key: cord-0988315-3e3hs9ay
authors: Barry, Mazin; Phan, My VT.; Akkielah, Layan; Al-Majed, Fahad; Alhetheel, Abdulkarim; Somily, Ali; Alsubaie, Sarah Suliman; McNabb, Scott JN.; Cotten, Matthew; Zumla, Alimuddin; Memish, Ziad A.
title: Nosocomial outbreak of the Middle East Respiratory Syndrome coronavirus: A phylogenetic, epidemiological, clinical and infection control analysis
date: 2020-06-27
journal: Travel Med Infect Dis
DOI: 10.1016/j.tmaid.2020.101807
sha: ecb8b9098f3361c9437cfb8f10997ace7d5c6647
doc_id: 988315
cord_uid: 3e3hs9ay

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 PCR-confirmed 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 of 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.

information is important for identifying the index case, source(s) of transmission, 2 transmission patterns, surveillance and evolution of MERS-CoV genomes (6, 7, 9, 13) . 3

Genomic sequencing of MERS-CoV and molecular epidemiology can reveal 4 spatiotemporal patterns that help identify whether all MERS-CoV infections originated 5 from a single or multiple source(s), with subsequent human-to-human transmission, or 6 from several sources. The focus of nosocomial outbreaks is usually on instituting 7 infection control measures, identification of the primary MERS case, preventing further 8 nosocomial spread between patients and healthcare workers (15 ) . Whilst clinical and 9 epidemiological information are usually available from outbreak response, obtaining 10 phylogenetic information remains challenging and has not been forthcoming from KSA 11 since 2015. In a review by Grant et.al. the prevalence of asymptomatic and mildly 12 symptomatic MERS amongst Health Care Workers (HCW) was 11% and 26% 13 respectively (16). The possible role of mildly symptomatic or asymptomatic MERS-CoV-14 infected healthcare workers as 'carriers' of MERS-CoV has been highlighted and needs 15 further investigation (15) (16) (17) (18) (19) . CoV. 50 μL of nucleic acid was generated from 200 μL of tracheal aspirate or from a 2 nasopharyngeal or throat swab with automated processing. PCR amplification of DNA 3 amplicons covering the entire MERS-CoV genome were prepared. The PCR amplicons 4 for each sample were pooled for Illumina library (Illumina, San Diego, CA, USA) 5 preparation with each sample processed to include a unique barcode sequence. 6

Standard MiSeq 150nt paired-end reads were generated. Sequence data were de-7 multiplexed into sample-specific readsets, processed to remove adapter and primer 8 sequences at the ends of reads, and trimmed from their 3′ end until the median Phred 9 quality score was >35, discarding reads smaller than 125 nucleotides using QUASR 10 (22). The processed readsets were de novo assembled into large contiguous 11 sequences (contigs) using SPAdes v.3.13.0 (23 

A total of 23 laboratory confirmed MERS cases were diagnosed during the outbreak: 10 11 were patients and 13 healthcare workers. The description of the outbreak is described 12 in terms of Cases # and HCW # in respect to chronological diagnosis: 13 14

The first identified MERS case (Case #1) was a male gentleman in his 40s-who 15 presented to an outside hospital with acute myocardial infarction, he was transferred to 16 our institution for coronary artery bypass grafting. On the first post-operative day he was 17 extubated and during the ensuing days he mobilized well and socialized with other 18 patients in neighbouring rooms in the cardiac surgery ward including patients who were 19 later identified as Case #2 and Case #3. 20

On the 4 th post-operative day Case #1 developed fever, chest pain, shortness of breath 21 (SOB), and was diagnosed with pneumonia and a MERS-CoV PCR test from a 22 respiratory sample returned to be positive. He was transferred to critical care unit 23 where he died four weeks later, he was identified epidemiologically as the index case, in 1 the meantime Case #2 was discharged home before onset of symptoms, only to return 2 to ER nine days later with fever and SOB, he was placed in RU without AIIR adjacent to 3

