Wen Hui Shaw1, Qianqian Lin1, Zikry Zhiwei Bin Roslee Muhammad1, Jia Jun Lee2, Wei Xin Khong3, Oon Tek Ng4, Eng Lee Tan5, Peng Li6. 1. Student, Centre for Biomedical and Life Sciences, Singapore Polytechnic , 500 Dover Road, Singapore . 2. Research Assistant, Department of Infectious Diseases, Tan Tock Seng Hospital , Singapore . 3. Scientific Officer, Department of Infectious Diseases, Tan Tock Seng Hospital , Singapore . 4. Consultant, Department of Infectious Diseases, Tan Tock Seng Hospital , Singapore . 5. 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 . 6. Project Leader, Centre for Biomedical and Life Sciences, Singapore Polytechnic , 500 Dover Road, Singapore .
Abstract
INTRODUCTION: 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. AIM: To leverage the NGS technology in order to improve current HIV-1 diagnosis and genotyping methods. MATERIALS AND 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. CONCLUSION: 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.
INTRODUCTION: 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. AIM: To leverage the NGS technology in order to improve current HIV-1 diagnosis and genotyping methods. MATERIALS AND METHODS: Ten blood samples were collected from HIV-1 infectedpatients 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. CONCLUSION: 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.
Entities:
Keywords:
Disease transmission; Drug resistance; Infectious diseases; Virus detection
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