1
|
Zou X, He J, Li X, Zheng J, Su X, Chen J, Chen X. Epidemic characteristics of local HIV-2 transmission across Hunan province, China. Virus Res 2024; 345:199385. [PMID: 38723949 PMCID: PMC11109882 DOI: 10.1016/j.virusres.2024.199385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
OBJECTIVE To elucidate the epidemiological features of HIV-2 in Hunan Province, China, utilizing sequence analysis. METHODS Thirteen individuals diagnosed with HIV-2 infection in Hunan Province, China, from 2017 to 2023 were included in this study. Amplification of HIV-2 env and pol regions was conducted, followed by Sanger sequencing. Phylogenetic and molecular transmission network analyses were performed to delineate molecular features and transmission dynamics. RESULTS All 14 individuals contracted HIV-2 through heterosexual intercourse, comprising 7 males and 7 females, with a median age of 58 years. Among them, three couples (HN001 and HN013, HN010 and HN011, HN008 and HN009) were identified, along with commercial sexual activity engagement reported for subject HN004. Notably, subjects HN001, HN003, HN008, and HN010 engaged in commercial sexual activities at the same location as subject HN004. Phylogenetic analysis of the pol gene revealed close proximity of sequences from all subjects to reference sequences from Gambia (Sub-type A). Employing a genetic distance threshold of 1.5 %, eight out of the 14 subjects formed a molecular transmission network, with HN002 and HN004 identified as central nodes. CONCLUSION From 2017 to 2023, all HIV-2-infected individuals in Hunan Province, China, acquired the virus through identifiable routes, indicating transmission of similar HIV-2 strains among them.
Collapse
Affiliation(s)
- Xiaobai Zou
- Hunan Provincial Center for Disease Control and Prevention, No. 861 Xinglian Road, Kaifu District, Changsha City, Hunan Province, 410005, PR China
| | - Jianmei He
- Hunan Provincial Center for Disease Control and Prevention, No. 861 Xinglian Road, Kaifu District, Changsha City, Hunan Province, 410005, PR China
| | - Xiaojun Li
- Hunan Provincial Center for Disease Control and Prevention, No. 861 Xinglian Road, Kaifu District, Changsha City, Hunan Province, 410005, PR China
| | - Jun Zheng
- Hunan Provincial Center for Disease Control and Prevention, No. 861 Xinglian Road, Kaifu District, Changsha City, Hunan Province, 410005, PR China
| | - Xiaolin Su
- Xiangtan City Center for Disease Control and Prevention, No. 12 North Second Ring Road, Yuhu District, Xiangtan City, 411200, PR China
| | - Jie Chen
- Hunan Provincial Center for Disease Control and Prevention, No. 861 Xinglian Road, Kaifu District, Changsha City, Hunan Province, 410005, PR China; Xiangtan City Center for Disease Control and Prevention, No. 12 North Second Ring Road, Yuhu District, Xiangtan City, 411200, PR China
| | - Xi Chen
- Hunan Provincial Center for Disease Control and Prevention, No. 861 Xinglian Road, Kaifu District, Changsha City, Hunan Province, 410005, PR China.
