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Faiz S, Irfan M, Farooq S, Khan IA, Iqbal H, Wahab AT, Shakeel M, Gong P, Iftner T, Choudhary MI. Study of drug resistance-associated genetic mutations, and phylo-genetic analysis of HCV in the Province of Sindh, Pakistan. Sci Rep 2023; 13:12213. [PMID: 37500705 PMCID: PMC10374889 DOI: 10.1038/s41598-023-39339-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023] Open
Abstract
Current management of HCV infection is based on Direct-Acting Antiviral Drugs (DAAs). However, resistance-associated mutations, especially in the NS3 and NS5B regions are gradually decreasing the efficacy of DAAs. The aim of the current study was to identify such mutations in the NS3, and NS5B genes in DAAs treatment-naïve Pakistani chronic HCV 3a patients. Peripheral blood samples were collected from 233 chronic HCV 3a patients at different tertiary care hospitals in Karachi, Pakistan, between August 2020 to September 2021. PCR-amplified target regions of the NS3/NS5B gene were subjected to Sanger sequencing to identify resistance-associated mutations. Phylogenetic analysis of the identified amino acid sequences was performed using HCV3a sequences of the global population in the virus pathogen resource (VIPR) database. Sequence analysis identified five amino acid mutations, Leu36Pro, Gln41His, Gln80Lys/Arg, Ala156Tyr, and Gln168Arg in the NS3 region, and two mutations Leu159Phe and Cys316Arg in the NS5B region. Phylogenetic analysis revealed a high genetic diversity in the studied isolates. Overall, the prevalence of resistance-associated substitutions was almost similar to other geographic regions worldwide. This data could be helpful in selecting the most effective treatment regimen for HCV chronically infected people in Pakistan.
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Affiliation(s)
- Sirmast Faiz
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Irfan
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, Jamil-ur-Rahman Center for Genome Research, University of Karachi, Karachi, 75270, Pakistan
| | - Saba Farooq
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan.
| | - Ishtiaq Ahmad Khan
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, Jamil-ur-Rahman Center for Genome Research, University of Karachi, Karachi, 75270, Pakistan.
| | - Hana'a Iqbal
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan
| | - Atia-Tul Wahab
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Shakeel
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, Jamil-ur-Rahman Center for Genome Research, University of Karachi, Karachi, 75270, Pakistan
| | - Peng Gong
- Wuhan Institute of Virology, Chinese Academy of Sciences, No.44 Xiao Hong Shan, Wuhan, 430071, Hubei, China
| | - Thomas Iftner
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital and Medical Faculty, Eberhard Karls University, Tuebingen, Germany
| | - M Iqbal Choudhary
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan.
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, Jamil-ur-Rahman Center for Genome Research, University of Karachi, Karachi, 75270, Pakistan.
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, H.E.J. Research Institute of Chemistry, University of Karachi, Karachi, 75270, Pakistan.
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Kiattanaphon A, Vipsoongnern Y, Kunthalert D, Sistayanarain A. Partial nonstructural 3 region analysis of hepatitis C virus genotype 3a. Mol Biol Rep 2022; 49:9437-9443. [PMID: 36002650 DOI: 10.1007/s11033-022-07803-5] [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: 04/19/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND The hepatitis C virus (HCV) is a major cause of illness around the world. HCV genotype 3a is the most prevalent genotype in Thailand. Direct-acting antiviral (DAA) drugs are available for treatment, and these drugs target the NS3, NS5A, and NS5b proteins of HCV. However, HCV variants that are resistant to NS3 protease inhibitors have been found during treatment. This resistance can be naturally occurring or in response to treatment. The purpose of this study is to analyze the codon positions of the main mutation of the partial NS3 gene region of HCV genotype 3a. METHODS In order to detect mutations and confirm the genotype of HCV genotype 3a, the nucleotide sequencing and amino acid portion of NS3 were analyzed. RESULTS Twenty-six samples were successfully sequenced and clustered within two sub-clades defined as 3a-1 and 3a-2. Through amino acid mutation analysis, the variations were detected at codon positions 122 (3.8%), 132 (84.6%), 168 (100%), 170 (92.3%), 174 (100%), and 175 (100%). CONCLUSIONS In conclusion, mutations at positions 168, 170, 174, and 175 of the NS3 region are common within the HCV genotype 3a. This information should be useful in the development of effective anti-viral drugs that can successfully treat HCV infection.
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Affiliation(s)
- Anusorn Kiattanaphon
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | | | - Duangkamol Kunthalert
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Anchalee Sistayanarain
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.
