Ruminants (PPR) Prevalence in Small Ruminant Populations of Pakistan from 2004 to 2023: A Systematic Review and Meta-Analysis

Peste des petits ruminants (PPR) is an extremely transmissible viral disease caused by the PPR virus that impacts domestic small ruminants, namely sheep and goats. This study aimed to employ a methodical approach to evaluate the regional occurrence of PPR in small ruminants in Pakistan and the contributing factors that influence its prevalence. A thorough search was performed in various databases to identify published research articles between January 2004 and August 2023 on PPR in small ruminants in Pakistan. Articles were chosen based on specific inclusion and exclusion criteria. A total of 25 articles were selected from 1275 studies gathered from different databases. The overall pooled prevalence in Pakistan was calculated to be 51% (95% CI: 42-60), with heterogeneity I2 = 100%, τ2 = 0.0495, and p = 0. The data were summarized based on the division into five regions: Punjab, Baluchistan, KPK, Sindh, and GB and AJK. Among these, the pooled prevalence of PPR in Sindh was 61% (95% CI: 46-75), I2 = 100%, τ2 = 0.0485, and p = 0, while in KPK, it was 44% (95% CI: 26-63), I2 = 99%, τ2 = 0.0506, and p < 0.01. However, the prevalence of PPR in Baluchistan and Punjab was almost the same. Raising awareness, proper surveillance, and application of appropriate quarantine measures interprovincially and across borders must be maintained to contain the disease.

Molecular Epidemiology of Peste Des Petits Ruminants Virus in West Africa: Is Lineage IV Replacing Lineage II in Burkina Faso?

This study aimed at investigating the genetic lineages of peste des petits ruminants virus (PPRV) currently circulating in Burkina Faso. As part of PPR surveillance in 2021 and 2022, suspected outbreaks in different regions were investigated. A risk map was produced to determine high-risk areas for PPR transmission. Based on alerts, samples were obtained from three regions and all sampled localities were confirmed to fall within PPR high risk areas. We collected swab samples from the eyes, mouth, and nose of sick goats. Some tissue samples were also collected from dead animals suspected to be infected by PPRV. In total, samples from 28 goats were analysed. Virus confirmation was performed with RT-PCR amplification targeting the nucleocapsid (N) gene. Partial N gene sequencing (350 bp) was carried out using the RT-PCR products of positives samples to characterise the circulating lineages. Eleven sequences, including ten new sequences, have been obtained. Our study identified the presence of the PPRV lineage IV in the three studied regions in Burkina Faso with a genetic heterogeneity recorded for the sequences analysed. Previously published data and results of this study suggest that PPRV lineage IV seems to be replacing lineage II in Burkina Faso.

Complete genome of a 2014 isolate of peste des petits ruminants virus from Ethiopia

This report describes the complete genome sequence of a peste des petits ruminants virus (PPRV) isolate from Ethiopia in 2014. The strain (PPRV/Ethiopia/Habru/2014), which showed a normal virulence and relatively low morbidity in the field, belongs to the North African subclade of Lineage IV.

Sero-Prevalence and Associated Risk Factors of Peste Des Petits Ruminants in Dera and Gerar Jarso Districts of Oromia Region, Ethiopia

Introduction

Peste des petits ruminants is a transboundary disease of major economic importance and imposes significant constraints on small ruminant production.

Methods

A cross-sectional study was employed in Dera and Gerar Jarso districts of the North Shewa zone, Oromia Region from February 2021 to March 2022, to estimate the antibody of PPRV and assess the associated risk factors. Blood samples (n = 662) were collected from sheep and goats. Cluster sampling strategy was employed to collect the data. Villages/Kebeles and individual small ruminants were randomly selected, while households were designated using a systematic random sampling method.

Results

An overall individual animal and flock level sero-prevalence was 10.3% (95% CI = 8.2-12.8) and 100% (95% CI = 96.3-100), respectively, from the c-ELISA test result. A sero-prevalence of 11.2% (95% CI = 8.7-14.4) in Dera and 8% (95% CI = 5-12.7) in Gerar Jarso districts was recorded.

