Enzootic patterns of Middle East respiratory syndrome coronavirus in imported African and local Arabian dromedary camels: a prospective genomic study

Abstract

Background The Middle East respiratory syndrome coronavirus (MERS-CoV) is a lethal zoonotic pathogen endemic to the Arabian Peninsula. Dromedary camels are a likely source of infection and the virus probably originated in Africa.We studied the genetic diversity, geographical structure, infection prevalence, and age-associated prevalence among camels at the largest entry port of camels from Africa into the Arabian Peninsula.Methods In this prospective genomic study, we took nasal samples from camels imported from Sudan and Djibouti into the Port of Jeddah in Jeddah, Saudi Arabia, over an almost 2-year period and local Arabian camels over 2 months in the year after surveillance of the port. We determined the prevalence of MERS-CoV infection, age-associated patterns of infection, and undertook phylogeographical and migration analyses to determine intercountry virus transmission after local lineage establishment. We compared all virological characteristics between the local and imported cohorts. We compared major gene deletions between African and Arabian strains of the virus. Reproductive numbers were inferred with Bayesian birth death skyline analyses. FindingsBetween Aug 10, 2016, and May 3, 2018, we collected samples from 1196 imported camels, of which 868 originated from Sudan and 328 from Djibouti, and between May 1, and June 25, 2018, we collected samples from 472 local camels, of which 189 were from Riyadh and 283 were from Jeddah, Saudi Arabia. Virus prevalence was higher in local camels than in imported camels (224 [47·5%] of 472 vs 157 [13·1%] of 1196; p<0·0001). Infection prevalence peaked among camels older than 1 year and aged up to 2 years in both groups, with 255 (66·9%) of 381 positive cases in this age group. Although the overall geographical distribution of the virus corresponded with the phylogenetic tree topology, some virus exchange was observed between countries corresponding with trade routes in the region. East and west African strains of the virus appear to be geographically separated, with an origin of west African strains in east Africa. African strains of the virus were not re-sampled in Saudi Arabia despite sampling approximately 1 year after importation from Africa. All local Arabian samples contained strains of the virus that belong to a novel recombinant clade (NRC) first detected in 2014 in Saudi Arabia. Reproduction number estimates informed by the sequences suggest sustained endemicity of NRC, with a mean R e of 1·16. Interpretation Despite frequent imports of MERS-CoV with camels from Africa, African lineages of MERS-CoV do not establish themselves in Saudi Arabia. Arabian strains of the virus should be tested for changes in virulence and transmissibility.

Middle East respiratory syndrome

“…[27][28][29] Full-genome phylogenetic analysis indicates that evolution of diverse MERS-CoV lineages in camels have caused human infections, perpetuating a low barrier for interspecies transmission. 21,29,30 However, African MERS-CoV lineages in camels imported into Saudi Arabia have not established themselves in camels in Saudi Arabia, 9,30 indicating potential differences in transmission dynamics and selection pressure. Analysis of population dynamics shows that Arabian viruses can maintain endemicity without introduction of additional lineages.…”

“…Analysis of population dynamics shows that Arabian viruses can maintain endemicity without introduction of additional lineages. 9,30 WHO is supporting molecular and serological studies at the dromedary-human interface in several countries in Africa and south Asia. 31 The phylogenetic relationship of complete genomes of MERS-CoV strains obtained from camels and humans has been published.…”

“…4 Given that MERS-CoV appears to be highly endemic among dromedary camels from geographically widespread areas of the Middle East and Africa, zoonotic transmission with consequent risk of human epidemics will most likely continue for years to come. 8,9 MERS-CoV endemic and at-risk countries must invest more in surveillance, in public health research, and in medical interventionsincluding human and camel vaccine development. The continued risk of human MERS-CoV outbreaks 7 years after its first discovery, effective human and camel MERS-CoV vaccines appear to be the ideal way to prevent continuing spread of MERS-CoV in dromedary camels in the Middle East and in humans at high risk of acquiring community and nosocomial MERS-CoV infection.…”

“…7 MERS-CoV is considered a zoonotic pathogen, with MERS-CoV-infected dromedary camels being the animal source of infection to humans. 8,9 Unlike SARS-CoV, which was contained within a year of emerging, MERS-CoV continues to circulate and cause human disease with intermittent sporadic cases, community clusters, and nosocomial outbreaks in the Middle East with considerable risk of spreading globally. 2,10 Several outbreaks of human-to-human MERS-CoV trans mission have occurred, the largest outside the Middle East occurring in South Korea in 2015.…”

COVID-19: A critical care perspective informed by lessons learnt from other viral epidemics

“…In addition, it is about 79% akin to severe acute respiratory syndrome coronavirus (SARS-CoV) and 50% related to Middle East respiratory syndrome coronavirus (MERS-CoV). The latter two coronaviruses have their immediate origins from civets and camels, respectively [4,5]. Although it is uncertain how COVID-19 transmission from animals to humans occurred, epidemiological studies suggested an intermediary wild animal host sold in the Huanan Seafood Wholesale Market [6].…”