Case #4 who was already in RU for an upper gastrointestinal bleed, nine days later she 4 developed SOB and fever . Case #3 who was still in cardiac surgery ward at the same 5 time developed fever and SOB and was transferred to ICU, all three new cases 6

nasopharyngeal swabs (NPS) tested positive by PCR for MERS-CoV, and all died. First 7 HCW identified be infected (HCW#1) developed fever and cough two days after caring 8

for Case #4 in RU. Case #5 was placed in RU between Case #2 and Case #4 in a 9

"disaster bed" without any barrier due to an overwhelmingly busy ER and was 10 transferred to cardiac ward prior to onset of respiratory symptoms that developed ten 11 days later in the form of cough, he ultimately recovered, while both other two cases 12 died. Second, third, fourth and fifth infected HCWs (HCW #2, HCW #3, HCW #4 and 13 HCW #5) cared for both Case #2 and Case #4 and were commonly mingling with HCW 14 #1. The 6 th HCW (HCW #6) did NPS for Case #4 without personal protective equipment 15 (PPE). Case #6 was in a common room in cardiac ward adjacent to Case #5. HCW #7 16 and HCW #8 worked in RU and cared for Case #2. Case #7 was diagnosed in a 17 separate ward and was not linked epidemiologically to any of the previous cases or 18

HCWs, she died. HCW# 9 worked in RU and cared for Case #4. HCW# 10 was in direct 19 contact with HCW #3. Case #8 was in also in a common room with Case #5 and Case 20 #6, both Case#8 and Case#6 died. HCW #11 was also in contact with Case #4. HCW 21 #12 was in contact with HCW#1 and was asymptomatic only detected by contact 22

tracing. Case #9 was admitted in a common room adjacent to Case #7, and ultimately 23 recovered. HCW #13 intubated Case #6 without PPE. Case #10 was admitted in a common room adjacent to Case #5. The outbreak primarily affected RU in ER and 1

Cardiac ward and was declared clear 14 days after the death of Case #10. 2 3 Eleven of the thirteen HCWs were symptomatic with only mild symptoms, one was 4 totally asymptomatic who was detected by contact tracing, and one had severe disease 5 that required ICU admission but ultimately recovered. 225 HCWs who were the total increasing space between patient beds to >3 meters in ER, placing a physical ceramic 19 barriers between beds in RU instead of curtains between beds, eliminating "disaster 20 beds", use of disposable curtains at bed entry points, allocating a new mobile building 21 outside ER for triaging and screening patients with acute respiratory illness (ARI), strict 22

adherence to IPC measures with log-in and log-out checklist for each personal 23 protective equipment (PPE) item used by HCW, 14-days of sick leave (the incubation 1 period) to all known MERS-CoV negative asymptomatic HCW contacts. Case #23, = Lineage A0) and the Case #2 genome were basal to Lineage A1 ( Figure  12 2A) This can also be seen in the pattern of SNPs across the genome set with all 13 genomes sharing SNPs or derived from earlier genomes by the additional of one or a 14 few SNPs (Figure 1b) . Of interest, Case #2 differed from Lineage A0 by a single 15 nucleotide (position 3932). Lineage A0 to A1 differed by a single nucleotide (Figure 1b) . 16 b. Within the clusters there were epidemiological features (shared room, contact, or 17 caregiver, with appropriate timing) that supported a transmission chain. For example, 18 the genomes from Case #6, Case #12 and Case #23 clustered closely phylogenetically, 19

and shared unique SNPs (Figure 1b) . The linked Case #6 and Case #12 shared a room 20

and Case #23 was in the next room. Furthermore Case #4 shared a room with Case #2 21 providing links to later cases and HCW_5 and HCW_11 cared for Case #4.

c. The genome from Case #2 appears basal to the cluster and this indicates that Case 1 #2 may be the source for the outbreak (rather than Case #1 which was implicated by 2 the clinic-epidemiological outbreak investigation). 3 d. The genome from HCW #16 has multiple SNPs that are not shared with any other 4 genomes (Figure 1b) . HCW #16 was mildly symptomatic and had contact with Case #4. suctioning 22 (33.3%); intubation 5 (7.6%); sputum induction 9 (13.6%); and handled 20 viral transport media (VTM) 5 (7.6%). HCW #5, HCW #11, HCW #16, HCW #19 did not 21 use N95 mask during aerosolizing procedure, HCW #22 used non-fit tested N95 mask 22 during intubation. (please refer to Materials and Methods for more info), based on which the nucleotide 28 differences from the putative index genome from Case 2 (16023_1_cs2_0734) were 29 identified. Nucleotide changes to A were marked in orange, to T in red, to G in dark 30

blue, to C in light blue and gaps in the second genome with marked in grey. The positions of the major MERS-CoV genes are shown in the upper panel. The major 1 cluster A1, the minor clusters A0 and B and the outlier genome from Case_#1 and 2 HCW#16 are marked to the right of the panel. 

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(16023_1_cs2_0734) were identified. Nucleotide changes to A were marked in orange, to T in red, to G in 11 dark blue, to C in light blue and gaps in the second genome with marked in grey. The positions of the 12 major MERS-CoV genes are shown in the upper panel