Nosocomial outbreak of the Middle East Respiratory Syndrome coronavirus: A phylogenetic, epidemiological, clinical and infection control analysis

Abstract

Background: Middle East Respiratory Syndrome coronavirus (MERS-CoV) continues to cause intermittent community and nosocomial outbreaks. Obtaining data on specific source(s) and transmission dynamics of MERS-CoV during nosocomial outbreaks has been challenging. We performed a clinical, epidemiological and phylogenetic investigation of an outbreak of MERS-CoV at a University Hospital in Riyadh, Kingdom of Saudi Arabia. Methods: Clinical, epidemiological and infection control data were obtained from patients and Healthcare workers (HCWs). Full genome sequencing was conducted on nucleic acid extracted directly from MERS-CoV PCRconfirmed clinical samples and phylogenetic analysis performed. Phylogenetic analysis combined with published MERS-CoV genomes was performed. HCWs compliance with infection control practices was also assessed. Results: Of 235 persons investigated, there were 23 laboratory confirmed MERS cases, 10 were inpatients and 13 HCWs. Eight of 10 MERS inpatients died (80% mortality). There were no deaths among HCWs. The primary index case assumed from epidemiological investigation was not substantiated phylogenetically. 17/18 MERS cases were linked both phylogenetically and epidemiologically. One asymptomatic HCW yielded a MERS-CoV genome not directly linked to any other case in the investigation. Five HCWs with mild symptoms yielded >75% full MERS-CoV genome sequences. HCW compliance with use of gowns was 62.1%, gloves 69.7%, and masks 57.6%. Conclusions: Several factors and sources, including a HCW MERS-CoV 'carrier phenomenon', occur during nosocomial MERS-CoV outbreaks. Phylogenetic analyses of MERS-CoV linked to clinical and epidemiological information is essential for outbreak investigation. The specific role of apparently healthy HCWs in causing nosocomial outbreaks requires further definition.

Clinical characteristics and outcomes of hospitalized COVID-19 patients in a MERS-CoV referral hospital during the peak of the pandemic

“…The Middle East Respiratory Syndrome Corona Virus (MERS-CoV) originated in KSA (Zaki et al, 2012) and is the only country in the world where it is still endemic, causing multiple nosocomial outbreaks (Alenazi et al, 2017;Amer et al, 2018;Assiri et al, 2013;Balkhy et al, 2016;Barry et al, 2020c;Drosten et al, 2015;Fagbo et al, 2015;Oboho et al, 2015). At the time of writing, the most recent reported case of MERS-CoV was on May 31, 2020 (Saudi Arabia Ministry of Health, n.d.a, n.d.b).…”

SARS-CoV-2 B.1.1.7 lineage-related perceptions, COVID-19 vaccine acceptance and travel worry among healthcare workers

“…These expatriate nurses usually reside in housing compounds with shared rooms and facilities [13], but during an epidemic, such arrangements can be hazardous to the health care system. A previous MERS-CoV hospital outbreak in Saudi Arabia was in part related to such accommodations [14]. Recently, HCWs in Saudi Arabia were exempted from the travel bans.…”

Structural modeling and phylogenetic analysis for infectious disease transmission pattern based on maximum likelihood tree approach

“…The pathogenic phylogeny structure may reflect the option of immunological strains, disease dynamics, and spatial spread patterns (Ragonnet-Cronin et al 2019 ). Evolutionary tree or phylogenetic tree analysis is a branching figure or tree presenting the evolutionary relationship between different biological species (Barry et al 2020 ). The phylogenetic tree characterizes the sampled pathogens clonal ancestry; its leaves are sampled pathogens, and interior nodes are the recent collective ancestors of the transmitted and sampled pathogens (de Bernardi Schneider et al 2020 ).…”