Genetic Evidence of Middle East Respiratory Syndrome Coronavirus (MERS-Cov) and Widespread Seroprevalence among Camels in Kenya

Abstract

We describe the first genome isolation of Middle East respiratory syndrome coronavirus (MERS-CoV) in Kenya. This fatal zoonotic pathogen was first described in the Kingdom of Saudi Arabia in 2012. Epidemiological and molecular evidence revealed zoonotic transmission from camels to humans and between humans. Currently, MERS-CoV is classified by the WHO as having high pandemic potential requiring greater surveillance. Previous studies of MERS-CoV in Kenya mainly focused on site-specific and archived camel and human serum samples for antibodies. We conducted active nationwide cross-sectional surveillance of camels and humans in Kenya, targeting both nasal swabs and plasma samples from 1,163 camels and 486 humans collected from January 2016 to June 2018. A total of 792 camel plasma samples were positive by ELISA. Seroprevalence increased with age, and the highest prevalence was observed in adult camels (82.37%, 95% confidence interval (CI) 79.50-84.91). More female camels were significantly seropositive (74.28%, 95% CI 71.14-77.19) than male camels (P < 0.001) (53.74%, 95% CI 48.48-58.90). Only 11 camel nasal swabs were positive for MERS-CoV by reverse transcription-quantitative PCR. Phylogenetic analysis of whole genome sequences showed that Kenyan MERS-CoV clustered within sub-clade C2, which is associated with the African clade, but did not contain signature deletions of orf4b in African viruses. None of the human plasma screened contained neutralizing antibodies against MERS-CoV. This study confirms the geographically widespread occurrence of MERS-CoV in Kenyan camels. Further one-health surveillance approaches in camels, wildlife, and human populations are needed.

Keywords: Kenya; Middle East respiratory syndrome coronavirus (MERS-CoV); One-health; Public health; Zoonosis.

Fig. 1

Map of Kenya showing the 13 counties surveyed in this study.

Fig. 2

Isolation of camel MERS-CoV C1215 and C1272. A Induction of cytopathic effect on Vero cells. The images were taken by NIS Elements F (ECLIPSE TS100, Nikon). Original magnification: 100 ×. B Successful isolation of camel MERS-CoV was confirmed by immunofluorescent antibody staining using rabbit antibody against the MERS-CoV N protein. The columns (from left to right) show staining of nuclei (blue), virus replication (red), and both nuclei and virus replication (merged double-stain images). The images were taken by a confocal microscope. Scale bar = 100 μm.

Fig. 3

Phylogenetic analysis of MERS-CoV full genomes using neighbor-joining method in MEGA7. Bootstrap values of nodes are shown. Bootstrap values along branches are for 1,000 replicates. The tree was rooted against a MERS-CoV related bat coronavirus Neoromicia/PML-PHE1/RSA/2011 (KC869678) from South Africa. To allow for greater resolution of the viruses of interest, the long branch of KC869678 was removed. Detected MERS-CoV viruses in this study are red colored and identified with circle node markers (●). Scale bar indicates nucleotide substitutions per site.

Fig. 4

Schematic diagram showing the alignment of orf4b from Kenya and other previously reported MERS-CoV strains from Africa compared to HCoV-EMC. Putative ORFs are represented in black and proteins are shown as gray bars. Stop codon are indicated by asterisks and amino acid lengths are indicated.