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

Abstract

Background: An 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.

Methods: We 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.

Results: Among 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.

Conclusions: The 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.

Keywords: Jordan; MERS-CoV; Middle East respiratory syndrome; coronavirus; emerging infectious disease; genome deletion; outbreak investigation; sero-epidemiology.

Figure 1.

Phylogenetic tree constructed from near complete Middle East respiratory syndrome coronavirus (MERS-CoV) genome sequences obtained from the 13 Jordan cases, indicated by solid-colored circles, and 240 previously published genome sequences in GenBank using the program MrBayes v3.2.6 [12] under a general time-reversible (GTR) model of nucleotide (nt) substitution with 4 categories of γ-distributed rate heterogeneity and a proportion of invariant sites (GTR + 4 + I). Clade-credibility values ≥70% are indicated at selected nodes. Circle colors correspond to transmitted deletion mutations: blue indicates 48-nt in-frame deletion in ORF4a; purple indicates 48-nt in-frame deletion in ORF4a and tandem 9-nt in-frame deletion in ORF3; and yellow indicates 48-nt in-frame deletion in ORF4a and tandem 726-nt out-of-frame deletion in ORF4b and 5. Case numbers assigned by the Jordan Ministry of Health are indicated within the circles. The scale bar shows the genetic distance as nt substitutions per site. ^aFor case 5, 2 sequence variants were detected: (i) a sequence with the ORF4a deletion only and (ii) a sequence with the ORF3 deletion and a tandem deletion in ORF3, 4a and 4b. Only the sequence with the ORF4a deletion is presented.

Figure 2.

Middle East respiratory syndrome coronavirus (MERS-CoV) deletion variants detected in individual cases, Jordan 2015. MERS-CoV deletions not drawn to scale. Deletion (∆): superscript numbers indicate genome assignment.

Figure 3.

Proposed transmission pathways and epidemiologic curve and for confirmed Middle East respiratory syndrome (MERS) cases, Jordan, 2015. Transmitted deletion variants are indicated by superimposed colored boxes. Box colors correspond to those used for case markers in Figure 1. The epidemiologic curve shows the date of illness onset or, for asymptomatic cases, the date of first positive MERS-CoV test. Case patients are indicated by the gray elements; element shape corresponds to the likely site of exposure. Case numbers are indicated within the elements, and “SA” indicates a patient detected in Saudi Arabia. A red outline indicates that the patient died. Arrows indicate likely epidemiologic links (dashed lines for likely healthcare links and solid lines for household links). For cases which may have overlapped in space or time but for which we have insufficient data to confidently propose direction of direct or indirect transmission links, no lines are displayed. *For case 5, 2 sequence variants were detected: (i) a sequence with the ORF4a deletion only and (ii) a sequence with the ORF3 deletion and a tandem deletion in ORF3, 4a and 4b.