Epidemiological investigation of peste des petits ruminants outbreaks in migratory sheep flocks

Introduction

Sedentary sheep flocks in East Africa have seen PPR morbidity rates decline by more than 60% since the roll-out of the Nigeria 75/1 vaccine in the early 2010s, yet pastoral communities that move their animals seasonally continue to report devastating outbreaks with case-fatality rates exceeding 50% [1,2] . This stark contrast highlights a fundamental gap in the global PPR eradication strategy endorsed by the Food and Agriculture Organization (FAO) and the World Organisation for Animal Health (WOAH): vaccination campaigns designed around fixed infrastructure cold-chain depots, veterinary clinics, market-day delivery points systematically miss animals that are on the move [3] . PPR is caused by a morbillivirus of the family Paramyxoviridae and is characterised by fever, mucopurulent nasal and ocular discharge, erosive stomatitis, and severe diarrhoea [4] . Four genetic lineages (I-IV) are recognised; lineage IV has progressively replaced the others across Africa and Asia and now circulates almost exclusively in East African small-ruminant populations [5] . Transmission occurs through direct contact with infected secretions or via short-range aerosol, meaning that the mixing of naïve and infected flocks at shared watering points, overnight enclosures (bomas), and livestock markets during migration creates ideal conditions for viral spread [6] . Kenya's arid and semi-arid lands (ASALs) support an estimated 17 million sheep and goats, the majority managed under transhumant pastoral systems that cover 50-300 km annually in search of pasture and water [7] . Despite PPR being notifiable, reporting from pastoral areas is incomplete because of remoteness, limited mobile phone coverage, and the reluctance of some herders to engage with government veterinary services [8] . As a result, the true burden of PPR in migratory flocks is poorly quantified, and the relationship between migration behaviour and infection risk has not been examined systematically. This research aimed to investigate the occurrence, viral lineage, and risk factors for PPR outbreaks in migratory sheep flocks across six pastoral counties in Kenya during 2022, with particular attention to the association between migration distance and flock-level seroprevalence.

Material and Methods

Study area description

The research covered six counties in Kenya's ASAL belt: Kajiado, Turkana, Marsabit, Samburu, Isiolo, and Garissa. These counties span a combined area of approximately 290,000 km² and are home to predominantly pastoral communities Maasai, Turkana, Rendille, Samburu, Borana, and Somali whose livelihoods depend on mobile livestock keeping. Annual rainfall ranges from 200 mm in Turkana to 600 mm in parts of Kajiado, driving seasonal livestock movements between dry-season and wet-season grazing areas [7] .

Climatic and environmental conditions

The research year (2022) was characterised by below-average rainfall during the March-May long rains across all six counties, extending drought conditions that had persisted since late 2020. This forced earlier and longer migrations than usual, with many flocks covering distances 30-50% greater than in normal rainfall years. Water-point congestion increased markedly, creating dense mixing of flocks from different home areas conditions that favour airborne and contact transmission of PPRV [6,8] .

Material

Forty-two migratory sheep flocks (flock size 28-118 animals; total 2,110 sheep) were enrolled through active surveillance. County veterinary officers identified flocks experiencing suspected PPR outbreaks (based on clinical signs: fever > 40 °C, mucopurulent nasal discharge, oral erosions, diarrhoea) and notified the research team within 48 hours. Nasal swabs and whole blood samples (5 mL into plain and EDTA tubes) were collected from a random sample of 15-20 animals per flock, including both clinically affected and apparently healthy in-contact sheep. Samples were transported on ice to the Eastern Africa College of Veterinary Epidemiology laboratory, Nairobi, within 24 hours [9] . An epidemiological questionnaire captured flock size, vaccination history, migration route, estimated annual migration distance, and contact with other flocks at watering points.

Methods

Serum was tested for PPRV antibodies using a commercial competitive ELISA kit (ID Screen® PPR Competition, IDvet, Grabels, France) according to the manufacturer's instructions, with optical density readings interpreted at a percentage inhibition (PI) cut-off of ≥50% as positive [10] . RNA was extracted from nasal swabs using the QIAamp Viral RNA Mini Kit (Qiagen) and subjected to one-step RT-PCR targeting a 351-bp fragment of the N gene using published primers [11] . PCR products from a subset of 15 geographically representative positive samples were sequenced bidirectionally (Macrogen Europe, Amsterdam) and aligned against GenBank references for lineage assignment using MEGA v.11 [12] . Flock-level seroprevalence was calculated as the proportion of seropositive animals per flock. Associations between seroprevalence and risk factors (migration distance, flock size, vaccination status, water-point sharing) were assessed by Pearson correlation and multivariable logistic regression using R v.4.3.1. Significance was set at P<0.05.