| |
Collapse
|
2
|
Diop-Ndiaye H, Sène PY, Coulibaly K, Diallo M, Diallo S, Diop K, Sow-Ndoye A, Fall M, Ndiaye AJS, Mathebula E, Ba AA, Lejeune C, Manga NMP, Camara M, Ndour CT, Kane CT. m-PIMA™ HIV1/2 VL: A suitable tool for HIV-1 and HIV-2 viral load quantification in West Africa. J Virol Methods 2024; 324:114872. [PMID: 38128833 DOI: 10.1016/j.jviromet.2023.114872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Point-of-Care for HIV viral RNA quantification seems to be a complementary strategy to the existing conventional systems. This study evaluated the performance of the m-PIMA™ HIV1/2 Viral Load for the quantification of both HIV-1 and HIV-2 RNA viral load. A total of 555 HIV-1 and 90 HIV-2 samples previously tested by Abbott RealTime HIV-1 (Abbott, Chicago, USA) and Generic HIV-2® Charge virale (Biocentric, France) were tested using the m-PIMA™ HIV1/2 Viral Load at the HIV National Reference lab in Senegal. For HIV-1, Pearson correlation and Bland-Altman plots showed a coefficient r = 0.97 and a bias of -0.11 log10 copies/ml (95% confidence interval [CI]: -0.086 to -0.133 log10 copies/ml) for the m-PIMA™ HIV1/2 Viral Load, respectively. Sensitivity and specificity at 3 log10 copies/ml (threshold of virological failure) were 93.6% (95%[CI]: 91.5% to 95.6%) and 99.1% (95%[CI]: 98.3% to 99.9%), respectively. For HIV-2, a correlation of r = 0.95 was also noted with a bias of - 0.229 log10 copies/ml (95%[CI]: -0.161 to -0.297 log10 copies/ml). Sensitivity and specificity at 3 log10 copies/ml were 97.6% (95%[CI]: 94.3% to 100%) and 93.9% (95%[CI]: 88.9% to 98.8%), respectively. These results confirmed that m-PIMA™ HIV1/2 VL could be a good alternative for HIV-1 and HIV-2 viral load testing in decentralized settings in Senegal.
Collapse
Affiliation(s)
- Halimatou Diop-Ndiaye
- Cheikh Anta Diop University and Bacteriology-Virology UTH Aristide le Dantec, Dakar, Senegal.
| | | | | | | | - Sada Diallo
- Bacteriology-Virology UTH Aristide le Dantec, Dakar, Senegal
| | - Karim Diop
- Division de Lutte contre le SIDA/IST, Dakar, Senegal
| | - Aissatou Sow-Ndoye
- Institut de Recherche en Santé, de surveillance épidémiologique et de Formation, Dakar, Senegal
| | - Mengue Fall
- Bacteriology-Virology UTH Aristide le Dantec, Dakar, Senegal
| | | | - Evans Mathebula
- School of Health Systems and Public Health, Faculty of Health Science, University of Pretoria, Pretoria, South Africa
| | | | | | | | - Makhtar Camara
- Cheikh Anta Diop University and Bacteriology-Virology UTH Aristide le Dantec, Dakar, Senegal
| | | | - Coumba Toure Kane
- Institut de Recherche en Santé, de surveillance épidémiologique et de Formation, Dakar, Senegal
| |
Collapse
|
3
|
Abdullah, Din M, Waris A, Khan M, Ali S, Muhammad R, Salman M. The contemporary immunoassays for HIV diagnosis: a concise overview. ASIAN BIOMED 2023; 17:3-12. [PMID: 37551202 PMCID: PMC10405330 DOI: 10.2478/abm-2023-0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Recent advances in human immunodeficiency virus (HIV) diagnostics have improved the management of disease progression significantly, which have also boosted the efficacy of antiviral therapies. The detection of HIV at the earliest is very important. A highly recognized and effective virological biomarker for acute HIV infections is p24 antigen. This brief overview is based on advances of HIV diagnosis while focusing on the latest HIV testing technologies including HIV-specific antigens detecting assays of both anti-HIV antibodies and p24 antigen. In addition to other emerging molecular diagnostics for acute HIV infection, the utilization of p24 antigen has been summarized. Moreover, it has been explained how these immunoassays have reduced the window period for detection of HIV in the acute stage of infection.