Discussion

Flock size, age, sex, communal grazing, and watering system, new small ruminant introduction into a flock, and mixed rearing were significantly associated with PPR sero-positivity in sheep and goats. The chance of PPR occurrence in goats was 4 times (OR = 4; P = 0.000) more than sheep. Female sheep and goats were more likely to be sero-positive to PPR by 3 times (OR = 3.2; P = 0.003) than males. The newly introduced small ruminants had 4 times more odds (OR = 4.4; P = 0.000) of sero-positivity than animals being born at home. Small ruminants kept under communal grazing and watering system were nearly 12 times (OR = 11.5; P = 0.024) more likely sero-positive than privately managed small ruminants. Likewise, sheep and goats reared together were almost 9 times (OR = 9.4; P = 0.000) a higher chance of being sero-positive compared with separately reared small ruminants.

Conclusion

The finding of PPR virus antibodies in small ruminants from all study areas indicates endemic circulation of the virus. The implementation of regular vaccination could minimize the occurrence of PPR.

Molecular Epidemiology and Phylogenetic Analysis of Peste des Petits Ruminants Virus Circulating in Sheep in Bangladesh

Peste des petits ruminants (PPR) is a viral disease of small ruminants that is highly contagious, severe, reportable, and economically important. The present study was conducted to detect the PPR virus (PPRV) circulating in sheep in Bangladesh to determine its association with epidemiological risk factors and the degree of relationship between the F and H genes of the PPRV of sheep with those of other sheep and goat isolates. A cross-sectional study was conducted in five selected districts of Bangladesh to collect data on locations, ecological zones, breeds, age, sex, sources, time period, and farming systems using a structured questionnaire accompanied by face-to-face interviews. During sampling, 250 nasal swab samples were collected from live sheep with the typical clinical signs of PPR. Thereafter, a reverse-transcriptase polymerase chain reaction (RT-PCR) assay was employed to detect PPRV using the F and H genes. Risk factors were determined using bivariable and multivariable logistic regression analyses. Phylogenetic analysis of the detected PPRV was performed using MEGA software after sequencing both F and H genes. Using RT-PCR, 35.6% (89/250, 95% CI: 29.6%-41.6%) of the samples were found to be positive for PPRV. Locations, breeds, sources, and feeding systems were identified as potential molecular epidemiological risk factors for PPRV infection in a multivariate logistic regression model. Nucleotide sequencing and phylogenetic analysis showed that the PPRV strain was genetically related to the lineage IV virus isolates. For the F gene, the sequence divergence of our gene and other selected genes ranged from 0.01% to 0.018% within lineage IV, and the similarity ranged from 98.2% to 99.0%. In the case of the H gene, similar results were also observed in divergence, ranging from 0.017% to 0.083% among lineage IV and others, and similarity varied from 91.7% to 98.3%. To the best of our knowledge, this is the first study in Bangladesh conducted to determine the RT-PCR-based molecular epidemiology of PPRV in sheep. This study highlights the importance of establishing successful interventions for managing PPRV infections in small ruminants in Bangladesh.

A Clinical, Pathological, Epidemiological and Molecular Investigation of Recent Outbreaks of Peste des Petits Ruminants Virus in Domestic and Wild Small Ruminants in the Abu Dhabi Emirate, United Arab Emirates

(1) Background: Peste des petits ruminants (PPR) is a highly contagious animal disease affecting small ruminants, leading to significant economic losses. There has been little published data on PPR virus (PPRV) infection in the United Arab Emirates (UAE); (2) Methods: four outbreaks reported in goats and Dama gazelle in 2021 were investigated using pathological and molecular testing; (3) Results: The infected animals showed symptoms of dyspnea, oculo-nasal secretions, cough, and diarrhea. Necropsy findings were almost similar in all examined animals and compliant to the classical forms of the disease. Phylogenetic analysis based on N gene and F gene partial sequences revealed a circulation of PPRV Asian lineage IV in the UAE, and these sequences clustered close to the sequences of PPRV from United Arab Emirates, Pakistan, Tajikistan and Iran; (4) Conclusions: PPRV Asian lineage IV is currently circulating in the UAE. To the best of our knowledge, this is a first study describing PPRV in domestic small ruminant in the UAE.

