title: Identification of HIV Mutation as Diagnostic Biomarker through Next Generation Sequencing.
abstract: BACKGROUND
  Current clinical detection of Human immunodeficiency virus 1 (HIV-1) is used to target viral genes and proteins. However, the immunoassay, such as viral culture or Polymerase Chain Reaction (PCR), lacks accuracy in the diagnosis, as these conventional assays rely on the stable genome and HIV-1 is a highly-mutated virus. Next generation sequencing (NGS) promises to be transformative for the practice of infectious disease, and the rapidly reducing cost and processing time mean that this will become a feasible technology in diagnostic and research laboratories in the near future. The technology offers the superior sensitivity to detect the pathogenic viruses, including unknown and unexpected strains.
  
  
  OBJECTIVE
  To leverage the NGS technology in order to improve current HIV-1 diagnosis and genotyping methods.
  
  
  METHODS
  Ten blood samples were collected from HIV-1 infected patients which were diagnosed by RT PCR at Singapore Communicable Disease Centre, Tan Tock Seng Hospital from October 2014 to March 2015. Viral RNAs were extracted from blood plasma and reversed into cDNA. The HIV-1 cDNA samples were cleaned up using a PCR purification kit and the sequencing library was prepared and identified through MiSeq.
  
  
  RESULTS
  Two common mutations were observed in all ten samples. The common mutations were identified at genome locations 1908 and 2104 as missense and silent mutations respectively, conferring S37N and S3S found on aspartic protease and reverse transcriptase subunits.
  
  
  CONCLUSIONS
  The common mutations identified in this study were not previously reported, therefore suggesting the potential for them to be used for identification of viral infection, disease transmission and drug resistance. This was especially the case for, missense mutation S37N which could cause an amino acid change in viral proteases thus reducing the binding affinity of some protease inhibitors. Thus, the unique common mutations identified in this study could be used as diagnostic biomarkers to indicate the origin of infection as being from Singapore.
authors.affiliation: Student, Centre for Biomedical and Life Sciences, Singapore Polytechnic , 500 Dover Road, Singapore .
authors.forename: Wen Hui
authors.initials: WH
authors.lastname: Shaw
authors.affiliation: Student, Centre for Biomedical and Life Sciences, Singapore Polytechnic , 500 Dover Road, Singapore .
authors.forename: Qianqian
authors.initials: Q
authors.lastname: Lin
authors.affiliation: Student, Centre for Biomedical and Life Sciences, Singapore Polytechnic , 500 Dover Road, Singapore .
authors.forename: Zikry Zhiwei Bin Roslee
authors.initials: ZZ
authors.lastname: Muhammad
authors.affiliation: Research Assistant, Department of Infectious Diseases, Tan Tock Seng Hospital , Singapore .
authors.forename: Jia Jun
authors.initials: JJ
authors.lastname: Lee
authors.affiliation: Scientific Officer, Department of Infectious Diseases, Tan Tock Seng Hospital , Singapore .
authors.forename: Wei Xin
authors.initials: WX
authors.lastname: Khong
authors.affiliation: Consultant, Department of Infectious Diseases, Tan Tock Seng Hospital , Singapore .
authors.forename: Oon Tek
authors.initials: OT
authors.lastname: Ng
authors.affiliation: Centre Director, Department of Paediatrics, University Children's Medical Institute, National University Hospital , Singapore, 119074 and Centre for Biomedical and Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore .
authors.forename: Eng Lee
authors.initials: EL
authors.lastname: Tan
authors.affiliation: Project Leader, Centre for Biomedical and Life Sciences, Singapore Polytechnic , 500 Dover Road, Singapore .
authors.forename: Peng
authors.initials: P
authors.lastname: Li
keywords: Disease transmission; Drug resistance; Infectious diseases; Virus detection