Osong Public Health and Research Perspectives

Original Article

Phylogenetic and genome-wide mutational analysis of SARS-CoV-2 strains circulating in Nigeria: no implications for attenuated COVID-19 outcomes: Daniel B. Kolawole, Malachy I. Okeke; Osong Public Health Res Perspect. 2022;13(2):101-113. Published online April 22, 2022; DOI: https://doi.org/10.24171/j.phrp.2021.0329

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Graphical Abstract Abstract PDF: Objectives
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The COVID-19 incidence and mortality rates are low in Nigeria compared to global trends. This research mapped the evolution of SARS-CoV-2 circulating in Nigeria and globally to determine whether the Nigerian isolates are genetically distinct from strains circulating in regions of the world with a high disease burden. Methods: Bayesian phylogenetics using BEAST 2.0, genetic similarity analyses, and genomewide mutational analyses were used to characterize the strains of SARS-CoV-2 isolated in Nigeria. Results: SARS-CoV-2 strains isolated in Nigeria showed multiple lineages and possible introductions from Europe and Asia. Phylogenetic clustering and sequence similarity analyses demonstrated that Nigerian isolates were not genetically distinct from strains isolated in other parts of the globe. Mutational analysis demonstrated that the D614G mutation in the spike protein, the P323L mutation in open reading frame 1b (and more specifically in NSP12), and the R203K/ G204R mutation pair in the nucleocapsid protein were most prevalent in the Nigerian isolates. Conclusion: The SARS-CoV-2 strains in Nigeria were neither phylogenetically nor genetically distinct from virus strains circulating in other countries of the world. Thus, differences in SARS-CoV-2 genomes are not a plausible explanation for the attenuated COVID-19 outcomes in Nigeria.

Review Article

Yersinia pestis antibiotic resistance: a systematic review: Chen Lei, Suresh Kumar; Osong Public Health Res Perspect. 2022;13(1):24-36. Published online February 18, 2022; DOI: https://doi.org/10.24171/j.phrp.2021.0288

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Yersinia pestis, the cause of plague and a potential biological weapon, has always been a threatening pathogen. Some strains of Y. pestis have varying degrees of antibiotic resistance. Thus, this systematic review was conducted to alert clinicians to this pathogen’s potential antimicrobial resistance. A review of the literature was conducted for experimental reports and systematic reviews on the topics of plague, Y. pestis, and antibiotic resistance. From 1995 to 2021, 7 Y. pestis isolates with 4 antibiotic resistance mechanisms were reported. In Y. pestis 17/95, 16/95, and 2180H, resistance was mediated by transferable plasmids. Each plasmid contained resistance genes encoded within specific transposons. Strain 17/95 presented multiple drug resistance, since plasmid 1202 contained 10 resistance determinants. Strains 16/95 and 2180H showed single antibiotic resistance because both additional plasmids in these strains carried only 1 antimicrobial determinant. Strains 12/87, S19960127, 56/13, and 59/13 exhibited streptomycin resistance due to an rpsl gene mutation, a novel mechanism that was discovered recently. Y. pestis can acquire antibiotic resistance in nature not only via conjugative transfer of antimicrobial-resistant plasmids from other bacteria, but also by gene point mutations. Global surveillance should be strengthened to identify antibiotic-resistant Y. pestis strains by whole-genome sequencing and drug susceptibility testing.

Citations

Citations to this article as recorded by

A situation analysis of the current plague outbreak in the Demographic Republic of Congo and counteracting strategies – Correspondence
Ranjit Sah, Abdullah Reda, Rachana Mehta, Ranjan K. Mohapatra, Kuldeep Dhama
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Original Articles

Genome-Wide Identification and Characterization of Point Mutations in the SARS-CoV-2 Genome: Jun-Sub Kim, Jun-Hyeong Jang, Jeong-Min Kim, Yoon-Seok Chung, Cheon-Kwon Yoo, Myung-Guk Han; Osong Public Health Res Perspect. 2020;11(3):101-111. Published online May 14, 2020; DOI: https://doi.org/10.24171/j.phrp.2020.11.3.05

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Abstract PDF

Objectives

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China, in December 2019 and has been rapidly spreading worldwide. Although the causal relationship among mutations and the features of SARS-CoV-2 such as rapid transmission, pathogenicity, and tropism, remains unclear, our results of genomic mutations in SARS-CoV-2 may help to interpret the interaction between genomic characterization in SARS-CoV-2 and infectivity with the host.

