Detection and molecular characterization of Peste des Petits Ruminants virus from outbreaks in Burundi, December 2017-January 2018

Prevalence and associated risk factors of peste des petits ruminants in selected districts of the northern border region of Pakistan

BACKGROUND

Peste des Petits Ruminants (PPR) is a world organization for animal health (WOAH) notifiable and economically important transboundary, highly communicable viral disease of small ruminants. PPR virus (PPRV) belongs to the genus Morbillivirus of the family Paramyxoviridae.

AIM

The present cross-sectional epidemiological investigation was accomplished to estimate the apparent prevalence and identify the risk factors linked with peste des petits ruminants (PPR) in the previously neglected northern border regions of Pakistan.

METHOD

A total of 1300 samples (serum = 328; swabs = 972) from 150 flocks/herds were compiled from sheep (n = 324), goats (n = 328), cattle (n = 324), and buffaloes (n = 324) during 2020-2021 and tested using ELISA for detection of viral antibody in sera or antigen in swabs.

RESULTS

An overall apparent prevalence of 38.7% (504 samples) and an estimated true prevalence (calculated by the Rogan and Gladen estimator) of 41.0% (95% CI, 38.0-44 were recorded in the target regions. The highest apparent prevalence of 53.4% (85 samples) and the true prevalence of 57.0%, 95% Confidence Interval (CI) were documented in the Gilgit district and the lowest apparent prevalence of 53 (25.1%) and the true prevalence of 26.0%, 95% Confidence Interval (CI), 19.0-33.0) was reported in the Swat district. A questionnaire was designed to collect data about associated risk factors that were put into a univariable logistic regression to decrease the non-essential assumed risk dynamics with a P-value of 0.25. ArcGIS, 10.8.1 was used to design hotspot maps and MedCalc's online statistical software was used to calculate Odds Ratio (OR). Some of the risk factors significantly different (P < 0.05) in the multivariable logistic regression were flock/herd size, farming methods, nomadic animal movement, and outbreaks of PPR. The odds of large-sized flocks/herds were 1.7 (OR = 1.79; 95% Confidence Interval (CI) = 0.034-91.80%) times more likely to be positive than small-sized. The odds of transhumance and nomadic systems were 1.1 (OR = 1.15; 95% Confidence Interval (CI) = 0.022-58.64%) and 1.0 (OR = 1.02; 95% Confidence Interval (CI) = 0.020-51.97%) times more associated to be positive than sedentary and mixed farming systems, respectively. The odds of nomadic animal movement in the area was 0.7 (OR = 0.57; 95% Confidence Interval (CI) = 0.014-38.06%) times more associated to be positive than in areas where no nomadic movement was observed. In addition, the odds of an outbreak of PPR in the area were 1.0 (OR = 1.00; 95% Confidence Interval (CI) = 0.018-46.73%) times more associated to be positive than in areas where no outbreak of PPR was observed.

CONCLUSIONS

It was concluded that many northern regions considered endemic for PPR, large and small ruminants are kept and reared together making numerous chances for virus transmission dynamic, so a big threats of disease spread exist in the region. The results of the present study would contribute to the global goal of controlling and eradicating PPR by 2030.

Development and Evaluation of a Nested PCR for Improved Diagnosis and Genetic Analysis of Peste des Petits Ruminants Virus (PPRV) for Future Use in Nascent PPR Eradication Programme

Peste des petits ruminants (PPR) is a highly contagious viral disease of small ruminants caused by PPR virus (PPRV). PPR is endemic in Asia, the Middle East and across large areas of Africa and is currently targeted for global eradication by 2030. The virus exists as four different lineages that are usually limited to specific geographical areas. However, recent reports of spread of PPRV, in particular of lineage IV viruses to infection-free countries and previously PPR endemic areas are noteworthy. A rapid and accurate laboratory diagnosis and reports on its epidemiological linkage for virus spread play a major role in the effective control and eradication of the disease. Currently, molecular assays, including conventional reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR (RT-qPCR) are usually used for diagnosis of PPR while the sequencing of part of the nucleocapsid gene is usually carried out for the viral lineage identification. However, it is difficult to diagnose and sequence the genetic material if the animal excreted a low level of virus at the initial stage of infection or if the PPRV is degraded during the long-distance transportation of samples to the reference laboratories. This study describes the development of a novel nested RT-PCR assay for the detection of the PPRV nucleic acid by targeting the N-protein gene, compares the performance of the assay with the existing conventional RT-PCR and also provides good-quality DNA suitable for sequencing in order to identify circulating lineages. The assay was evaluated using cell culture propagated PPRVs, field samples from clinically infected animals and samples from experimentally infected animals encompassing all four lineages (I-IV) of PPRV. This assay provides a solution with an easy, accurate, rapid and cost-effective PPR diagnostic and partial genome sequencing for use in resource-limited settings.

