key: cord-0003038-0p7cdj5v authors: Pan, Chao-Yang; Padilla, Tasha; Yagi, Shigeo; Lewis, Linda S.; Ng, Terry Fei Fan; Marine, Rachel L.; Nix, William Allan; Wadford, Debra A. title: Whole-Genome Sequence of Human Rhinovirus C47, Isolated from an Adult Respiratory Illness Outbreak in Butte County, California, 2017 date: 2018-02-01 journal: Genome Announc DOI: 10.1128/genomea.01579-17 sha: c6e964e7a3f4cb45e146546ae2aef10017fe69d4 doc_id: 3038 cord_uid: 0p7cdj5v Here, we report the full coding sequence of rhinovirus C47 (RV-C47), obtained from a patient respiratory sample collected during an acute respiratory illness investigation in Butte County, California, in January 2017. This is the first whole-genome sequence of RV-C47 to be reported. family of nonenveloped single-stranded positive-sense RNA viruses. RV-C was first described in 2006 in patients with influenza-like illness, defined as fever of Ͼ38°C with cough and/or pharyngitis (1, 2) . RV-C has been associated with more severe respiratory illness (3) than have RV-A and RV-B species and is also distinct from RV-A and RV-B in not being culturable by conventional cell culture methods (4). In January 2017, an acute respiratory illness outbreak occurred at a long-term care facility in Butte County, California, affecting 12 residents and 4 staff members and causing symptoms, including fever, cough, malaise, and congestion. Three patients were diagnosed with pneumonia, with one requiring hospitalization. Nasopharyngeal (NP) samples from five of the outbreak patients were submitted to the California Department of Public Health Viral and Rickettsial Disease Laboratory (VRDL) for virus testing by real-time PCR. VRDL detected RV-C in four of the five patients by methods previously described (5) . No respiratory virus was detected from the fifth patient's specimen. We used a next-generation sequencing (NGS) approach to characterize the RV-C isolate from a single patient. Briefly, the NP sample was clarified, filtered through a 0.45-M column, and nuclease treated before nucleic acid extraction using the NucliSENS EasyMAG system (bioMérieux, Inc., Durham, NC). Extracted nucleic acid was treated with DNase to remove DNA. Reverse-transcription PCR, cDNA PCR, and PCR were performed using the sequence-independent single-primer amplification method (6) . Nextera XT libraries were prepared and sequenced on an Illumina MiSeq 300-cycle paired-end run. Sequence data were processed through a bioinformatics pipeline modified from a previous study (7) . The complete genome sequence of RV-C was obtained from the specimen and typed as RV-C47 with the strain designation CA-RGDS-1001. Based on the VP1 region, CA-RGDS-1001 shares 96% nucleotide identity (NI) with the only other available RV-C47 VP1 sequence (PNG7254-3947) (GenBank accession number JF519760); CA-RGDS-1001 has Ͻ80% NI with VP1s from other RV-C genotypes. The rhinovirus genome can be divided into one structural (P1-capsid) and two nonstructural (P2 and P3) regions. The P1, P2, and P3 regions of CA-RGDS-1001 share 67 to 79%, 65 to 79%, and 65 to 80% NI with other RV-C genotypes, respectively. Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections MassTag polymerase-chain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness in New York State during Rhinovirus associated with severe lower respiratory tract infections in children A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illnesses in infants Laboratory testing for Middle East respiratory syndrome coronavirus, California High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage Highthroughput next-generation sequencing of polioviruses