Methods

A total of 4,254 genomic sequences of SARS-CoV-2 were collected from the Global Initiative on Sharing all Influenza Data (GISAID). Multiple sequence alignment for phylogenetic analysis and comparative genomic approach for mutation analysis were conducted using Molecular Evolutionary Genetics Analysis (MEGA), and an in-house program based on Perl language, respectively.

Results

Phylogenetic analysis of SARS-CoV-2 strains indicated that there were 3 major clades including S, V, and G, and 2 subclades (G.1 and G.2). There were 767 types of synonymous and 1,352 types of non-synonymous mutation. ORF1a, ORF1b, S, and N genes were detected at high frequency, whereas ORF7b and E genes exhibited low frequency. In the receptor-binding domain (RBD) of the S gene, 11 non-synonymous mutations were observed in the region adjacent to the angiotensin converting enzyme 2 (ACE2) binding site.

Conclusion

It has been reported that the rapid infectivity and transmission of SARS-CoV-2 associated with host receptor affinity are derived from several mutations in its genes. Without these genetic mutations to enhance evolutionary adaptation, species recognition, host receptor affinity, and pathogenicity, it would not survive. It is expected that our results could provide an important clue in understanding the genomic characteristics of SARS-CoV-2.

Citations

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Geographical distribution of host's specific SARS-CoV-2 mutations in the early phase of the COVID-19 pandemic
Mohammad Khalid, David Murphy, Maryam Shoai, Jonahunnatha Nesson George-William, Yousef Al-ebini
Gene.2023; 851: 147020. CrossRef
Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor‐binding domain mutations: Receptor affinity versus neutralization of receptor interaction
Monique Vogel, Gilles Augusto, Xinyue Chang, Xuelan Liu, Daniel Speiser, Mona O. Mohsen, Martin F. Bachmann
Allergy.2022; 77(1): 143. CrossRef
Peptides and peptidomimetics as therapeutic agents for Covid‐19
Achyut Dahal, Jafrin Jobayer Sonju, Konstantin G. Kousoulas, Seetharama D. Jois
Peptide Science.2022;[Epub] CrossRef
Emergence of unique SARS-CoV-2 ORF10 variants and their impact on protein structure and function
Sk. Sarif Hassan, Kenneth Lundstrom, Ángel Serrano-Aroca, Parise Adadi, Alaa A.A. Aljabali, Elrashdy M. Redwan, Amos Lal, Ramesh Kandimalla, Tarek Mohamed Abd El-Aziz, Pabitra Pal Choudhury, Gajendra Kumar Azad, Samendra P. Sherchan, Gaurav Chauhan, Murta
International Journal of Biological Macromolecules.2022; 194: 128. CrossRef
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Ananda Vardhan Hebbani, Swetha Pulakuntla, Padmavathi Pannuru, Sreelatha Aramgam, Kameswara Rao Badri, Vaddi Damodara Reddy
Archives of Microbiology.2022;[Epub] CrossRef
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Boon Zhan Sia, Wan Xin Boon, Yoke Yee Yap, Shalini Kumar, Chong Han Ng
F1000Research.2022; 11: 9. CrossRef
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Xiao-wen Cheng, Jie Li, Lu Zhang, Wen-jun Hu, Lu Zong, Xiang Xu, Jin-ping Qiao, Mei-juan Zheng, Xi-wen Jiang, Zhi-kun Liang, Yi-fan Zhou, Ning Zhang, Hua-qing Zhu, Yuan-hong Xu
Frontiers in Medicine.2022;[Epub] CrossRef
Promising inhibitors against main protease of SARS CoV-2 from medicinal plants: In silico identification
OLUWAKEMI EBENEZER, MICHAEL SHAPI
Acta Pharmaceutica.2022; 72(2): 159. CrossRef
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Karl R. Franke, Robert Isett, Alan Robbins, Carrie Paquette-Straub, Craig A. Shapiro, Mary M. Lee, Erin L. Crowgey, Pierre Roques
PLOS ONE.2022; 17(1): e0262573. CrossRef
The importance of accessory protein variants in the pathogenicity of SARS-CoV-2
Sk. Sarif Hassan, Pabitra Pal Choudhury, Guy W. Dayhoff, Alaa A.A. Aljabali, Bruce D. Uhal, Kenneth Lundstrom, Nima Rezaei, Damiano Pizzol, Parise Adadi, Amos Lal, Antonio Soares, Tarek Mohamed Abd El-Aziz, Adam M. Brufsky, Gajendra Kumar Azad, Samendra P
Archives of Biochemistry and Biophysics.2022; 717: 109124. CrossRef
The mutational dynamics of the SARS-CoV-2 virus in serial passages in vitro
Sissy Therese Sonnleitner, Stefanie Sonnleitner, Eva Hinterbichler, Hannah Halbfurter, Dominik B.C. Kopecky, Stephan Koblmüller, Christian Sturmbauer, Wilfried Posch, Gernot Walder
Virologica Sinica.2022; 37(2): 198. CrossRef
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Nastiti Wijayanti, Faris Muhammad Gazali, Endah Supriyati, Mohamad Saifudin Hakim, Eggi Arguni, Marselinus Edwin Widyanto Daniwijaya, Titik Nuryastuti, Matin Nuhamunada, Rahma Nabilla, Sofia Mubarika Haryana, Tri Wibawa