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.

Virus distribution and early pathogenesis of highly pathogenic peste-des-petits-ruminants virus in experimentally infected goats

INTRODUCTION

Despite causing one of the most dreaded diseases of small ruminants, relatively little is known about the pathogenic events, antigen distribution and the cells responsible for the uptake and transmission of peste-des-petits-ruminants virus (PPRV) during primitive stages of infection.

OBJECTIVES

We aimed at deciphering the sequential tissue tropism, pathological events and putative role of M2c macrophages during incubatory, prodromal and invasive stages of PPRV infection.

METHODOLOGY

A total of 10 goats were sequentially sacrificed at 1, 2, 3, 4, and 5 days post-infection (dpi, n = 2 per time-point) following intranasal inoculation with a highly virulent strain of PPRV (lineage IV PPRV/Izatnagar/94). Histological evaluation to assess PPRV mediated pathologies, RT-qPCR and immunohistochemistry (IHC) to decipher sequential virus distribution, and dual immunolabelling to determine the role of M2c macrophage in early PPRV uptake and transmission was performed.

RESULTS

PPRV/Izatnagar/94 caused major pathologies in the lung tissues. Unprecedentedly, PPRV nucleic acid and antigens were detected in various tissues as early as one dpi. RT-qPCR revealed PPRV in the nasal cavity, trachea, bronchi, tongue and lymph nodes draining these tissues from 1 dpi. IHC affirms cells residing in the lamina propria and submucosa of the respiratory tract and tongue and peribronchiolar areas of lungs as the primary target of PPRV. Following initial replication in the respiratory tract, PPRV is transmitted to the regional lymph nodes where primary viral amplification occurs. After viraemia and secondary replication in generalized lymphoid tissues, PPRV infects and replicates in the epithelial cells. Further, we localized CD163⁺ M2c macrophages in the goat tissues, but dual IHC elucidated that M2c macrophages do not facilitate uptake and transmission of PPRV during the early stages of infection.

CONCLUSION

Our study substantiates the disease establishment process and pathogenesis of PPRV/Izatnagar/94 during the incubatory and prodromal stages of infection. Further, we have also observed M2c macrophage distribution in the goat tissues and demonstrated that they do not pick and transmit 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.

Serological Evidence of Exposure to Peste des Petits Ruminants in Small Ruminants in Rwanda

The status of Peste des Petits Ruminants (PPR) in Rwanda is unknown, despite its prevalence in neighboring countries. A cross-sectional sampling of goats and sheep was carried out in five districts of Rwanda located closer to neighboring countries endemic to PPR. Serum samples were analyzed using a commercial ELISA, to detect antibodies to PPR virus (PPRV). Sixty-eight samples [14.8, 95% Confidence Interval (CI): 11.7–18.4] were seropositive for PPR, of which 17.4% (95% CI: 11.6–24.6; 25/144) were from sheep, whereas 13.6% (95% CI: 10.0–17.9; 43/316) were from goats. Seropositivity ranged from 8.9 to 17.3% (goats) and from 10.5 to 25.8% (sheep) in sampled districts. Seropositivity was slightly higher in males than females in both goats (15.7 vs. 12.4%) and sheep (17.7 vs. 17.1%), and were significantly marked in goats and sheep aged more than 15 months (goats: 17.9, 95% CI: 12.9–24.0; sheep: 22.2, 95% CI: 14.1–32.2) than those between 6 and 15 months (goats: 6.1, 95% CI: 2.5–12.1; sheep: 9.3, 95% CI: 3.1–20.3). Sampling was non-randomized and results are not representative of the true prevalence of PPR antibody in small ruminants. Thus, data does not allow to fully discuss the findings beyond the presence/absence certitude and the comparisons made must be interpreted with caution. The presence of specific antibodies to PPRV may, however, be linked to one or a combination of following scenarios: (1) prevalence and persistence of PPRV in sampled regions which would cause low level of clinical cases and/or mortalities that go unnoticed; (2) introduction of PPRV to herds through movements of livestock from neighboring infected countries, and/or (3) events of disease outbreaks that are underreported by farmers and veterinarians. In addition to strengthen veterinary surveillance mechanisms, further studies using robust sampling methods and integrating livestock and wildlife, should be carried out to fully elucidate PPR epidemiology in Rwanda.

