title: Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting.
abstract: Norovirus is a highly transmissible infectious agent that causes epidemic gastroenteritis in susceptible children and adults. Norovirus infections can be severe and can be initiated from an exceptionally small number of viral particles. Detailed genome sequence data are useful for tracking norovirus transmission and evolution. To address this need, we have developed a whole-genome deep-sequencing method that generates entire genome sequences from small amounts of clinical specimens. This novel approach employs an algorithm for reverse transcription and PCR amplification primer design using all of the publically available norovirus sequence data. Deep sequencing and de novo assembly were used to generate norovirus genomes from a large set of diarrheal patients attending three hospitals in Ho Chi Minh City, Vietnam, over a 2.5-year period. Positive-selection analysis and direct examination of protein changes in the virus over time identified codons in the regions encoding proteins VP1, p48 (NS1-2), and p22 (NS4) under positive selection and expands the known targets of norovirus evolutionary pressure.
  
  
  OBJECTIVE
  The high transmissibility and rapid evolutionary rate of norovirus, combined with a short-lived host immune responses, are thought to be the reasons why the virus causes the majority of pediatric viral diarrhea cases. The evolutionary patterns of this RNA virus have been described in detail for only a portion of the virus genome and never for a virus from a detailed urban tropical setting. We provide a detailed sequence description of the noroviruses circulating in three Ho Chi Minh City hospitals over a 2.5-year period. This study identified patterns of virus change in known sites of host immune response and identified three additional regions of the virus genome under selection that were not previously recognized. In addition, the method described here provides a robust full-genome sequencing platform for community-based virus surveillance.
authors: The Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors: Matthew
authors: M
authors: Cotten
authors: The Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors: Velislava
authors: V
authors: Petrova
authors: Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
authors: My V T
authors: MV
authors: Phan
authors: Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom.
authors: Maia A
authors: MA
authors: Rabaa
authors: The Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors: Simon J
authors: SJ
authors: Watson
authors: The Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors: Swee Hoe
authors: SH
authors: Ong
authors: The Wellcome Trust Sanger Institute, Hinxton, United Kingdom Division of Infection & Immunity, University College London, London, United Kingdom pk5@sanger.ac.uk.
authors: Paul
authors: P
authors: Kellam
authors: Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam The London School of Hygiene and Tropical Medicine, London, United Kingdom Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom.
authors: Stephen
authors: S
authors: Baker
mesh_terms: D005075:Biological Evolution; D017250:Caliciviridae Infections / Q000821:virology; D002648:Child; D002675:Child, Preschool; D002947:Cities; D003062:Codon; D003967:Diarrhea / Q000821:virology; D005759:Gastroenteritis / Q000821:virology; D015870:Gene Expression; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007223:Infant; D029322:Norovirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D014744:Vietnam; D017361:Viral Nonstructural Proteins / Q000235:genetics
chemical_list: D003062:Codon; D012367:RNA, Viral; D017361:Viral Nonstructural Proteins