International Microbiology.2022; 25(3): 531. CrossRef
Prediction of the effects of the top 10 nonsynonymous variants from 30229 SARS-CoV-2 strains on their proteins
Boon Zhan Sia, Wan Xin Boon, Yoke Yee Yap, Shalini Kumar, Chong Han Ng
F1000Research.2022; 11: 9. CrossRef
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Mohamed G. Seadawy, Reem Binsuwaidan, Badriyah Alotaibi, Thanaa A. El-Masry, Bassem E. El-Harty, Ahmed F. Gad, Walid F. Elkhatib, Maisra M. El-Bouseary
Frontiers in Microbiology.2022;[Epub] CrossRef
Genomic surveillance, evolution and global transmission of SARS-CoV-2 during 2019–2022
Nadim Sharif, Khalid J. Alzahrani, Shamsun Nahar Ahmed, Afsana Khan, Hamsa Jameel Banjer, Fuad M. Alzahrani, Anowar Khasru Parvez, Shuvra Kanti Dey, Jayanta Bhattacharya
PLOS ONE.2022; 17(8): e0271074. CrossRef
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Tiana M. Scott, Antonio Solis-Leal, J. Brandon Lopez, Richard A. Robison, Bradford K. Berges, Brett E. Pickett
Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef
The Delta and Omicron Variants of SARS-CoV-2: What We Know So Far
Vivek P. Chavda, Rajashri Bezbaruah, Kangkan Deka, Lawandashisha Nongrang, Tutumoni Kalita
Vaccines.2022; 10(11): 1926. CrossRef
SARS-CoV-2’NİN SÜREGELEN EVRİMİ: PANDEMİNİN SONUNA NE KADAR YAKINIZ?
Elmas Pınar KAHRAMAN KILBAŞ, Mustafa ALTINDİŞ
JOURNAL OF BIOTECHNOLOGY AND STRATEGIC HEALTH RESE.2022;[Epub] CrossRef
Complete Genomic Characterisation and Mutation Patterns of Iraqi SARS-CoV-2 Isolates
Jivan Qasim Ahmed, Sazan Qadir Maulud
Diagnostics.2022; 13(1): 8. CrossRef
Comprehensive annotations of the mutational spectra of SARS‐CoV‐2 spike protein: a fast and accurate pipeline
Mohammad Shaminur Rahman, Mohammad Rafiul Islam, Mohammad Nazmul Hoque, Abu Sayed Mohammad Rubayet Ul Alam, Masuda Akther, Joynob Akter Puspo, Salma Akter, Azraf Anwar, Munawar Sultana, Mohammad Anwar Hossain
Transboundary and Emerging Diseases.2021; 68(3): 1625. CrossRef
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Christian Luke D. C. Badua, Karol Ann T. Baldo, Paul Mark B. Medina
Journal of Medical Virology.2021; 93(3): 1702. CrossRef
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Malik Sallam, Nidaa A. Ababneh, Deema Dababseh, Faris G. Bakri, Azmi Mahafzah
Heliyon.2021; 7(1): e06035. CrossRef
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Eman Serag, Marwa El-Zeftawy
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Microbiology Research.2021; 12(1): 138. CrossRef
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Szu-Wei Huang, Sheng-Fan Wang
International Journal of Molecular Sciences.2021; 22(6): 3060. CrossRef
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Aysun Urhan, Thomas Abeel
Scientific Reports.2021;[Epub] CrossRef
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Sally Esmail, Wayne R. Danter
Computational and Structural Biotechnology Journal.2021; 19: 1701. CrossRef
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Journal of Translational Medicine.2021;[Epub] CrossRef
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Mirriam M. Nzivo, Nancy L.M. Budambula
Journal of Pure and Applied Microbiology.2021; 15(2): 524. CrossRef
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Danijela Miljanovic, Ognjen Milicevic, Ana Loncar, Dzihan Abazovic, Dragana Despot, Ana Banko
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mBio.2021;[Epub] CrossRef
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Sagar Dholariya, Deepak Narayan Parchwani, Ragini Singh, Amit Sonagra, Anita Motiani, Digishaben Patel
Indian Journal of Clinical Biochemistry.2021; 36(4): 451. CrossRef
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Marios Mejdani, Kiandokht Haddadi, Chester Pham, Radhakrishnan Mahadevan
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Heliyon.2021; 7(8): e07866. CrossRef
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Comparison of Three Different Methods for Detection of IL28 rs12979860 Polymorphisms as a Predictor of Treatment Outcome in Patients with Hepatitis C Virus: Abolfazl Fateh, Mohammadreza Aghasadeghi, Seyed D. Siadat, Farzam Vaziri, Farzin Sadeghi, Roohollah Fateh, Hossein Keyvani, Alireza H. Tasbiti, Shamsi Yari, Angila Ataei-Pirkooh, Seyed H. Monavari; Osong Public Health Res Perspect. 2016;7(2):83-89. Published online April 30, 2016; DOI: https://doi.org/10.1016/j.phrp.2015.11.004

