Multihospital Outbreak of a Middle East Respiratory Syndrome Coronavirus Deletion Variant, Jordan: A Molecular, Serologic, and Epidemiologic Investigation

Abstract

BackgroundAn outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) in Jordan in 2015 involved a variant virus that acquired distinctive deletions in the accessory open reading frames. We conducted a molecular and seroepidemiologic investigation to describe the deletion variant’s transmission patterns and epidemiology.MethodsWe reviewed epidemiologic and medical chart data and analyzed viral genome sequences from respiratory specimens of MERS-CoV cases. In early 2016, sera and standardized interviews were obtained from MERS-CoV cases and their contacts. Sera were evaluated by nucleocapsid and spike protein enzyme immunoassays and microneutralization.ResultsAmong 16 cases, 11 (69%) had health care exposure and 5 (31%) were relatives of a known case; 13 (81%) were symptomatic, and 7 (44%) died. Genome sequencing of MERS-CoV from 13 cases revealed 3 transmissible deletions associated with clinical illness during the outbreak. Deletion variant sequences were epidemiologically clustered and linked to a common transmission chain. Interviews and sera were collected from 2 surviving cases, 23 household contacts, and 278 health care contacts; 1 (50%) case, 2 (9%) household contacts, and 3 (1%) health care contacts tested seropositive.ConclusionsThe MERS-CoV deletion variants retained human-to-human transmissibility and caused clinical illness in infected persons despite accumulated mutations. Serology suggested limited transmission beyond that detected during the initial outbreak investigation.

Genomic characterization of a novel SARS-CoV-2

“…The finding heavily supports an intense requirement for additional prompt, inclusive investigations that combine genomic detail, epidemiological information and graph records of the clinical features of patients with COVID-19 (Payne et al, 2018). In the future, mining these resources and establishing a statistical framework based on epidemiological, antigenic, and genetic information could provide further insights into the rules that govern the emergence and establishment of antigenically novel variants and improve the potential for SARS-CoV-2 prevention and control (Ge et al, 2013;Yang et al, 2015).…”

Scope and extent of healthcare-associated Middle East respiratory syndrome coronavirus transmission during two contemporaneous outbreaks in Riyadh, Saudi Arabia, 2017

“…28 The use of serologic testing to detect unrecognized infections in asymptomatic or mildly symptomatic individuals may be limited. 29 In both outbreaks, rapid identification of contacts, symptom monitoring, and repeated testing allowed for efficient detection of secondary HCP cases and provided information to guide outbreak management. Of the 25 HCP-cases, 10 were detected on initial rRT-PCR testing and 15 by repeated rRT-PCR testing, including multiple HCP cases who initially tested rRT-PCRnegative up to 7 days after known case exposure, indicating that asymptomatic or mildly symptomatic HCP may require repeated screening to rule out infection.…”

Molecular Evolution and Structural Mapping of N-Terminal Domain in Spike Gene of Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

“…Coronaviruses are known to undergo recombination [52], and it is considered to be related to an increase in pathogenicity in other animal RNA viruses [53]. There is, however, little evidence that recombination in MERS-CoV has caused substantial changes in human-to-human transmission.…”