Epidemiology, risk factors and molecular characterization of small ruminant morbillivirus in Haryana, India

Peste des petitis ruminants is an economically important transboundary and notifiable viral disease of sheep and goats. In this study, 14 PPR suspected outbreaks among sheep and goats were investigated in four districts of Haryana, India, during July 2020 to October, 2021. The causative agent of the disease; small ruminant morbillivirus was detected by Reverse Transcription Polymerase Chain Reaction targeting full gene sequences of fusion protein gene and confirmed by sequencing. The overall morbidity and cumulative mortality in these outbreaks were 37.56% and 12.09%, respectively. Risk factor analysis identified significant difference in mortality based on age with higher mortality in young ones; 21% as compared to adults; 7.55%. Analysis of the vaccination status revealed significant difference in morbidity and mortality with higher morbidity and mortality in un-vaccinated animals as compared to vaccinated ones. The sequencing and phylogenetic analysis of representative samples revealed that the strains of the present study fall in lineage IV (96.6-99.1%) along with other Indian isolates but made a separate cluster (sub-lineage). The comparison of deduced amino acid (aa) sequence analysis of fusion protein of circulating field strains with reference vaccine strain and other lineage IV strains revealed four N-linked glycosylation sites instead of three. The findings of the present study revealed changes in fusion protein of some of the circulating field strains of SRMV in Haryana, India. Further detailed studies are warranted to delineate the molecular details of these circulating field strains and to evaluate the effectiveness of currently used vaccine against these mutated strains.

Isolation and Molecular Characterization of Peste des Petits Ruminants Virus from Outbreaks in Southern Ethiopia, 2020

Peste des petits ruminants (PPR) is one of the most important transboundary diseases of small ruminants. In this study, nasal and oral swabs (n = 24) were collected from sheep (n = 7) and goats (n = 17) with clinical signs in southern Ethiopia in March 2020. PPR virus was isolated on Vero dog cells expressing the signaling lymphocyte activation molecule (VDS) and screened using RT-qPCR. Positive samples were confirmed by conventional RT-PCR followed by sequencing of a partial nucleoprotein (N) gene segment. Results revealed that 54% (n = 13/24) of the tested samples were PPRV-positive Phylogenetic analysis revealed that the viruses belonged to lineage IV and lineage II. The lineage IV viruses were similar, although not identical, to other lineage IV viruses previously reported in Ethiopia and other East African countries while the lineage II viruses have been reported for the first time in Ethiopia showed a high nucleotide identity (99.06%) with the vaccine (Nigeria 75/1) that is currently used in Ethiopia for the prevention of PPR. Further investigations are therefore recommended in order to fully understand the true nature of the lineage II PPRVs in Ethiopia.

Wide circulation of peste des petits ruminants virus in sheep and goats across Nigeria

Peste des petits ruminants (PPR) is a highly contagious viral disease that mainly affects goats and sheep in Asia, Africa and the Middle East, and threatens Europe [R.E.1]. The disease is endemic on the African continent, particularly in West Africa, and is a major factor driving food insecurity in low-income populations. The aim of this research study was to carry out surveillance, genetic characterisation and isolation of recently circulating PPR viruses (PPRV) in sheep and goats from the six agro-ecological zones of Nigeria. A total of 268 post-mortem tissue samples of lung and mesenteric ganglia were collected from clinically suspected sheep and goats in 18 different states, of which five never previously sampled. The presence of PPRV was confirmed using a reverse-transcription coupled with a polymerase chain reaction (RT-PCR) assay. A total of 72 samples, 17 sheep (6%) and 55 goats (21%), were found to be PPR positive. Positive samples were distributed in almost all states, except Kano, where PPR was detected in previous studies. The PPRV-positive samples were further confirmed by sequencing or virus isolation in areas where the infection had never previously been detected. These results confirm the active circulation of PPRV across all six agro-ecological zones of Nigeria, and consequently, the need for introducing strict measures for the control and prevention of the disease in the country.

Prioritizing smallholder animal health needs in East Africa, West Africa, and South Asia using three approaches: Literature review, expert workshops, and practitioner surveys

Managing the health needs of livestock contributes to reducing poverty and improving the livelihoods of smallholder and pastoralist livestock keepers globally. Animal health practitioners, producers, policymakers, and researchers all must prioritize how to mobilize limited resources. This study employed three approaches to prioritize animal health needs in East and West Africa and South Asia to identify diseases and syndromes that impact livestock keepers. The approaches were a) systematic literature review, b) a series of expert workshops, and c) a practitioner survey of veterinarians and para-veterinary professionals. The top constraints that emerged from all three approaches include endo/ ectoparasites, foot and mouth disease, brucellosis, peste des petits ruminants, Newcastle disease, and avian influenza. Expert workshops additionally identified contagious caprine pleuropneumonia, contagious bovine pleuropneumonia, mastitis, and reproductive disorders as constraints not emphasized in the literature review. Practitioner survey results additionally identified nutrition as a constraint for smallholder dairy and pastoralist small ruminant production. Experts attending the workshops agreed most constraints can be managed using existing veterinary technologies and best husbandry practices, which supports a shift away from focusing on individual diseases and new technologies towards addressing systemic challenges that limit access to veterinary services and inputs. Few research studies focused on incidence/ prevalence of disease and impact, suggesting better incorporation of socio-economic impact measures in future research would better represent the interests of livestock keepers.

