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Li X, Tamim S, Trovão NS. The emergence and circulation of human immunodeficiency virus (HIV)-1 subtype C. J Med Microbiol 2024; 73. [PMID: 38757423 DOI: 10.1099/jmm.0.001827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
Introduction. Human immunodeficiency virus (HIV)-1 subtype C is the most prevalent globally and is thought to have originated in non-human primates in the Democratic Republic of Congo.Hypothesis/Gap Statement. Although the global dominance of HIV-1 subtype C is well established, a thorough understanding of its evolutionary history and transmission dynamics across various risk populations remains elusive. The current knowledge is insufficient to fully capture the global diversification and dissemination of this subtype.Aim. We for the first time sought to investigate the global evolutionary history and spatiotemporal dynamics of HIV-1 subtype C using a selection of maximum-likelihood-based phylodynamic approaches on a total of 1210 near full-length genomic sequences sampled from 32 countries, collected in 4 continents, with sampling dates between 1986-2019 among various risk groups were analysed.Methodology. We subsampled the HIV-1 subtype C genomic datasets based on continent and risk group traits, and performed nucleotide substitution model selection analysis, maximum likelihood (ML) phylogenetic reconstruction, phylogenetic tree topology similarity analysis, temporal signal analysis and traced the timings of viral spread both geographically and by risk group.Results. Based on the phylodynamic analyses of four datasets (full1210, locrisk626, loc562 and risk393), we inferred the time to the most recent common ancestor (TMRCA) in the 1930s and an evolutionary rate of 0.0023 substitutions per site per year. The total number of introduction events of HIV-1 subtype C between continents and between risk groups is estimated to be 71 and 115, respectively. The largest number of introductions occurred from Africa to Europe (n=32), from not-recorded to heterosexual (n=40) and from heterosexual to not-recorded (n=51) risk groups.Conclusion. Our results emphasize that HIV subtype C has mainly spread from Africa to Europe, likely through heterosexual transmission.
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Affiliation(s)
- Xingguang Li
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, 315000, PR China
| | - Sana Tamim
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Nídia S Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
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Tamim S, Adeel SS, Trevan T, Ikram A, Jadoon N, Zaman A, Mehmood R, Ashfaq QM, Mushtaq A, Shaukat M, Nimra M, Hamid S, Shabbir I. Implementing High-Reliability Organization Principles at Biological Diagnostic Laboratories: Case Study at National Institute of Health, Islamabad. Appl Biosaf 2022; 27:33-41. [PMID: 36032320 PMCID: PMC9402247 DOI: 10.1089/apb.2021.0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Introduction Healthcare organizations are complex systems where healthcare professionals, patients, biological materials, and equipment constantly interact and provide feedback with highly consequential outcomes. These are the characteristics of a complex adaptive system. Healthcare delivery requires coordination but it necessarily relies on delegation of essential functions. It is thus essential to have an engaged workforce to ensure optimal outcomes for patients. Thus human performance factors play a key role in ensuring both the presence of excellent healthcare provision and the absence of outcomes that must be avoided-"never events." Methods The commitment of management was a precondition for the implementation of the high-reliability organization (HRO) principles. A team from middle management was engaged and provided with appropriate management tools for identifying, prioritizing, assessing, and applying solutions for the safety concern in their operating systems. Results This article documents efforts at the National Institute of Health (NIH) to adapt the principles of HROs to diagnostic laboratories and vaccine production facilities at its campus in Islamabad, Pakistan, and seeks to draw some lessons for how this approach can be usefully replicated in such facilities elsewhere. Conclusion Public health institutes such as NIH deliver vital products and services that are inherently risky to produce, where the consequence of failure can be catastrophic. Adopting the HRO principles is an approach to improving not just safety, but also the overall organizational performance in any setting, including low-resource settings, and can serve as an implementable process for other institutions.