Collapse
Affiliation(s)
- Abdullah
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar25000, Pakistan
| | - Misbahud Din
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad45320, Pakistan
| | - Abdul Waris
- Department of Biomedical Sciences, City University of Hong Kong, Shezhen518057, Hong Kong SAR
| | - Muddasir Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar25120, Pakistan
| | - Sajjad Ali
- Department of Zoology, University of Buner, Buner19281, Pakistan
| | - Riaz Muhammad
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar25000, Pakistan
- Department of Zoology, Government Degree College Lakarai, Mohmand24651, Pakistan
| | - Muhammad Salman
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar25000, Pakistan
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok10330, Thailand
| |
Collapse
|
4
|
Ramalingam VV, Fletcher GJ, Kasirajan A, Demosthenes JP, Rupali P, Varghese GM, Pulimood SA, Rebekah G, Kannangai R. Can In-house HIV-2 Viral Load Assay be a Reliable Alternative to Commercial Assays for Clinical and Therapeutic Monitoring? Curr HIV Res 2022; 20:274-286. [PMID: 35692165 DOI: 10.2174/1570162x20666220609155237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/11/2022] [Accepted: 04/01/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Currently, there is a global contemplation to end the AIDS epidemic by 2030. HIV-2 poses unique challenges to this end. The burden of HIV-2 is higher in resource-limited countries, and it is intrinsically resistant to NNRTI drugs. In addition, there is no FDA-approved plasma viral load assay to monitor disease progression and therapeutic efficacy. To overcome these challenges, we have developed and evaluated an in-house quantitative HIV-2 viral load assay. METHODS Blood samples were collected from 28 HIV-2 treatment-naïve monoinfected individuals and tested using an in-house qPCR HIV-2 viral load assay. The extracted RNA was amplified using Quantifast pathogen + IC kit. RESULTS The in-house qPCR has a limit of detection of 695 copies/ml. The intra- and inter-assay variation (% CV) of the assay was 0.61 and 0.95, respectively. The in-house assay quantified HIV-2 NIBSC accurately (1000 IU) with a mean of 1952 copies/mL. Among the 28 samples tested by in-house qPCR assay, 11 (39.2%) samples were quantified, whereas 17 (60.7%) samples were not detected. In comparison with Altona RealStar HIV-2 RT PCR and Exavir Load RT assay, the results were 96.4% and 69.6% concordant, respectively. No significant (p = 0.99 and p = 0.13) difference in quantifying viral load between the three assays. Based on clinical and immunological (CD4) staging, the performance characteristics were comparable. CONCLUSION To the best of our knowledge, this is the first in-house qPCR developed in India. The performance characteristics of the in-house assay are comparable to the commercial assays, and they can be used assertively to monitor HIV-2 patients.
Collapse
Affiliation(s)
| | | | - Anand Kasirajan
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - John Paul Demosthenes
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - Priscilla Rupali
- Department of Infectious Diseases, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - George Mannil Varghese
- Department of Infectious Diseases, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | | | - Grace Rebekah
- Department of Biostatistics, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - Rajesh Kannangai
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| |
Collapse
|
5
|
Evaluation of a Quantitative Taqman Real-Time PCR Assay to Measure Proviral load from Human Immunodeficiency Virus Type 1 individuals. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human Immunodeficiency Virus (HIV) is a virus belonging to the family Retroviridae. HIV – 1 is found to be predominant in India and many parts of Africa. The intention of this study was to quantify the HIV Proviral Deoxyribonucleic Acid (DNA) from newly infected HIV-1 individuals. Fifty patients who were tested positive for HIV were included in this study. Proviral Ribo Nucleic Acid (RNA) was extracted by QIAmp® RNA Mini Kit (QIAGEN, Germany) method. Complementary Deoxyribo Nucleic Acid (cDNA) was synthesized by using Invitrogen Superscript III cDNA synthesis Kit (USA). This cDNA was subjected to Polymerase Chain Reaction (PCR) and Gene cloning by transformation method. The quantification of Real time PCR was done by Applied Bio-System (ABI)-Prism 7700. A linear standard curve was obtained 10 copies to 106 copies per reaction. The assay had good analytic sensitivity and linear dynamic range greater than 6 logs. From the results obtained in this study, It was concluded that Taqman Real-Time PCR Assay plays a major role in monitoring the HIV infected patients in routine diagnostics and clinical practice.
