Diversity of Middle East respiratory syndrome coronaviruses in 109 dromedary camels based on full-genome sequencing, Abu Dhabi, United Arab Emirates

Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) was identified on the Arabian Peninsula in 2012 and is still causing cases and outbreaks in the Middle East. When MERS-CoV was first identified, the closest related virus was in bats; however, it has since been recognized that dromedary camels serve as a virus reservoir and potential source for human infections. A total of 376 camels were screened for MERS-Cov at a live animal market in the Eastern Region of the Emirate of Abu Dhabi, UAE. In all, 109 MERS-CoV-positive camels were detected in week 1, and a subset of positive camels were sampled again weeks 3 through 6. A total of 126 full and 3 nearly full genomes were obtained from 139 samples. Spike gene sequences were obtained from 5 of the 10 remaining samples. The camel MERS-CoV genomes from this study represent 3 known and 2 potentially new lineages within clade B. Within lineages, diversity of camel and human MERS-CoV sequences are intermixed. We identified sequences from market camels nearly identical to the previously reported 2015 German case who visited the market during his incubation period. We described 10 recombination events in the camel samples. The most frequent recombination breakpoint was the junctions between ORF1b and S. Evidence suggests MERS-CoV infection in humans results from continued introductions of distinct MERS-CoV lineages from camels. This hypothesis is supported by the camel MERS-CoV genomes sequenced in this study. Our study expands the known repertoire of camel MERS-CoVs circulating on the Arabian Peninsula.

A systematic review of MERS-CoV seroprevalence and RNA prevalence in dromedary camels: Implications for animal vaccination

“…All available studies followed animals that were found to be MERS-CoV RNA positive at the first instance of sampling and the duration of shedding prior to sampling is unknown. Further to this, intermittent RNA shedding, and evidence of potential rapid reinfection/ coinfection has been observed (Muhairi et al, 2016;Yusof et al, 2017).…”

“…Our search found that dromedary populations in 16 countries have been tested for MERS-CoV RNA, 13 of which report positive results indicating active infection. These include KSA (0.12-56%) (Alagaili et al, 2014;Khalafalla et al, 2015;Sabir et al, 2016;Alfuwaires et al, 2017;Kasem et al, 2018a, b), UAE (0-29% (Wernery et al, 2015a, b;Yusof et al, 2015;Li et al, 2017;Yusof et al, 2017) or 0-100% if dromedaries epidemiologically linked to human MERS-CoV cases are included(Al Hammadi et al, 2015;Muhairi et al, 2016;Paden et al, 2018)), Qatar (22-79%) Reusken et al, 2014a;Farag et al, 2015;Mohran et al, 2016), Oman (7%) (Nowotny and Kolodziejek, 2014), Iraq (15%) (Al Salihi and Alrodhan, 2017), and Jordan (62%) (van Doremalen et al, 2017), as well as Egypt (4-15%) , Ali et al, 2017a, Ethiopia (10%) (Miguel et al, 2017), Kenya (0.35-0.95%) (Kiambi et al, 2018;Ommeh et al, 2018), Nigeria (3-11%) So et al, 2018), Burkina Faso (5%) (Miguel et al, 2017), Morocco (2%) (Miguel et al, 2017), and Pakistan (3%) . See Fig.…”

“…We found 10 longitudinal studies describing 9 incidences of natural infection on farms and in quarantine facilities -1 in Egypt (Ali et al, 2017b), 4 in KSA (Azhar et al, 2014;Hemida et al, 2014a;Memish et al, 2014;Hemida et al, 2017a), 5 in UAE (Al Hammadi et al, 2015;Wernery et al, 2015a;Meyer et al, 2016;Muhairi et al, 2016;Yusof et al, 2017) and 1 study taking monthly samples of 430 dromedaries in Kenya (Kiambi et al, 2018).…”

“…Four studies of natural infection measured viral shedding in dromedaries at approximately weekly intervals. The maximum time window in which all consecutive nasal samples taken were positive for MERS-CoV RNA ranged from 7 to 45 days across published studies, with most positive animals becoming negative within 2 weeks (Al Hammadi et al, 2015;Wernery et al, 2015a;Muhairi et al, 2016;Yusof et al, 2017). All available studies followed animals that were found to be MERS-CoV RNA positive at the first instance of sampling and the duration of shedding prior to sampling is unknown.…”

Genetic diversity of MERS-CoV spike protein gene in Saudi Arabia

“…The emergence of dominant and recombinant MERS-CoV which caused a human outbreak in 2015 has been reported from camel [3]. The zoonotic introduction was suspected after the MERS-CoV identification [18] and in a recent study from UAE the genetic diversity of MERS-CoV full-genome from both human and dromedary camel was analyzed, and very closed sequence similarity was observed which confirms the zoonotic introductions [20,21]. Additionally, the zoonotic introduction time and seasons play an important role in the disease spread.…”