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Abstract PDF

Objectives
This study aimed to evaluate the specificity, sensitivity, cost, and turn-around time of three methods of gene polymorphism analysis and to study the relationship between IL28B rs12979860 and SVR rate to pegIFN-α/RVB therapy among patients with chronic hepatitis C.
Methods
A total of 100 samples from chronic hepatitis C patients were analyzed in parallel using the three methods: direct sequencing, real-time polymerase chain reaction (PCR), amplification refractory mutation system (ARMS)-PCR.
Results
The different profiles for IL28B rs12979860 alleles (CC, CT, and TT) obtained with PCR-RFLP, ARMS-PCR, and direct sequencing were consistent among the three methods. Prevalence of rs12979860 genotypes CC, CT and TT in HCV genotype 1a was 10(19.6%), 35(68.6%), and six (11.8%), respectively, and in HCV genotype 31, it was 13(26.5%), 31(63.3%), and five (10.2%), respectively. No significant difference was seen between rs12979860 genotype and HCV genotype (p = 0.710).
Conclusion
Screening by ARMS – PCR SNOP detection represents the most efficient and reliable method to determine HCV polymorphisms in routine clinical practice.

Citations

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Mohsen Moghoofei, Sohrab Najafipour, Shayan Mostafaei , Ahmad Tavakoli , Farah Bokharaei-Salim , Saied Ghorbani, Davod Javanmard, Hadi Ghaffari , Seyed Hamidreza Monavari
Current HIV Research.2021; 19(1): 27. CrossRef
Occult hepatitis C virus infection in hemophilia patients and its correlation with interferon lambda 3 and 4 polymorphisms
Amir Hossein Nafari, Ahmad Ayadi, Zahra Noormohamadi, Fatemeh Sakhaee, Farzam Vaziri, Seyed Davar Siadat, Abolfazl Fateh
Infection, Genetics and Evolution.2020; 79: 104144. CrossRef
Polymerase Chain Reaction Assay Using the Restriction Fragment Length Polymorphism Technique in the Detection of Prosthetic Joint Infections: A Multi-Centered Study
Ataollah Moshirabadi, Mohammad Razi, Peyman Arasteh, Mohammad Mahdi Sarzaeem, Saman Ghaffari, Saied Aminiafshar, Kami Hosseinian Khosroshahy, Fatemeh Maryam Sheikholeslami
The Journal of Arthroplasty.2019; 34(2): 359. CrossRef
One-Step ARMS-PCR for the Detection of SNPs—Using the Example of the PADI4 Gene
Ehnert, Linnemann, Braun, Botsch, Leibiger, Hemmann, Nussler
Methods and Protocols.2019; 2(3): 63. CrossRef
Epstein–Barr virus and risk of breast cancer: a systematic review and meta-analysis
Mohammad Farahmand, Seyed Hamidreza Monavari, Zabihollah Shoja, Hadi Ghaffari, Mehdi Tavakoli, Ahmad Tavakoli
Future Oncology.2019; 15(24): 2873. CrossRef
Modeling suggests that microliter volumes of contaminated blood caused an outbreak of hepatitis C during computerized tomography