Collapse
|
6
|
Long S, Berkemeier B. Ultrasensitive detection and quantification of viral nucleic acids with Raindance droplet digital PCR (ddPCR). Methods 2022; 201:49-64. [PMID: 33957204 PMCID: PMC8563494 DOI: 10.1016/j.ymeth.2021.04.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
Sensitive detection of viral nucleic acids is critically important for diagnosis and monitoring of the progression of infectious diseases such as those caused by SARS-CoV2, HIV-1, and other viruses. In HIV-1 infection cases, assessing the efficacy of treatment interventions that are superimposed on combination antiretroviral therapy (cART) has benefited tremendously from the development of sensitive HIV-1 DNA and RNA quantitation assays. Simian immunodeficiency virus (SIV) infection of Rhesus macaques is similar in many key aspects to human HIV-1 infection and consequently this non-human primate (NHP) model has and continues to prove instrumental in evaluating HIV prevention, treatment and eradication approaches. Cell and tissue associated HIV-1 viral nucleic acids have been found to serve as useful predictors of disease outcome and indicators of treatment efficacy, highlighting the value of and the need for sensitive detection of viruses in cells/tissues from infected individuals or animal models. However, viral nucleic acid detection and quantitation in such sample sources can often be complicated by high nucleic acid input (that is required to detect ultralow level viruses in, for example, cure research) or inhibitors, leading to reduced detection sensitivity and under-quantification, and confounded result interpretation. Here, we present a step-by-step procedure to quantitatively recover cell/tissue associated viral DNA and RNA, using SIV-infected Rhesus macaque cells and tissues as model systems, and subsequently quantify the viral DNA and RNA with an ultrasensitive SIV droplet digital PCR (ddPCR) assay and reverse transcription ddPCR (RT-ddPCR) assay, respectively, on the Raindance ddPCR platform. The procedure can be readily adapted for a broad range of applications where highly sensitive nucleic acid detection and quantitation are required.
Collapse
Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States.
| | - Brian Berkemeier
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States
| |
Collapse
|
7
|
Kibirige CN, Manak M, King D, Abel B, Hack H, Wooding D, Liu Y, Fernandez N, Dalel J, Kaye S, Imami N, Jagodzinski L, Gilmour J. Development of a sensitive, quantitative assay with broad subtype specificity for detection of total HIV-1 nucleic acids in plasma and PBMC. Sci Rep 2022; 12:1550. [PMID: 35091568 PMCID: PMC8799642 DOI: 10.1038/s41598-021-03016-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/28/2021] [Indexed: 11/09/2022] Open
Abstract
An LTR-based quantitative PCR (qPCR) assay was modified and optimized for the quantification of total HIV-1 nucleic acids in plasma and PBMC. TaqMan qPCR primers and probes were designed against the NCBI/LANL HIV-1 compendium database by analyzing sequences used in assays for sensitive cross-clade detection of HIV-1 as reported in the literature and elucidating regions of improved cross-subtype specificity. Inosine and mixed nucleotide bases were included at polymorphic sites. Real-time RT-qPCR and qPCR were performed on plasma viral RNA and cellular lysates. A step-up amplification approach to allow binding of primers across polymorphic regions showed improved sensitivity compared to universal cycling. Unlike a lead competing laboratory-developed assay, all major HIV-1 subtypes, and a wide range of recombinants from a 127-member diversity panel were detected and accurately quantified in spiked plasmas. Semi-nested PCR increased detection sensitivity even further. The assay was able to detect down to 88 copies/mL of HIV-1 in plasma with 95% efficiency or the equivalent of a single infected cell. The PCR assay will be valuable in studies that monitor very low viral levels including residual or break through HIV-1 in patients receiving antiretroviral therapy, in HIV-1 cure, and in other research studies.
Collapse
Affiliation(s)
- C N Kibirige
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK.
