WIDESPREAD OUTBREAK OF MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS IN A CAMEL COHORT AND ASSOCIATED SPILLOVER TO HUMANS IN KENYA

ABSTRACT

Background: Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging coronavirus that is endemic in dromedary camels. Kenya's >3 million camels have high seroprevalence of antibodies against MERS-CoV, with scant evidence of human infection, possibly due to a lower zoonotic potential of Clade C viruses, predominantly found in African camels. Methods: Between April 2018-March 2020, we followed camels aged 0-24 months from 33 camel-keeping homesteads within 50Km of Marsabit town through collecting deep nasal swabs and documenting signs of illness in camels every two weeks. Swabs were screened for MERS-CoV by reverse transcriptase (RT)-polymerase chain reaction (PCR) testing and virus isolation performed on PCR positive samples with cycle threshold (CT) <20. Both the isolates and swab samples (CT <30) were subjected to whole genome sequencing. Human camel handlers were also swabbed and screened for symptoms monthly and samples tested for MERS-CoV by RT-PCR. Results: Among 243 calves, 68 illnesses were recorded in 58 camels (53.9%);50/68 (73.5%) of illnesses were recorded in 2019, and 39 (57.3%) were respiratory symptoms (nasal discharge, hyperlacrimation and coughing). A total of 124/4,702 camel swabs (2.6%) from 83 (34.2%) calves in 15 (45.5%) enrolled compounds were positive for MERS-CoV RNA. Cases were detected between May-September 2019 with three infection peaks, a similar period when three (1.1%) human PCR-positive but asymptomatic cases were detected among 262 persons handling these herds. Sequencing of camel specimens revealed a Clade C2 virus with identical 12 nucleotide deletion at the 3' end of OFR3 region and one nucleotide insertion at the 5' region but lacked the signature ORF4b deletions of other Clade C viruses. Interpretation: We found high levels of transmission of distinct Clade C MERS-CoV among camels in Northern Kenya, with likely spillover infection to humans. These findings update our understanding of MERS-CoV epidemiology in this region.