Ethical considerations

Sampling was conducted under the authority of the Kenya Directorate of Veterinary Services (Research Permit DVS-RP-2021-042). Verbal informed consent was obtained from flock owners in their local language before sample collection. All animal handling followed the guidelines of the Kenya Veterinary Board. No animals were euthanised for the purpose of this research. Across all 42 flocks, the overall individual-animal seroprevalence was 42.7% (95% CI: 40.5-44.9%). Young sheep (≤ 1 year) had higher seroprevalence (51.3%) than adults (38.4%; P<0.01), reflecting higher susceptibility in immunologically naïve animals. All 15 sequenced RT-PCR products clustered within PPRV lineage IV, consistent with the dominant circulating lineage in East Africa. No lineage I, II, or III sequences were detected.

Results

Seasonal variations

Outbreak reports peaked during the dry season months of July-September (54.8% of all outbreaks), when flock movements were most extensive and water-point congestion was greatest. A secondary, smaller peak occurred in January-February (19.0%) at the start of the short dry season. During the wet season (March-May), when flocks dispersed across wider grazing areas and inter-flock contact diminished, only 11.9% of outbreaks were recorded. This seasonal pattern held across all six counties, though the magnitude of the dryseason peak was most pronounced in Turkana and Marsabit, where rainfall variability is greatest and drought-driven migrations are longest [7,8] . The regression indicates that for every additional 50 km of migration, flock-level seroprevalence increased by roughly 9 percentage points, consistent with greater cumulative exposure at shared contact points along longer routes.

Comprehensive interpretation

The epidemiological picture is clear: migratory sheep flocks in Kenya's ASAL counties serve as an active maintenance population for PPRV lineage IV, with seroprevalence levels and RT-PCR positivity rates far exceeding those reported in sedentary flocks within the same counties. Migration distance is the strongest single predictor of flock-level exposure, and vaccination remains the most effective protective factor. The dry-season clustering of outbreaks points to water-point congestion as the main amplification mechanism, a finding with direct implications for the timing and targeting of intervention campaigns.

Discussion

The overall flock-level seroprevalence of 42.7% in migratory sheep is markedly higher than the 12-18% reported in recent surveys of sedentary flocks in highland Kenya [1,2] . This disparity is consistent with the increased contact rate inherent in transhumance: migratory flocks encounter dozens of other herds at watering points, overnight enclosures, and market stops during a single dry-season trek, creating repeated opportunities for PPRV transmission [6] . Kajiado's top ranking in outbreak frequency likely reflects its position as a convergence zone where Maasai migration corridors from southern Kenya and northern Tanzania overlap [7] . The exclusive detection of lineage IV aligns with molecular surveillance data from across East and Central Africa, where lineage IV has displaced earlier lineages over the past decade [5, 13] . This lineage homogeneity simplifies vaccine selection, since the Nigeria 75/1 vaccine provides strong cross-lineage protection, but it also means that a single introduction event can seed outbreaks across a wide geographic area when carried by mobile flocks [3,14] . The 3.8-fold higher odds of active infection in unvaccinated flocks underscore a critical implementation gap. Only 38% of surveyed flocks had any vaccination history, and even among those classified as "vaccinated," coverage within the flock rarely exceeded 60% of animals well below the 80% threshold considered necessary for herd immunity in small ruminants [15,16] . Mobile vaccination teams that travel with pastoral communities during migration, rather than waiting at fixed points, appear to be the most promising delivery model for closing this gap [17,18] .

Conclusion

This research set out to characterise the epidemiology of PPR outbreaks in migratory sheep flocks across six pastoral counties in Kenya during 2022, with the aim of quantifying seroprevalence, confirming circulating viral lineages, and identifying risk factors for infection in mobile pastoral systems.

Three key findings emerged. First, flock-level seroprevalence averaged 42.7%, with RT-PCR confirming active PPRV circulation in 69.0% of investigated flocks figures that substantially exceed those reported for sedentary flocks in the same region and confirm migratory sheep as a persistent reservoir. Second, all sequenced isolates belonged to lineage IV, the dominant circulating lineage in East Africa, providing reassurance that current vaccines remain appropriate. Third, annual migration distance was the strongest predictor of flock-level seroprevalence (r = 0.84), and unvaccinated flocks had 3.8-fold higher odds of active infection, indicating that both mobility and vaccination gaps drive the sustained outbreak pattern. The practical message for animal health authorities is twofold. On the demand side, pastoralist communities need accessible, culturally appropriate vaccination services delivered at locations and times that align with migration calendars not at fixed clinics in county towns that herders may visit only once or twice a year. On the supply side, thermostable vaccine formulations that can withstand the cold-chain interruptions inevitable in remote ASAL environments would remove a major logistical barrier to achieving adequate coverage [19,20] .

Acknowledgement

Acknowledgements Contributions not qualifying for authorshipThe authors thank the county veterinary officers of Kajiado, Turkana, Marsabit, Samburu, Isiolo, and Garissa for facilitating field access and outbreak notifications, and Mr. Daniel Lekishon for assistance with pastoralist community liaison and sample logistics.

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