Peste des petits ruminants in Africa: a review of currently available molecular epidemiological data, 2020

Small ruminants (e.g., sheep and goats) contribute considerably to the cash income and nutrition of small farmers in most countries in Africa and Asia. Their husbandry is threatened by the highly infectious transboundary viral disease peste des petits ruminants (PPR) caused by peste-des-petits-ruminants virus (PPRV). Given its social and economic impact, PPR is presently being targeted by international organizations for global eradication by 2030. Since its first description in Côte d’Ivoire in 1942, and particularly over the last 10 years, a large amount of molecular epidemiological data on the virus have been generated in Africa. This review aims to consolidate these data in order to have a clearer picture of the current PPR situation in Africa, which will, in turn, assist authorities in global eradication attempts.

Prevalence and molecular characterization of some circulating strains of the peste-des-petits-ruminants virus in Saudi Arabia between 2014-2016

Background

The peste-des-petits-ruminants virus (PPRV) is a highly devastating virus of small ruminants in many parts of the world, including the Kingdome of Saudi Arabia. Therefore, our objectives were (1) to conduct a molecular prevalence study of PPRV in sheep and goat across the KSA and (2) to isolate and identify currently circulating PPRV lineages. Swabs and tissue specimens were collected from 97 herds suspected to be infected with PPRV across the Kingdome of Saudi Arabia (KSA). Testing for the presence of the virus was done by the real-time PCR. Confirmation of the identity of the reactions was done by the gel-based-PCR then by sequencing of the partial PPRV genome.

Results

Our results revealed that 24.1% of the tested specimens were PPRV-positive. Isolation of PPRV was successful from samples using the Vero cell line. Sequence analysis of some partial PPRV genes (N, F, M, L, P, and H) revealed that these strains were belonging to lineage IV of the PPRV.

Conclusions

This is the first study to conduct both the nationwide prevalence, isolation, and molecular characterizations of the PPRV in the KSA. Continuous surveillance and monitoring of the circulating strains of PPRV among sheep and goats will contribute substantially to the global eradication campaign of such a virus.

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.

Spatial Multicriteria Evaluation for Mapping the Risk of Occurrence of Peste des Petits Ruminants in Eastern Africa and the Union of the Comoros

Peste des petits ruminants virus (PPRV), responsible for peste des petits ruminants (PPR), is widely circulating in Africa and Asia. The disease is a huge burden for the economy and development of the affected countries. In Eastern Africa, the disease is considered endemic. Because of the geographic proximity and existing trade between eastern African countries and the Comoros archipelago, the latter is at risk of introduction and spread, and the first PPR outbreaks occurred in the Union of the Comoros in 2012. The objective of this study was to map the areas suitable for PPR occurrence and spread in the Union of the Comoros and four eastern African countries, namely Ethiopia, Uganda, Kenya, and Tanzania. A Geographic Information System (GIS)-based Multicriteria Evaluation (MCE) was developed. Risk factors for PPR occurrence and spread, and their relative importance, were identified using literature review and expert-based knowledge. Corresponding geographic data were collected, standardized, and combined based on a weighted linear combination to obtain PPR suitability maps. The accuracy of the maps was assessed using outbreak data from the EMPRES database and a ROC curve analysis. Our model showed an excellent ability to distinguish between absence and presence of outbreaks in Eastern Africa (AUC = 0.907; 95% CI [0.820-0.994]), and a very good performance in the Union of the Comoros (AUC = 0.889, 95% CI: [0.694-1]). These results highlight the efficiency of the GIS-MCE method, which can be applied at different geographic scales: continental, national and local. The resulting maps provide decision support tools for implementation of disease surveillance and control measures, thus contributing to the PPR eradication goal of OIE and FAO by 2030.