Figure 1

Figure 1. Biphasic Middle East respiratory syndrome coronavirus (MERS-CoV) incidence in dromedaries sampled in an abattoir hub, northern Kenya, 2022–2023. A) MERS-CoV RNA detection rates in nasal swab specimens from dromedary camels...

Our sampling site was an abattoir hub in Isiolo, northern Kenya, where camels from Marsabit, Samburu, and Isiolo counties are slaughtered (Appendix Figure 1). During September 2022–September 2023, we took samples from 10–15 dromedary camels 4–5 days per week (Appendix). The camels (n = 2,711) were originally from 12 different administrative wards, mainly from Laisamis in Marsabit County (n = 1,841, 67.9%) and Burat in Isiolo County (n = 578, 21.3%) (Table; Appendix Figure 1). MERS-CoV RNA was detected in 36/2,711 (1.3%) (Table; Figure 1) camels using quantitative reverse transcription PCR, which amplifies the upstream of the envelope E gene, and confirmed by open reading frame (ORF) 1ab quantitative reverse transcription PCR or sequencing (Appendix). The cumulative RNA positivity rate was higher in September–October 2022 at 19/381 (5.0%) compared with 17/727 (2.3%) in January–March 2023 (Figure 1). Incidence was biphasic, showing detection peaks in the first weeks of October 2022 (7/60, 11.7%) and February 2023 (7/58, 12.1%) (Figure 1, panel B). For 9/36 MERS-CoV–positive samples, we obtained ORF1ab sequences and performed phylogenetic analysis. The 9 ORF1ab sequences were highly similar (>99.93% nucleotide identity) and had 99.75%–99.78% nucleotide identity with the closest MERS-CoV relative identified in Akaki, Ethiopia, in 2019 (9). Phylogenetic analysis showed that the 9 sequences clustered as a monophyletic group within clade C2.2, which encompasses East Africa strains initially detected in Kenya in 2018 (10) (Appendix Figure 2). Those sequences represent 3 putative MERS-CoV outbreaks occurring contemporarily in camels in Kenya (Appendix Table 1).

To test whether biphasic MERS-CoV RNA–positivity is accompanied by increased MERS-CoV IgG levels, we tested randomized camel serum samples (n = 369/2,711) by MERS-CoV S1 ELISA (Appendix). MERS-CoV IgG levels showed a median optical density ratio (ODR) of 2.14 (95% CI 0.59–3.48) and a seroprevalence of 80.76% (298/369) (Appendix Figure 3, panel A). Lowest IgG levels were identified in June (median ODR 1.28, 95% CI 0.20–3.31), whereas the highest levels were seen in March (median ODR 2.72, 95% CI 1.67–3.76). MERS-CoV IgG levels were negatively associated with RNA-positivity (Odds ratio [OR] 0.20, 95% CI 0.09–0.44; p<0.0001) (Appendix Figure 3, panel B). RNA-positivity was negatively associated with the season (dry vs. wet, OR 0.14, 95% CI 0.06–0.30; p<0.0001). Male camels were more likely to be RNA positive (OR 3.94, 95% CI 0.86–29.2; p = 0.11) and less likely to be seropositive (OR 0.27, 95% CI 0.08–0.77; p = 0.021) than were female camels. Older animals (>3 years of age) were more likely to be seropositive (86%) than were animals ≤3 years of age (72%), but this difference was not statistically significant.

Figure 2

Figure 2. MERS-CoV immune responses in camel-exposed abattoir workers in Isiolo, Kenya. A) Results of commercial MERS-CoV S1-protein ELISA to detect IgG responses in 48 serum samples (diluted 1:100) from Isiolo abattoir...

Seroepidemiologic studies have suggested that abattoir workers in contact with dromedaries are at increased risk for MERS-CoV exposure (11). Seroconversion of subclinical MERS cases might be missed when diagnostically implemented ELISA cutoffs of commercial kits (e.g., ODR = 1.1 for IgG positives) are applied (11,12). We identified MERS-CoV S1 IgG reactivity (ODR >0.2) in 7/48 (14.6%) of Isiolo abattoir workers (Figure 2, panel A). We excluded SARS-CoV-2 infection– or vaccine–induced antibody cross-reactivity with MERS-CoV S1 by comparison of ELISA ODRs of MERS-CoV S1–based with SARS-CoV-2 S1–based ELISA (Appendix Table 2, Figure 4). A control cohort (n = 12) with no history of camel exposure showed no MERS-CoV S1 IgG reactivity (0/12; 0%) despite high SARS-CoV-2 S1 IgG levels (11/12; 92%) (Appendix Table 2).

Neutralization tests (NT) based on GFP-encoding vesicular stomatitis virus pseudoparticles (VSVpp) carrying the MERS-CoV S protein from clade A EMC/2012 or clade C2.2 (Kenya) showed that 1/7 serum samples (1:20 dilution) had a VSVpp-NT 50% reduction of foci-forming units for EMC/2012 and a 90% reduction for Kenya VSVpp-S (Figure 2, panel B). A MERS-CoV EMC/2012-based plaque-reduction neutralization test (PRNT) showed a 50% PRNT at the 1:20 dilution, fulfilling the World Health Organization criteria for a confirmed MERS-CoV seroconversion. None of 6 selected MERS-CoV S1 ELISA-negative abattoir samples showed neutralizing capacity when tested by VSVpp-NT and PRNT (Appendix Table 2).

Our sustained sampling of dromedary camels showed a biphasic MERS-CoV incidence in northern Kenya not observed in previous studies (1,10,13). One explanation might be the short time of virus excretion in MERS-CoV–infected dromedaries (14), making viral RNA detection difficult without daily surveillance. Phylogenetic analysis suggests that we identified >3 MERS-CoV clusters over 3 different weeks in dromedaries originating from different wards. The first potential factor likely influencing the outbreaks is increased animal-to-animal interactions, because camels from different herds are transported to Isiolo and kept in holding pens together before slaughter, which could enhance MERS-CoV outbreaks. Second, increased interactions between immunologically naive and infected animals during transport and in holding pens increases the probability of transmitting MERS-CoV. That hypothesis is supported by the high percentage of IgG–negative adult camels (19.24%, ODR<0.3) (1,7). Although identifying the exact MERS-CoV transmission scenario between camels is logistically difficult, rapid point-of-care tests might help trace infections even in resource-limited conditions.

The overall biphasic MERS-CoV incidence might be linked to seasonal factors, such as the biannual alternating wet and dry seasons in northern Kenya. During dry seasons, herds congregate using limited forage, then migrate back to the point of origin in wet seasons. Because calves are mainly born during the 2 wet seasons, the loss of protection by maternal antibodies coincides with the dry seasons. Of note, the 2 dry seasons during July–October 2022 and January–February 2023 matched the peaks of MERS-CoV RNA–positivity in October 2022 and February 2023. The combination of immunologically naive, possibly infected camel calves and the dry season–specific increased population density and probability of contact at limited waterholes might encourage MERS-CoV infections and transmissions among camels.

We identified 7/48 abattoir workers with putative MERS-CoV exposure or past subclinical infection by implementing ELISA ODR cutoffs previously shown to be suitable for seroepidemiologic studies outside clinical settings. In 1/7 cases, we confirmed MERS-CoV neutralizing antibodies by VSVpp-based NT and PRNT. None of the abattoir workers experienced severe symptoms in recent years, supporting the hypothesis that clade C strains might have limited pathogenicity and transmissibility (15). Identifying defined factors that drive MERS-CoV outbreaks will assist in predictive epidemiology, risk assessment, and timely precautionary interventions for public and occupational health.