Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates

Abstract

Camels are known carriers for many viral pathogens, including Middle East respiratory syndrome coronavirus (MERS-CoV). It is likely that there are additional, as yet unidentified viruses in camels with the potential to cause disease in humans. In this study, we performed metagenomic sequencing analysis on nasopharyngeal swab samples from 108 MERS-CoV-positive dromedary camels from a live animal market in Abu Dhabi, United Arab Emirates. We obtained a total of 846.72 million high-quality reads from these nasopharyngeal swab samples, of which 2.88 million (0.34%) were related to viral sequences while 512.63 million (60.5%) and 50.87 million (6%) matched bacterial and eukaryotic sequences, respectively. Among the viral reads, sequences related to mammalian viruses from 13 genera in 10 viral families were identified, including Coronaviridae, Nairoviridae, Paramyxoviridae, Parvoviridae, Polyomaviridae, Papillomaviridae, Astroviridae, Picornaviridae, Poxviridae, and Genomoviridae. Some viral sequences belong to known camel or human viruses and others are from potentially novel camel viruses with only limited sequence similarity to virus sequences in GenBank. A total of five potentially novel virus species or strains were identified. Co-infection of at least two recently identified camel coronaviruses was detected in 92.6% of the camels in the study. This study provides a comprehensive survey of viruses in the virome of upper respiratory samples in camels that have extensive contact with the human population.

A systematic review of MERS-CoV (Middle East Respiratory Syndrome Coronavirus) seroprevalence and viral RNA prevalence in dromedary camels: implications for animal vaccination

“…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%) (45, 46, 49-51, 70), UAE (0-29% (62–66) or 0-100% if dromedaries epidemiologically linked to human MERS-CoV cases are included(67–69)), Qatar (22-79%) (15, 58, 71, 72), Oman (7%) (55), Iraq (15%) (34), and Jordan (62%) (39), as well as Egypt (4-15%) (27, 29, 30), Ethiopia (10%) (23), Kenya (0.35-0.95%) (43, 44), Nigeria (3-11%) (53, 54), Burkina Faso (5%) (23), Morocco (2%) (23), and Pakistan (3%) (57). See Fig 4 for a map of RNA prevalence, and Table 1).…”

A Preliminary Study of the Virome of the South American Free-Tailed Bats (Tadarida brasiliensis) and Identification of Two Novel Mammalian Viruses

“…In addition, in previous studies, the authors aimed to establish nine genera within the family Genomoviridae based on pairwise comparisons of complete genome sequences [70]. CRESS DNA viruses, including genomoviruses, have been found in association with a great variety of animal species, such as camels [98], bats [89], mongooses, badgers [99], wolves [100], pigs [101], and humans [102], as well as in environmental-associated [103] and plant-associated [104] samples. However, no direct implication with a disease has been demonstrated so far.…”

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

“…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.…”