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Dimonte S, Babakir-Mina M, Hama-Soor T, Ali S. Genetic Variation and Evolution of the 2019 Novel Coronavirus. Public Health Genomics 2021; 24:54-66. [PMID: 33406522 PMCID: PMC7900485 DOI: 10.1159/000513530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/27/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION SARS-CoV-2 is a new type of coronavirus causing a pandemic severe acute respiratory syndrome (SARS-2). Coronaviruses are very diverting genetically and mutate so often periodically. The natural selection of viral mutations may cause host infection selectivity and infectivity. METHODS This study was aimed to indicate the diversity between human and animal coronaviruses through finding the rate of mutation in each of the spike, nucleocapsid, envelope, and membrane proteins. RESULTS The mutation rate is abundant in all 4 structural proteins. The most number of statistically significant amino acid mutations were found in spike receptor-binding domain (RBD) which may be because it is responsible for a corresponding receptor binding in a broad range of hosts and host selectivity to infect. Among 17 previously known amino acids which are important for binding of spike to angiotensin-converting enzyme 2 (ACE2) receptor, all of them are conservative among human coronaviruses, but only 3 of them significantly are mutated in animal coronaviruses. A single amino acid aspartate-454, that causes dissociation of the RBD of the spike and ACE2, and F486 which gives the strength of binding with ACE2 remain intact in all coronaviruses. DISCUSSION/CONCLUSION Observations of this study provided evidence of the genetic diversity and rapid evolution of SARS-CoV-2 as well as other human and animal coronaviruses.
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Affiliation(s)
| | | | - Taib Hama-Soor
- Technical College of Health, Sulaimani Polytechnic University, KGR, Sulaimani, Iraq
| | - Salar Ali
- Technical College of Health, Sulaimani Polytechnic University, KGR, Sulaimani, Iraq
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D'Costa J, Gooey M, Richards N, Sameer R, Lee E, Chibo D. Analysis of transmitted HIV drug resistance from 2005 to 2015 in Victoria, Australia: a comparison of the old and the new. Sex Health 2019. [PMID: 28641707 DOI: 10.1071/sh16190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Background Baseline genotyping is part of standard-of-care treatment. It reveals that transmitted drug resistance (TDR) continues to be important for the management of HIV infection. Attention is typically focused on determining whether resistance to the protease inhibitors (PI) and reverse transcriptase inhibitors (RTI) occurs. However, the increasing use of integrase inhibitors (INIs) raises a concern that TDR to this class of antiretroviral drug may also occur. METHODS PI and RTI drug resistance genotyping was performed on blood samples collected between 2005 and 2015 from 772 treatment-naïve Victorian patients infected with HIV within the previous 12 months. Integrase genotyping was performed on 461 of the 485 patient samples collected between 2010 and 2015. RESULTS In the period 2005-10, 39 of 343 patients (11.4%) had at least one PI- or RTI-associated mutation, compared with 34 of 429 (7.9%) during the period 2011-15. Compared with 2005-10, during 2011-15 there was a significant decline in the prevalence of the non-nucleoside-associated mutation K103N and the nucleoside-associated mutations at codons M41 and T215. One patient was detected with a major INI resistance mutation, namely G118R. However, this mutation is rare and its effect on susceptibility is unclear. A small number of patients (n=12) was infected with HIV containing accessory resistance mutations in the integrase gene. CONCLUSIONS The lack of transmitted resistance to INIs is consistent with a low level of resistance to this class of drugs in the treated population. However, continued surveillance in the newly infected population is warranted as the use of INIs increases.
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Affiliation(s)
- Jodie D'Costa
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute, Locked Bag 815, Carlton South, Vic. 3053, Australia
| | - Megan Gooey
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute, Locked Bag 815, Carlton South, Vic. 3053, Australia
| | - Nicole Richards
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute, Locked Bag 815, Carlton South, Vic. 3053, Australia
| | - Rizmina Sameer
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute, Locked Bag 815, Carlton South, Vic. 3053, Australia
| | - Elaine Lee
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute, Locked Bag 815, Carlton South, Vic. 3053, Australia
| | - Doris Chibo
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute, Locked Bag 815, Carlton South, Vic. 3053, Australia
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Sayan M, Gündüz A, Ersöz G, İnan A, Deveci A, Özgür G, Sargın F, Karagöz G, İnci A, İnan D, Ülçay A, Karaoğlan I, Kaya S, Kutlu SS, Süer K, Çağatay A, Akalın H. Integrase Strand Transfer Inhibitors (INSTIs) Resistance Mutations in HIV-1 Infected Turkish Patients. HIV CLINICAL TRIALS 2016; 17:109-13. [PMID: 27125365 DOI: 10.1080/15284336.2016.1153303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
OBJECTIVES Integrase strand transfer inhibitor (INSTI) is a new class of antiretroviral (ARV) drugs designed to block the action of the integrase viral enzyme, which is responsible for insertation of the HIV-1 genome into the host DNA. The aim of this study was to evaluate for the first time INSTI resistance mutations in Turkish patients. METHODS This study was conducted in Turkey, between April 2013 and April 2015 using 169 HIV-1-infected patients (78 ARV naive patients and 91 ARV-experienced patients). Laboratory and clinical characteristics of ARV naive and ARV-experienced patients were as follows: gender (M/F): 71/7 and 80/11, median age: 38 and 38.4; median CD4(+) T-cell: 236 and 216 cells/mm(3), median HIV-1 RNA: 4.95+E5 and 1.08E+6 copies/ml. Population-based seqeunces of the reverse transcriptase, protease, and integrase domains of the HIV-1 pol gene were used to detect HIV-1 drug resistance mutations. RESULT INSTI resistance mutations were not found in recently diagnosed HIV-1-infected patients. However, ARV-experienced patients had major resistance mutations associated with raltegravir and elvitegravir; the following results were generated:F121Y, Y143R, Q148R and E157Q (6/91 - 6.6%). CONCLUSIONS The prevalence of INSTI resistant mutations in ART-experienced patients suggested that resistance testing must be incorporated as an integral part of HIV management with INSTI therapies.