A Review of the Current Status of Peste des Petits Ruminants Epidemiology in Small Ruminants in Tanzania

Peste des petits ruminants (PPR) is a highly contagious viral disease of sheep and goats with high mortality. The disease is of considerable economic importance in countries such as Tanzania, where small ruminant products are important for sustainable livelihoods. This review assesses current knowledge regarding the epidemiology of PPRV in Tanzania, highlighting the challenges with respect to control and suggesting possible interventions. Thirty-three articles were identified after literature searches using Google Scholar and PubMed. Studies revealed that PPRV is endemic in sheep and goats in Tanzania, although seropositivity has also been reported in cattle, camels, buffalo, Grant's gazelle, wildebeest and impala, but with no clinical manifestation. Three lineages (lineage II to IV) of PPRV have been identified in Tanzania, implying at least two separate introductions of the virus. Diagnosis of PPR in Tanzania is mostly by observation of clinical signs and lesions at post mortem. Risk factors in Tanzania include age, sex, species, and close contact of animals from different farms/localities. Although there is an efficacious vaccine available for PPR, poor disease surveillance, low vaccine coverage, and uncontrolled animal movements have been the bane of control efforts for PPR in Tanzania. There is need for collaborative efforts to develop interventions to control and eradicate the disease. The establishment of a national reference laboratory for PPR, conduct of surveillance, the development of high-quality DIVA vaccines, as well as execution of a carefully planned national vaccination campaign may be key to the control and subsequent eradication of PPR in Tanzania and achieving the global goal of eradicating PPR by 2030.

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.

Characterisation of Peste Des Petits Ruminants Disease in Pastoralist Flocks in Ngorongoro District of Northern Tanzania and Bluetongue Virus Co-Infection

Peste des petits ruminants (PPR) disease was first confirmed in Tanzania in 2008 in sheep and goats in Ngorongoro District, northern Tanzania, and is now endemic in this area. This study aimed to characterise PPR disease in pastoralist small ruminant flocks in Ngorongoro District. During June 2015, 33 PPR-like disease reports were investigated in different parts of the district, using semi-structured interviews, clinical examinations, PPR virus rapid detection test (PPRV-RDT), and laboratory analysis. Ten flocks were confirmed as PPRV infected by PPRV-RDT and/or real-time reverse transcription-polymerase chain reaction (RT-qPCR), and two flocks were co-infected with bluetongue virus (BTV), confirmed by RT-qPCR. Phylogenetic analysis of six partial N gene sequences showed that the PPR viruses clustered with recent lineage III Tanzanian viruses, and grouped with Ugandan, Kenyan and Democratic Republic of Congo isolates. No PPR-like disease was reported in wildlife. There was considerable variation in clinical syndromes between flocks: some showed a full range of PPR signs, while others were predominantly respiratory, diarrhoea, or oro-nasal syndromes, which were associated with different local disease names (olodua-a term for rinderpest, olkipiei-lung disease, oloirobi-fever, enkorotik-diarrhoea). BTV co-infection was associated with severe oro-nasal lesions. This clinical variability makes the field diagnosis of PPR challenging, highlighting the importance of access to pen-side antigen tests and multiplex assays to support improved surveillance and targeting of control activities for PPR eradication.

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.

Genetic Parameters for Growth and Kid Survival of Indigenous Goat under Smallholding System of Burundi

The goal of this study was to estimate genetic parameters for the growth, conformation, and survival of goat kids raised in smallholder farming systems in Burundi. To do this, measurements were taken on live weight, thoracic perimeter, length, and height at birth (n = 1538 animals), at 3 months (n = 1270 animals), at 6 months (n = 992 animals), at 9 months (n = 787 animals), and at 12 months (n = 705 animals). Kids were born between 2016 and 2019, from 645 dams and 106 bucks. Three bivariate animal models were used to estimate genetic parameters of body weight and conformation measurements as potential indicators of this weight. According to the measure, heritability was estimated between 15 and 17% and genetic correlations between 65 and 79%. An accelerated failure time animal model was used to estimate the heritability of survival for kids under one year, adjusted for birth weight. Goat survival was significantly prolonged by 0.64 days per kilogram of birth weight. The estimated heritability for this trait was 2%. Overall, these results suggest that a selection program could be implemented to improve animal growth, either directly on weight or indirectly on conformational traits. At the same time, efforts need to be made to improve rearing conditions to increase the survival of kids.

Peste des petits ruminants viruses of lineages II and III identified in the Democratic Republic of the Congo

Understanding the molecular epidemiology and evolution of peste des petits ruminants virus (PPRV), the causative agent of Peste des petits ruminants, can assist in the control of the transboundary spread of this economically important disease. To date, despite having been reported in the majority of northern and central African countries, no molecular epidemiological data on PPRVs are available for the Democratic Republic of the Congo (DRC). This study reports the collection and analysis of 11 samples collected from three provinces of the DRC in 2016 and 2018. Sequence analysis identified two (i.e. II and III) of the four known lineages of PPRV in the country providing important information that will assist in the global eradication of PPR.

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.