key: cord-0972818-l44dytci
authors: Taboada, B. T.; Isa, P.; Espinoza, M. A.; Aponte, F. E.; Arias-Ortiz, M. A.; Monge-Martínez, J.; Rodríguez-Vázquez, R.; Díaz-Hernández, F.; Zárate-Vidal, F.; Wong-Chew, R. M.; Firo-Reyes, V.; del Río-Almendárez, C. N.; Gaitán-Meza, J.; Villaseñor-Sierra, A.; Martínez-Aguilar, G.; García-Borjas, M.; Noyola, D. E.; Pérez-Gónzalez, L. F.; López, S.; Santos-Preciado, J. I.; Arias, C. F.
title: Complete Genome Sequence of Human Coronavirus OC43 Isolated from Mexico
date: 2016-11-10
journal: Genome Announc
DOI: 10.1128/genomea.01256-16
sha: c36f5134f23a74677ed9d3a39f2eb8b4b19ad6e5
doc_id: 972818
cord_uid: l44dytci

We report the complete genome sequence of the first Mexican human coronavirus (HCoV) OC43, obtained by new-generation sequencing and a metagenomic approach, isolated from a child hospitalized with pneumonia. The genome is closely related to the other OC43 genome sequences available, ranging from 99.8% to 98.2% nucleotide sequence identity.

coronavirus (HCoV) OC43 belongs to the Betacoronavirus genus of the Coronaviridae and its genome is formed by a positivesense, single-stranded RNA of ca. 31.5 kb (1) . HCoV OC43 and HCoV 229E are responsible for one-third of all common colds, infecting all age groups (2), but there have been reports of a more severe lower respiratory tract involvement (3, 4) . The aim of the present study was to determine the full-length genome of the first HCoV OC43 isolated from Mexico, which was obtained from a viral metagenomic analysis of a nasal washing from a child who required hospitalization due to clinical or radiological signs of pneumonia of unknown origin, negative for commonly associated respiratory viruses and bacteria, using the xTAG Bioplex respiratory viral panel and multiplex PCR Seeplex Pneumobacter ACE detection kit, respectively (5) .

Nucleic acids from the sample were extracted with the PureLink Viral RNA/DNA kit. Before extraction, the sample was treated with Turbo DNase and RNase, and a random-primer amplification of the genetic material was performed as previously described (5) . The sequencing was carried out with the Illumina Genome Analyzer IIx single-end platform. A total of 12,330,418 reads were generated and 1,657,101 (13.44%) were mapped to the consensus sequence of HCoV OC43. Mapping was accomplished by SMALT v.0.7.6 (6) with default parameters (only Ϫy set to 0.8).

The whole viral genome sequence was obtained with an average coverage of 3,368ϫ. The same genome sequence was obtained by de novo assembly using Velvet (7) . The complete Mexican HCoV OC43 genome was composed of 30,712 nucleotides, with an average GϩC content of 35.51%. The strain shows the typical OC43 organization, with the following 5= untranslated region (UTR) (nt 1 to 199), genes: orf1ab (nt 200 to Accession number(s). The complete genome sequence of the Mexican OC43 strain was deposited at GenBank under the accession number KX344031.

Reverse genetics of the largest RNA viruses

Human coronaviruses: a brief review

An outbreak of coronavirus OC43 respiratory infection in Normandy, France

Coronavirus-related nosocomial viral respiratory infections in a neonatal and paediatric intensive care unit: a prospective study

Is there still room for novel viral pathogens in pediatric respiratory tract infections?

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

We thank the Instituto de Biotecnología-UNAM for its computer cluster and Verónica Jiménez-Jacinto and Jerome Verleyen for their computer support.This work was supported by grants 153639 (J. I. Santos) and "Influenza 2009" (C. F. Arias) from the National Council for Science and Technology-Mexico (CONACYT).