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Affiliation(s)
- M Sayan
- a Faculty of Medicine, Clinical Laboratory, PCR Unit , University of Kocaeli , Kocaeli , Turkey.,b Research Center of Experimental Health Sciences, University of Near East , Nicosia , Northern Cyprus
| | - A Gündüz
- c Clinic of Infectious Diseases , Sisli Etfal, Educational and Research Hospital , Istanbul , Turkey
| | - G Ersöz
- d Faculty of Medicine, Department of Infectious Diseases , University of Mersin , Mersin , Turkey
| | - A İnan
- e Clinic of Infectious Diseases , Haydarpasa Numune, Educational and Research Hospital , Istanbul , Turkey
| | - A Deveci
- f Faculty of Medicine, Department of Infectious Diseases , University of 19 Mayis , Samsun , Turkey
| | - G Özgür
- g Clinic of Infectious Diseases , Samsun Educational and Research Hospital , Samsun , Turkey
| | - F Sargın
- h Clinic of Infectious Diseases , Medeniyet University, Goztepe Educational and Research Hospital , Istanbul , Turkey
| | - G Karagöz
- i Clinic of Infectious Diseases , Umraniye Educational and Research Hospital , İstanbul , Turkey
| | - A İnci
- j Clinic of Infectious Diseases , Istanbul Kanuni Sultan Süleyman, Educational and Research Hospital , Istanbul , Turkey
| | - D İnan
- k Faculty of Medicine, Department of Infectious Diseases , University of Akdeniz , Antalya , Turkey
| | - A Ülçay
- l Clinic of Infectious Diseases , Gulhane Military Medical Academy , Istanbul , Turkey
| | - I Karaoğlan
- m Faculty of Medicine, Department of Infectious Diseases , University of Gaziantep , Gaziantep , Turkey
| | - S Kaya
- n Faculty of Medicine, Department of Infectious Disease , University of Karadeniz Technical , Trabzon , Turkey
| | - S S Kutlu
- o Faculty of Medicine, Department of Infectious Diseases , University of Pamukkale , Denizli , Turkey
| | - K Süer
- p Faculty of Medicine, Department of Infectious Diseases , University of Near East , Nicosia , Northern Cyprus
| | - A Çağatay
- q Faculty of Medicine, Department of Infectious Diseases , University of Istanbul , İstanbul , Turkey
| | - H Akalın
- r Faculty of Medicine, Department of Infectious Diseases , University of Uludag , Bursa , Turkey
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Katlama C, Assoumou L, Valantin MA, Soulie C, Duvivier C, Chablais L, Kolta S, Pialoux G, Mercie P, Simon A, Costagliola D, Peytavin G, Marcelin AG, Katlama C, Simon A, Valantin MA, Assoumou L, Costagliola D, Soulie C, Calvez V, Marcelin AG, Peytavin G, Katlama C, Simon A, Valantin MA, Assoumou L, Costagliola D, Chablais L, Peytavin G, Capeau J, Bastard JP, Kolta S, Soulie C, Calvez V, Marcelin AG, Couffin Cadiergues S, Saillard J, Rey-Coquais X, Durand F, Lemarchand C, Cuzin L, Aboulker JP, Fisher H. Maraviroc plus raltegravir failed to maintain virological suppression in HIV-infected patients with lipohypertrophy: results from the ROCnRAL ANRS 157 study. J Antimicrob Chemother 2014; 69:1648-52. [DOI: 10.1093/jac/dkt536] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Dimonte S, Babakir-Mina M, Aquaro S. HIV-1 B-subtype capsid protein: a characterization of amino acid's conservation and its significant association with integrase signatures. Virus Genes 2014; 48:429-37. [PMID: 24474329 DOI: 10.1007/s11262-014-1039-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 01/12/2014] [Indexed: 11/26/2022]
Abstract
The HIV-1 pre-integration phase and the subsequent integration of viral genome to the host of nuclear chromosomes are not well analyzed so far. Many studies are discussing the question of pre- and post-nuclear viral entry which is to support the assumption that HIV-1 integrase (IN) is maintained in the volume of intact conical structure's capsids through HIV entry. The aim of the current study is to identify the prevalence of capsid's (CA) signatures among drug-naïve and antiretroviral (ARV)-treated patients in a cohort of 827 HIV-1 B-subtype-infected individuals, and subsequently the relationship between IN and CA amino acid's changes was evaluated. These analyses suggest a conceivable co-evolution of IN-CA sequences, especially in relation to steps of nuclear viral entry. The frequency of mutations was calculated, and statistically has been compared between treatment-naïve and ARV-treated patients. The binomial correlation coefficient was used to assess covariation among CA and IN mutations; then, the average linkage hierarchical agglomerative clustering was performed. The results show a detailed conservation of HIV-1 CA protein both in drug-naïve and in ARV-treated patients. Moreover, the specific CA substitutions are significantly associated with different IN signatures at the amino acid level and the topology of the dendrogram has revealed the existence of two strong sub-clusters associated with hypothetical different mutational pathways. The in vitro and in vivo studies are necessary to exclude the hypothetical statistical false positive results and in order to confirm that some CA amino acid signatures are going to establish specific and precise implication in the HIV life cycle.
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