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Frequency distribution of HCV resistance-associated variants in infected patients treated with direct-acting antivirals. Int J Infect Dis 2021; 115:171-177. [PMID: 34902582 DOI: 10.1016/j.ijid.2021.12.320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/11/2021] [Accepted: 12/05/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) is a global public health problem. Second-generation direct-acting antivirals targeting non-structural regions on the viral genome are the cornerstone for treatment of chronic infection. However, resistance-associated variants (RAVs) have been reported to be associated with therapeutic failure. The aim of this study was to assess the frequency of variants, including RAVs, in the NS3, NS5A and NS5B regions at baseline in Brazilian patients with chronic hepatitis C with HCV genotypes 1a, 1b and 3a. METHODS Serum samples from 13 patients were used to obtain viral RNA. Massively parallel sequencing was performed using genotype-specific amplicons and a panel of Ampliseq technology for all genotypes. RESULTS Several non-synonymous substitutions were detected at baseline for 11 responders and pre-/post-treatment for two non-responders. HCV genotype 3a was found to have significantly more non-synonymous substitutions than HCV genotype 1 in the NS3 and NS5A regions. Analyses were conducted using quantitative and qualitative inter- and intrapatient comparisons. Variants that confer resistance to the treatment used by the patients were found in both responders and non-responders. CONCLUSIONS A wide frequency distribution of RAVs was found at baseline, and this did not interfere with the achievement of a sustained response. Evaluation of the presence of RAVs requires additional study in order to determine clinical relevance.
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Cela-Dablanca R, Santás-Miguel V, Fernández-Calviño D, Arias-Estévez M, Fernández-Sanjurjo MJ, Álvarez-Rodríguez E, Núñez-Delgado A. SARS-CoV-2 and other main pathogenic microorganisms in the environment: Situation in Galicia and Spain. ENVIRONMENTAL RESEARCH 2021; 197:111049. [PMID: 33753078 PMCID: PMC7979271 DOI: 10.1016/j.envres.2021.111049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 05/19/2023]
Abstract
In the context of the current COVID-19 pandemic, and mostly taking a broad perspective, it is clearly relevant to study environmental factors that could affect eventual future outbreaks due to coronaviruses and/or other pathogenic microorganisms. In view of that, the authors of this manuscript review the situation of SARS-CoV-2 and other main pathogenic microorganisms in the environment, focusing on Galicia and Spain. Overall, in addition to showing local data, it is put in evidence that, summed to all efforts being carried out to treat/control this and any other eventual future epidemic diseases, both at local and global levels, a deep attention should be paid to ecological/environmental aspects that have effects on the planet, its ecosystems and their relations/associations with the probability of spreading of eventual future pandemics.
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Affiliation(s)
- Raquel Cela-Dablanca
- Dept. Soil Science and Agricultural Chemistry, Engineering Polytechnic School, Univ. Santiago de Compostela, 27002, Lugo, Spain
| | - Vanesa Santás-Miguel
- Soil Science and Agricultural Chemistry, Fac. Sciences, Univ. Vigo, 32004, Ourense, Spain
| | | | - Manuel Arias-Estévez
- Soil Science and Agricultural Chemistry, Fac. Sciences, Univ. Vigo, 32004, Ourense, Spain
| | - María J Fernández-Sanjurjo
- Dept. Soil Science and Agricultural Chemistry, Engineering Polytechnic School, Univ. Santiago de Compostela, 27002, Lugo, Spain
| | - Esperanza Álvarez-Rodríguez
- Dept. Soil Science and Agricultural Chemistry, Engineering Polytechnic School, Univ. Santiago de Compostela, 27002, Lugo, Spain
| | - Avelino Núñez-Delgado
- Dept. Soil Science and Agricultural Chemistry, Engineering Polytechnic School, Univ. Santiago de Compostela, 27002, Lugo, Spain.
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Franklyne JS, Gopinath PM, Mukherjee A, Chandrasekaran N. Nanoemulsions: The rising star of antiviral therapeutics and nanodelivery system-current status and prospects. Curr Opin Colloid Interface Sci 2021; 54:101458. [PMID: 33814954 PMCID: PMC8007535 DOI: 10.1016/j.cocis.2021.101458] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nanoemulsions (NEs) of essential oil (EO) have significant potential to target microorganisms, especially viruses. They act as a vehicle for delivering antiviral drugs and vaccines. Narrowing of drug discovery pipeline and the emergence of new viral diseases, especially, coronavirus disease, have created a niche to use NEs for augmenting currently available therapeutic options. Published literature demonstrated that EOs have an inherent broad spectrum of activity across bacterial, fungal, and viral pathogens. The emulsification process significantly improved the efficacy of the active ingredients in the EOs. This article highlights the research findings and patent developments in the last 2 years especially, in EO antiviral activity, antiviral drug delivery, vaccine delivery, viral resistance development, and repurposing EO compounds against SARS-CoV-2.
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Affiliation(s)
| | | | - Amitava Mukherjee
- Centre for Nanobiotechnology, VIT University, Vellore, 32014, Tamil Nadu, India
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