Increase in Middle East Respiratory Syndrome-Coronavirus Cases in Saudi Arabia Linked to Hospital Outbreak With Continued Circulation of Recombinant Virus, July 1–August 31, 2015

Assiri, Abdullah M.; Biggs, Holly M.; Abedi, Glen R.; Lu, Xiaoyan; Bin Saeed, Abdulaziz; Abdalla, Osman; Mohammed, Mutaz; Al-Abdely, Hail M.; Algarni, Homoud S.; Alhakeem, Raafat F.; Almasri, Malak M.; Alsharef, Ali A.; Nooh, Randa; Erdman, Dean D.; Gerber, Susan I.; Watson, John T.

Genome sequencing was performed on specimens from 6 MERS cases with dates of illness onset ranging from June 27 to August 19, 2015 ( Figure 1A ). All 6 cases were either from Riyadh or had traveled to Riyadh within the exposure period. Four of the 6 cases were exposed to Hospital A as patients or visitors. Phylogenetic and recombinational analysis revealed that all 6 viruses were members of a recently described novel recombinant clade (NRC-2015). Sequences from cases linked to Hospital A were genetically similar ( Figure 1B) and distinct from 2 cases not linked to Hospital A. Of cases not linked to Hospital A, one had visited a relative (not a MERS case) in a Riyadh hospital where limited transmission had occurred, but the patient denied contact with a known MERS-CoV case. The other case was an 83-year-old man who resided in Jeddah, but he had visited Riyadh during the exposure period and had healthcare contact in both Riyadh (not Hospital A) and Jeddah for a chronic illness. The MERS-CoV sequence from this patient possessed a unique 20-nucleotide frameshift deletion spanning positions 387/388 to 407/408 of the nonstructural protein gene ORF5. Whereas native ORF5 is predicted to encode a 224-amino acid (aa) protein, the deletion would predict a 147-aa truncated protein consisting of the amino-terminal 129 aa of ORF5 plus 18 non-ORF5 residues prematurely terminating in an out-of-frame stop codon. This sequence clustered most closely with MERS-CoV sequences derived from 3 camels in April 2015 from Taif, SA, that lacked the deletion [4] (Figure 1B) . No definitive link to camels was identified for this patient; however, the patient was deceased and the interview was conducted with a relative.