key: cord-1034742-3gzkaqud
authors: Kandeil, Ahmed; Shehata, Mahmoud M.; El Shesheny, Rabeh; Gomaa, Mokhtar R.; Ali, Mohamed A.; Kayali, Ghazi
title: Complete Genome Sequence of Middle East Respiratory Syndrome Coronavirus Isolated from a Dromedary Camel in Egypt
date: 2016-04-28
journal: Genome Announc
DOI: 10.1128/genomea.00309-16
sha: 794b00331ade89870f1475a4c765b8c32ac855b5
doc_id: 1034742
cord_uid: 3gzkaqud

We generated the near-full genome sequence of Middle East respiratory syndrome coronavirus (MERS-CoV) from a collected nasal sample of dromedary camel in Egypt. The newly characterized Egyptian strain has high similarity to the previously characterized Egyptian virus and both of viruses fell into a cluster distinct from other MERS-CoVs.

CoV) is a new member of the Betacoronavirus genus. It was first detected in 2012 in samples of an infected human and was later found to be related to camels (1, 2) . MERS-CoV is a positivesense, single-stranded RNA (2) .

The first complete genome of MERS-CoV from an infected dromedary camel (Camelus dromedarius) in Egypt was named NRCE-HKU205 and deposited in GenBank under accession number KJ477102 (3). Here, we report the near full genome sequence of another MERS-CoV detected through systematic surveillance in Egypt. It was detected in the nasal swab from a healthy adult dromedary camel collected on 17 December 2014 from an abattoir in Cairo, Egypt.

Viral RNA was extracted using a QIAmp viral RNA minikit (Qiagen, Germany). Reverse transcription was performed using the Superscript III system (Invitrogen, Carlsbad, CA) with random hexamers. The cDNA was subjected to 11 PCRs to generate overlapping amplicons covering the full-length MERS-CoV genome as previously described (4) . The PCR products were purified from agarose gels using a QIAquick gel extraction kit (Qiagen). Purified amplicons were Sanger sequenced according to the primer/amplicon combinations (123 sequencing reactions) as shown previously (4) To further investigate the genetic relationship between Egyptian MERS-CoVs and other strains whose genomes are available in GenBank, we performed whole-genome phylogenetic analysis using MEGA 5 (5) . Egyptian strains fell into a cluster distinct from other MERS-CoVs detected elsewhere.

Sequence analysis was performed using BioEdit (6) . Egyptian MERS-CoVs had 14 characteristic amino acids (aa) in the ORF1ab protein (Y581, F664, F1024, F1583, T1911, L1970, I2000, V2333,  C2481, L2639, T2676, S3361, I3721, M5537) . No specific aa variations were identified in the S, ORF3, ORF4a, ORF4b, E, M, and N proteins. An aa deletion that was previously identified at site 1,293 of the S protein of NRCE-HKU205 (3) was not identified in NRC163. The biological impact of such differences among MERS-CoV strains needs to be fully examined.

Nucleotide sequence accession number. The complete genome sequence of the MERS-CoV/Egypt/NRC163/2014 was deposited in GenBank under the accession number KU740200.

Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia

Middle East respiratory syndrome coronavirus: a comprehensive review

MERS coronaviruses in dromedary camels

MERS-CoV PCR/sequencing primers

MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods

BioEdit: a user-friendly biological sequence alignment editor and analysis for Windows 95/98/NT

We express gratitude to the field personnel who conduct the MERS CoV surveillance in Egypt and the laboratory personnel who conduct the laboratory screening at the National Research Centre in Egypt.

This work, including the efforts of Mohamed Ahmed Ali, was funded by the Egyptian Science and Technology Development Fund (contract no. 5175). This work, including the efforts of Ghazi Kayali, was funded by the National Institute of Allergy and Infectious Diseases (contract no. HHSN272201400006C).