Eyal Shteyer, Louis Shekhtman, Tal Zinger, Sheri Harari, Inna Gafanovich, Dana Wolf, Hefziba Ivgi, Rima Barsuk, Ilana Dery, Daniela Armoni, Mila Rivkin, Rahul Pipalia, Michal Cohen Eliav, Yizhak Skorochod, Gabriel S. Breuer, Ran Tur-kaspa, Yonit Weil Wien
PLOS ONE.2019; 14(1): e0210173. CrossRef
Correlation of CD81 and SCARB1 polymorphisms on virological responses in Iranian patients with chronic hepatitis C virus genotype 1
Milad Nafari, Shiva Irani, Farzam Vaziri, Safoora Gharibzadeh, Fatemeh Sakhaee, Mohammad Khazeni, Naser Kalhor, Fatemeh Rahimi Jamnani, Seyed Davar Siadat, Abolfazl Fateh
Infection, Genetics and Evolution.2018; 62: 296. CrossRef
First detection of human hepegivirus-1 (HHpgV-1) in Iranian patients with hemophilia
Yazdan Bijvand, Mohammad Reza Aghasadeghi, Fatemeh Sakhaee, Parviz Pakzad, Farzam Vaziri, Alireza Azizi Saraji, Fatemeh Rahimi Jamnani, Seyed Davar Siadat, Abolfazl Fateh
Scientific Reports.2018;[Epub] CrossRef
Evaluation of TRIM5 and TRIM22 polymorphisms on treatment responses in Iranian patients with chronic hepatitis C virus infection
Setareh Mobasheri, Nazanin Irani, Abbas Akhavan Sepahi, Fatemeh Sakhaee, Fatemeh Rahimi Jamnani, Farzam Vaziri, Seyed Davar Siadat, Abolfazl Fateh
Gene.2018; 676: 95. CrossRef
Data Mining and Machine Learning Algorithms Using IL28B Genotype and Biochemical Markers Best Predicted Advanced Liver Fibrosis in Chronic Hepatitis C
Hend Ibrahim Shousha, Abubakr Hussein Awad, Dalia Abdelhamid Omran, Mayada Mohamed Elnegouly, Mahasen Mabrouk
Japanese Journal of Infectious Diseases.2018; 71(1): 51. CrossRef
IL28B rs12980275 and HLA rs4273729 genotypes as a powerful predictor factor for rapid, early, and sustained virologic response in patients with chronic hepatitis C
Parvaneh Sedighimehr, Shiva Irani, Fatemeh Sakhaee, Farzam Vaziri, Mohammadreza Aghasadeghi, Seyed Mehdi Sadat, Fatemeh Rahimi Jamnani, Abolfazl Fateh, Seyed Davar Siadat
Archives of Virology.2017; 162(1): 181. CrossRef
Comparison of Direct Sequencing, Real-Time PCR-High Resolution Melt (PCR-HRM) and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) Analysis for Genotyping of Common Thiopurine Intolerant Variant Alleles NUDT15 c.415C>T and TPMT c.719A>G (TPMT*3C)
Wai-Ying Fong, Chi-Chun Ho, Wing-Tat Poon
Diagnostics.2017; 7(2): 27. CrossRef
Effect of IL15 rs10833 and SCARB1 rs10846744 on virologic responses in chronic hepatitis C patients treated with pegylated interferon-α and ribavirin
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Infectivity of Homologous Recombinant HIV-1 Pseudo-virus with Reverse Transcriptase Inhibitor-related Mutations from Highly Active Antiretroviral Therapy Experienced Patients: Oh-Kyung Kwon, Ju-yeon Choi, Eun-Jin Kim, Sung Soon Kim; Osong Public Health Res Perspect. 2011;2(1):23-28. Published online June 30, 2011; DOI: https://doi.org/10.1016/j.phrp.2011.04.006

