Outbreak of Middle East Respiratory Syndrome Coronavirus in Camels and Probable Spillover Infection to Humans in Kenya

Abstract

The majority of Kenya’s > 3 million camels have antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV), although human infection in Africa is rare. We enrolled 243 camels aged 0−24 months from 33 homesteads in Northern Kenya and followed them between April 2018 to March 2020. We collected and tested camel nasal swabs for MERS-CoV RNA by RT-PCR followed by virus isolation and whole genome sequencing of positive samples. We also documented illnesses (respiratory or other) among the camels. Human camel handlers were also swabbed, screened for respiratory signs, and samples were tested for MERS-CoV by RT-PCR. We recorded 68 illnesses among 58 camels, of which 76.5% (52/68) were respiratory signs and the majority of illnesses (73.5% or 50/68) were recorded in 2019. Overall, 124/4692 (2.6%) camel swabs collected from 83 (34.2%) calves in 15 (45.5%) homesteads between April−September 2019 screened positive, while 22 calves (26.5%) recorded reinfections (second positive swab following ≥ 2 consecutive negative tests). Sequencing revealed a distinct Clade C2 virus that lacked the signature ORF4b deletions of other Clade C viruses. Three previously reported human PCR positive cases clustered with the camel infections in time and place, strongly suggesting sporadic transmission to humans during intense camel outbreaks in Northern Kenya.

Keywords: Horn of Africa; MERS-CoV epidemiology; Middle East respiratory syndrome coronavirus; spillover events; zoonosis.

Figure 1

Study flow chart showing screening, enrollment, and follow-up of the linked camel–human cohort.

Figure 2

(A) Net enrollment, number of swabs tested, respiratory illness signs, and PCR positive swabs enrolled camels; (B) Net enrollment, number of swabs tested, respiratory illness signs, and PCR positive swabs enrolled camel handlers.

Figure 2

(A) Net enrollment, number of swabs tested, respiratory illness signs, and PCR positive swabs enrolled camels; (B) Net enrollment, number of swabs tested, respiratory illness signs, and PCR positive swabs enrolled camel handlers.

Figure 3

Spot-map of the study area showing the location of enrolled camel homesteads (black spots), herds involved in the MERS-CoV outbreak (yellow spots), and human infections (red dots). The three human MERS-CoV infections clustered with camel infections.

Figure 4

Phylogenetic tree of camel-derived MERS-CoV sequences from Clade C. The sequences indicated by the green and blue colored dots were isolated from camels in Kenya in earlier studies. Sequences denoted by the red dots were isolated from our study and were based on whole genome sequences (sequences measuring 30,112 kilobases).