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facilitate early recognition of suspect cases, followed by imple- mentation of appropriate infection prevention and control (IPC) measures.4 MERS-CoV may be transmitted by close contact that likely includes respiratory droplets, but transmission routes are still not fully understood.7 Both the Saudi Arabia Ministry of Health (MoH) and the World Health Organization (WHO) recommend MERS-CoV-specific precautions for healthcare set- tings to reduce the risk of healthcare-associated transmission.8,9 From May 28 through June 19, 2017, 2 hospitals in Riyadh,
Saudi Arabia, reported MERS CoV outbreaks; epidemiologic links between the 2 hospitals were not apparent, and the extent of circulation was unknown. The outbreaks were initially reported by WHO in July 2017.10 The MoH and US Centers for Disease Control and Prevention (CDC) conducted an investigation to describe the scope of healthcare-associated transmission using epidemiologic, molecular, and serologic methods.
Methods Setting
The investigation was conducted at 4 healthcare facilities in Riyadh, Saudi Arabia, where cases presented: (1) hospital A, a 1,200-bed tertiary-care MoH hospital with 140 intensive-care unit (ICU) beds and a busy emergency department (ED); (2) hospital B, a 200-bed MoH specialty pulmonary hospital; (3) clinic C, an outpatient clinic; and (4) an outpatient dialysis unit.
Outbreak investigation
We defined a case as any patient with laboratory-confirmed MERS-CoV infection and an epidemiologic connection to the affected healthcare facilities as a patient, HCP, visitor or family member of a patient from May 28 through June 19, 2017. Laboratory confirmation was performed either at the MoH using a rRT-PCR assay targeting both the region upstream of the E gene (UpE) and open reading frame (ORF) 1a11,12 or at the CDC by genome sequencing. An indeterminate rRT-PCR result was defined as positive result on only 1 of the 2 gene targets required for confirmation. We defined a superspreading event as any inter- action in which a MERS case transmitted to ≥5 subsequent cases. Patients with symptoms consistent with MERS and contacts
exposed to identified cases were tested. Contact investigations were performed by hospital infection control personnel, local public health authorities, and MoH personnel. MoH recommends MERS-CoV testing of HCP identified with prolonged, close contact with a MERS case (ie, >10 minutes within 1.5m) if not properly wearing personal protective equipment (PPE).13 In addition to recommended testing, ad hoc testing of HCP contacts with various levels of exposure and PPE use occurred. We reviewed available medical and public health records for all cases and conducted key-informant interviews with HCP. We collected sera and interviewed available HCP cases and
HCP identified as rRT-PCR–negative contacts. Interview forms included questions related to demographics, occupation, expo- sures, PPE use, symptoms, and underlying medical conditions.
Methods Genome sequencing and phylogenetic analysis
Available MERS-CoV rRT-PCR–positive samples from confirmed cases collected from May 28 through June 19, 2017, were stored at
Khalid H. Alanazi et al
−80°C and shipped to the CDC for further molecular analysis. Sample aliquots (200 µL) were extracted on a NucliSens Easy- MAG (BioMerieux, Marcy-l'Étoile, France), and 100 µL of total nucleic acid was recovered. The specimen extracts were retested by MERS-CoV N2 and/or N3 real-time rRT-PCR assays,14 and genome sequencing was performed on positive samples with sufficient viral load using the previously described primer sets and protocol.15,16 The nucleotide sequences were first aligned in MAFFT version
7.013 multiple-sequence alignment software. Phylogenetic trees were inferred using the maximum likelihood (ML) method with PhyML version 3.0 software,17 assuming a general time-reversible (GTR) model with a discrete γ-distributed rate variation among sites (γ4) and an SPR tree-swapping algorithm and visualized using MEGA version 6 software.18
Serology
Serum samples were tested at the CDC for anti-MERS-CoV antibodies using indirect ELISAs for nucleocapsid (N) and spike (S) proteins followed by a confirmatory microneutralization test (MNT) as previously described.19 At the optical density cutoffs used by our laboratory, the N ELISA has a sensitivity of 88.9% and a specificity of 92.2%, and the S ELISA has a sensitivity of 90.8% and a specificity of 90.8% (unpublished data). MERS-CoV seropositivity was defined as having 2 of 3 positive assays, including N-ELISA, S-ELISA, and MNT, or positive by MNT alone. Indeterminate seropositivity was defined as S ELISA positive, but N ELISA and MNT-negative.
Ethics
This investigation was determined by MoH and CDC to be public health response, not research, and therefore was not subject to institutional review board (IRB) review. Signed consent was obtained from seroepidemiologic investigation participants. Inter- views were conducted in Arabic, English, Filipino, or Malayalam.
Results Outbreak investigation
We identified 48 MERS cases, including 38 linked to hospital A and 10 linked to hospital B (Fig. 1 and Table 1). At both hospitals, transmission was traced to a single introduction by the respective index cases (Fig. 2). Index patient A presented at hospital A on May 28, and index patient B presented at hospital B on June 2. No epidemiologic link was established between these cases. Respiratory specimens from 36 MERS-CoV cases were received
by the CDC: 35 were confirmed positive by rRT-PCR and 1 positive specimen could not be confirmed by MERS-CoV N2 and/or N3 rRT-PCR assays but was confirmed by sequencing the spike gene. Phylogenetic analysis of 95 MERS-CoV genomes, including 21 complete or nearly complete genomes in this study, showed clus- tering of the outbreak sequences in lineage 5 within clade B15,20 (Fig. 4). The outbreak sequences from each hospital formed a mono- phyletic group and separated into 2 distinct clusters, suggesting 2 distinct outbreaks. The hospital A cluster appears to have been closely related to camel MERS-CoV (KT368879) and human MERS-CoV (MG011358) sampled at Riyadh in 2015 and 2016 respectively. The hospital B cluster appears to have been more
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