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Objectives
In this study, the viral fitness of pseudo-viruses with a drug-resistant site in the reverse transcriptase (RT) region of the genome was investigated. The pseudo-viruses were derived from highly active antiretroviral therapy (HAART)-experienced HIV/AIDS patients.
Methods
HIV-1 RNA was extracted from the plasma of HAART-experienced (KRB9149, KRB7021, KRC1097) and HAART-naïve (KRC5180, KRC5123) HIV-1 patients. The RT gene from the extracted viral RNA was amplified and the polymerase chain reaction product was cloned from the pHXB2Δ2-261 RT vector. C8166 and TZM-bl cell lines were used as the HIV-1 replication capacity measurement system. To quantify the infectivity of homologous recombinant HIV-1, the infectivity derived from each pseudo-virus was compared with the infectivity of the reference strain HXB2.
Results
Patient-derived HIV-1 was cotransfected into C8166 cells and the expression level of the p24 antigen was measured. The expression was high in the HIV-1 isolates from patients KRC5180 and KRB9149 and low in patients KRB7021, KRC5123, and KRC1097, when compared with the reference strain. The infectivity of the pseudo-virus measured in TZM-bl cells decreased in the order, reference strain HXB2 > KRC5180 > KRC5123 > KRB9149 > KRB7021 > KRC1097.
Conclusion
In this study, HIV-1 infectivity of the drug-resistant strain isolated from HAART-experienced patients with HIV/AIDS was found to be lower than the infectivity of the reference strain HXB2. This study provides useful data for the phenotypic susceptibility assay in HAART-experienced patients infected with HIV-1.

Citations

Citations to this article as recorded by

Discrimination and Stigma
Hae-Wol Cho, Chaeshin Chu
Osong Public Health and Research Perspectives.2015; 6(3): 141. CrossRef
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Osong Public Health and Research Perspectives.2013; 4(6): 291. CrossRef
The Road Less Traveled
Chaeshin Chu
Osong Public Health and Research Perspectives.2011; 2(1): 1. CrossRef

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