| | - M Manak
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD, 20910, USA
- Turesol Consulting, 314 S. Henderson Road, King of Prussia, PA, 19406, USA
| | - D King
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - B Abel
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - H Hack
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD, 20910, USA
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - D Wooding
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - Y Liu
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD, 20910, USA
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - N Fernandez
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - J Dalel
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - Steve Kaye
- Molecular Diagnostics Unit, Imperial College London, Jefferiss Trust Laboratory, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - N Imami
- Centre for Immunology and Vaccinology, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - L Jagodzinski
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD, 20910, USA
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - J Gilmour
- IAVI, Human Immunology Laboratory, Imperial College London, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| |
Collapse
|
8
|
Xie C, Chen S, Zhang L, He X, Ma Y, Wu H, Zou B, Zhou G. Multiplex detection of blood-borne pathogens on a self-driven microfluidic chip using loop-mediated isothermal amplification. Anal Bioanal Chem 2021; 413:2923-2931. [PMID: 33712918 DOI: 10.1007/s00216-021-03224-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/02/2021] [Accepted: 02/06/2021] [Indexed: 01/13/2023]
Abstract
Detection of blood-borne pathogens such as hepatitis C virus (HCV), hepatitis B virus (HBV) and human immunodeficiency virus (HIV) is essential to ensure the safety of blood transfusion. However, traditional PCR-based pathogen nucleic acid detection methods require relatively high experimental facilities and are difficult to apply in areas with limited resources. In this study, a self-driven microfluidic chip was designed to carry out multiplex detection of HBV, HCV and HIV by using loop-mediated isothermal amplification (LAMP). Benefitting from the air permeability of the polydimethylsiloxane material, the chip could accomplish sample loading within 12 min driven by the pressure difference between the reaction chambers and vacuum chambers in the chip without using pumps or any injection devices. Multiplex detection is achieved by presetting LAMP primers specific to different targets in different reaction chambers. Calcein was used as an indicator to indicate the positive amplification reaction, and the result can be recorded by a smartphone camera. After 50 min of isothermal amplification at 63 °C, 2 copies/μL of HBV, HCV and HIV target nucleic acids could be detected. The results of HBV detection of 20 clinical plasma samples by using the chip are consistent with that of the qPCR-based kit, indicating that the LAMP-based self-driven chip has the clinical application potential for blood-borne pathogen detection, especially in resource-limited areas.
Collapse
Affiliation(s)
- Chunmei Xie
- Department of Clinical Pharmacy, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Shan Chen
- Department of Clinical Pharmacy, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Likun Zhang
- Department of Clinical Pharmacy, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Xiangpeng He
- Department of Clinical Pharmacy, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Yi Ma
- Department of Clinical Pharmacy, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Haiping Wu
- Department of Clinical Pharmacy, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China.
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China.
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210093, Jiangsu, China.
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China.
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210093, Jiangsu, China.
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| |
Collapse
|
9
|
Long S, Berkemeier B. Development of a reverse transcription droplet digital PCR (RT-ddPCR) assay for sensitive detection of simian immunodeficiency virus (SIV). Virol J 2021; 18:35. [PMID: 33588884 PMCID: PMC7883996 DOI: 10.1186/s12985-021-01503-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/01/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Simian immunodeficiency virus (SIV)-infected rhesus macaques constitute an excellent model of human HIV infection. Sensitive detection of SIV RNA in cell and tissue samples from infected animals subjected to treatment regimens becomes especially critical in determining which therapeutic attempts are successful, and consequently, which interventions should be prioritized in HIV cure research. RESULTS In this report, we describe the design and testing of a Raindance ddPCR platform-based, sensitive SIV reverse transcription droplet digital PCR (RT-ddPCR) assay by exploring the combinations of various priming conditions and reverse transcriptases, and testing one-step vs. two-step procedures, to eliminate background signal(s) and enable detection and quantification of low level target signals. CONCLUSIONS Similar reaction conditions and assay validation procedures can be explored for potential development of additional assays for other applications that require sensitive detection of low-level targets in RNA samples.
Collapse
Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
| | - Brian Berkemeier
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| |
Collapse
|
10
|
Moeis MR, Rahayu AP, Ihsani N, Pertiwi W. Coronavirus-SARS-CoV-2: Biology and Problems in rRT-PCR Detection. BORNEO JOURNAL OF PHARMACY 2020. [DOI: 10.33084/bjop.v3ispecial-1.1429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) first appeared in China in December 2019 and was declared a pandemic by the World Health Organization. COVID-19 is caused by Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2), a new virus previously unknown to humans. Here we look at what is known about this virus, the main method for detecting the presence of this virus in a person who is used as a golden standard, and the problems that could arise in this detection method. Understanding the biology of the virus and the strengths and weaknesses of the detection method are important for patient management and for overcoming the pandemic.
Collapse
|