A25 Phylogenetic analysis of the nucleocapsid and RNA-dependent RNA polymerase fragments of the first imported case of middle east respiratory syndrome coronavirus (MERS-CoV) infection in the Philippines from Saudi Arabia, February 2015

We report the first laboratory-confirmed case of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection from a patient returning to the Philippines from the Kingdom of Saudi Arabia (KSA). MERS-CoV was first identified in 2012 circulating in Middle Eastern countries with outbreaks occurring in KSA, the United Arab Emirates (UAE), and South Korea, plus sporadic imported cases in at least 20 other countries. The Philippines is at risk for MERS-CoV transmission from frequent travelers, such as overseas Filipino workers and Hajj pilgrims, coming from Middle Eastern countries. Throat swabs, sputum samples, and a rectal swab were collected from the index case within 13 to 22 days after the onset of symptoms. MERS-CoV testing was performed using a real-time reverse transcription polymerase chain reaction (RT-qPCR) screening assay targeting regions upstream of the envelope gene (upE) and the nucleocapsid gene (N2), a confirmatory RT-qPCR assay targeting regions within the open reading frame 1a gene (ORF1a) and another region of the N gene (N3), and Sanger sequencing of regions of the N and RNA-dependent polymerase (RdRp) genes. The index case tested weakly positive for MERS-CoV in a sputum sample until day 19 of illness. Sequences of the N and RdRp gene regions reveal 100 and 99% similarity with MERS-CoV sequences obtained in KSA and UAE, respectively, confirming that the infection originated from Middle Eastern strains. Two unique synonymous/silent mutations (T15259A and T15265C) were identified in the RdRp sequence fragments. Whole genome sequencing of the strain may identify other mutations across the genome and determine the most probable origin of the strain.