title: Next-generation whole genome sequencing identifies the direction of norovirus transmission in linked patients.
abstract: BACKGROUND
  Noroviruses are a highly transmissible and major cause of nosocomial gastroenteritis resulting in bed and hospital-ward closures. Where hospital outbreaks are suspected, it is important to determine the routes of spread so that appropriate infection-control procedures can be implemented. To investigate a cluster of norovirus cases occurring in children undergoing bone marrow transplant, we undertook norovirus genome sequencing by next-generation methods. Detailed comparison of sequence data from 2 linked cases enabled us to identify the likely direction of spread.
  
  
  METHODS
  Norovirus complementary DNA was amplified by overlapping polymerase chain reaction (PCR) from 13 stool samples from 5 diagnostic real-time PCR-positive patients. The amplicons were sequenced by Roche 454, the genomes assembled by de novo assembly, and the data analyzed phylogenetically.
  
  
  RESULTS
  Phylogenetic analysis indicated that patients were infected by viruses similar to 4 distinct GII.4 subtypes and 2 patients were linked by the same virus. Of the 14 sites at which there were differences between the consensus sequences of the 2 linked viral genomes, 9 had minor variants present within one or the other patient. Further analysis confirmed that minor variants at all 9 sites in patient B w ere present as the consensus sequence in patient A.
  
  
  CONCLUSIONS
  Phylogenetic analysis excluded a common source of infection in this apparent outbreak. Two of 3 patients on the same ward had closely related viruses, raising the possibility of cross-infection despite protective isolation. Analysis of deep sequencing data enabled us to establish the likely direction of nosocomial transmission.
authors: Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom. samit.kundu@ucl.ac.uk
authors: Samit
authors: S
authors: Kundu
authors: Julianne
authors: J
authors: Lockwood
authors: Daniel P
authors: DP
authors: Depledge
authors: Yasmin
authors: Y
authors: Chaudhry
authors: Antony
authors: A
authors: Aston
authors: Kanchan
authors: K
authors: Rao
authors: John C
authors: JC
authors: Hartley
authors: Ian
authors: I
authors: Goodfellow
authors: Judith
authors: J
authors: Breuer
mesh_terms: D017250:Caliciviridae Infections / Q000453:epidemiology / Q000635:transmission* / Q000821:virology*; D002648:Child; D002675:Child, Preschool; D016000:Cluster Analysis; D003428:Cross Infection / Q000453:epidemiology / Q000635:transmission / Q000821:virology; D005260:Female; D005759:Gastroenteritis / Q000453:epidemiology / Q000821:virology*; D016679:Genome, Viral; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007223:Infant; D008297:Male; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D029322:Norovirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*
chemical_list: D012367:RNA, Viral
keywords: next-generation sequencing; norovirus; nosocomial transmission; whole genome
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