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Affiliation(s)
- Sana Tamim
- Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan.,Address correspondence to: Sana Tamim, Department of Virology/Immunology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 45500, Pakistan,
| | - Syeda Shazia Adeel
- Quality Assurance Department, National Institute of Health, Islamabad, Pakistan
| | - Tim Trevan
- Chrome Biorisk Management Consulting, Washington, District of Columbia, USA
| | - Aamer Ikram
- Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan
| | - Nadira Jadoon
- Department of Hematology, National Institute of Health, Islamabad, Pakistan
| | - Ayesha Zaman
- Department of Microbiology, National Institute of Health, Islamabad, Pakistan
| | - Rashid Mehmood
- Drugs Control and Traditional Medicine Division, National Institute of Health, Islamabad, Pakistan
| | - Qazi Muhammad Ashfaq
- Drugs Control and Traditional Medicine Division, National Institute of Health, Islamabad, Pakistan
| | - Atifa Mushtaq
- Drugs Control and Traditional Medicine Division, National Institute of Health, Islamabad, Pakistan
| | - Maria Shaukat
- Biological Production Division, National Institute of Health, Islamabad, Pakistan
| | - Mehak Nimra
- Biological Production Division, National Institute of Health, Islamabad, Pakistan
| | - Saima Hamid
- Nutrition Division, National Institute of Health, Islamabad, Pakistan
| | - Iqra Shabbir
- Nutrition Division, National Institute of Health, Islamabad, Pakistan
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Tamim S, Trovao NS, Thielen P, Mehoke T, Merritt B, Ikram A, Salman M, Alam MM, Umair M, Badar N, Khurshid A, Mehmood N. Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan. Infect Genet Evol 2021; 94:105003. [PMID: 34271187 PMCID: PMC8277555 DOI: 10.1016/j.meegid.2021.105003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/08/2021] [Accepted: 07/11/2021] [Indexed: 11/30/2022]
Abstract
Genomic epidemiology of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has provided global epidemiological insight into the COVID-19 pandemic since it began. Sequencing of the virus has been performed at scale, with many countries depositing data into open access repositories to enable in-depth global phylogenetic analysis. To contribute to these efforts, we established an Oxford Nanopore Technologies (ONT) sequencing capability at the National Institutes of Health (NIH), Pakistan. This study highlights multiple SARS-CoV-2 lineages co-circulating during the peak of a second COVID-19 wave in Pakistan (Nov 2020-Feb 2021), with virus origins traced to the United States of America and Saudi Arabia. Ten SARS-CoV-2 positive samples were used for ONT library preparation. Sequence and phylogenetic analysis determined that the patients were infected with lineage B.1.1.250, originally identified in the United Kingdom and Bangladesh during March and April of 2020, and in circulation until the time of this study in Europe, USA and Australia. Lineage B.1.261 was originally identified in Saudi Arabia with widespread local dissemination in Pakistan. One sample clustered with the parental B.1 lineage and the other with lineage B.6 originally from Singapore. In the future, monitoring the evolutionary dynamics of circulating lineages in Pakistan will enable improved tracing of the viral spread, changing trends of their expansion trajectories, persistence, changes in their demographic dynamics, and provide guidance for better implementation of control measures.
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Affiliation(s)
- Sana Tamim
- Department of Virology/Immunology, National Institute of Health, Park Road, Chak Shahzad, Islamabad 45500, Pakistan.
| | - Nidia S Trovao
- Fogarty International Centre, National Institute of Health, Bethesda, MD, USA
| | - Peter Thielen
- Johns Hopkins University Applied Physics Laboratory, USA
| | - Tom Mehoke
- Johns Hopkins University Applied Physics Laboratory, USA
| | - Brian Merritt
- Johns Hopkins University Applied Physics Laboratory, USA
| | - Aamer Ikram
- Department of Virology/Immunology, National Institute of Health, Park Road, Chak Shahzad, Islamabad 45500, Pakistan
| | - Muhammad Salman
- Department of Virology/Immunology, National Institute of Health, Park Road, Chak Shahzad, Islamabad 45500, Pakistan
| | - Muhammad Masroor Alam
- WHO Regional Reference Laboratory, Polio eradication Initiative, National Institute of Health, Islamabad, Pakistan
| | - Massab Umair
- Department of Virology/Immunology, National Institute of Health, Park Road, Chak Shahzad, Islamabad 45500, Pakistan
| | - Nazish Badar
- Department of Virology/Immunology, National Institute of Health, Park Road, Chak Shahzad, Islamabad 45500, Pakistan
| | - Adnan Khurshid
- WHO Regional Reference Laboratory, Polio eradication Initiative, National Institute of Health, Islamabad, Pakistan
| | - Nayab Mehmood
- WHO Regional Reference Laboratory, Polio eradication Initiative, National Institute of Health, Islamabad, Pakistan
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Sharif S, Ikram A, Khurshid A, Salman M, Mehmood N, Arshad Y, Ahmed J, Safdar RM, Rehman L, Mujtaba G, Hussain J, Ali J, Angez M, Alam MM, Akthar R, Wasif Malik M, Iqbal Baig MZ, Suleman Rana M, Usman M, Qaisar Ali M, Ahad A, Badar N, Umair M, Tamim S, Ashraf A, Tahir F, Ali N. Detection of SARs-CoV-2 in wastewater using the existing environmental surveillance network: A potential supplementary system for monitoring COVID-19 transmission. PLoS One 2021; 16:e0249568. [PMID: 34185787 PMCID: PMC8241060 DOI: 10.1371/journal.pone.0249568] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/19/2021] [Indexed: 12/14/2022] Open
Abstract
The ongoing COVID-19 pandemic is caused by SARs-CoV-2. The virus is transmitted from person to person through droplet infections i.e. when infected person is in close contact with another person. In January 2020, first report of detection of SARS-CoV-2 in faeces, has made it clear that human wastewater might contain this virus. This may illustrate the probability of environmentally facilitated transmission, mainly the sewage, however, environmental conditions that could facilitate faecal oral transmission is not yet clear. We used existing Pakistan polio environment surveillance network to investigate presence of SARs-CoV-2 using three commercially available kits and E-Gene detection published assay for surety and confirmatory of positivity. A Two-phase separation method is used for sample clarification and concentration. An additional high-speed centrifugation (14000Xg for 30 min) step was introduced, prior RNA extraction, to increase viral RNA yield resulting a decrease in Cq value. A total of 78 wastewater samples collected from 38 districts across Pakistan, 74 wastewater samples from existing polio environment surveillance sites, 3 from drains of COVID-19 infected areas and 1 from COVID 19 quarantine center drainage, were tested for presence of SARs-CoV-2. 21 wastewater samples (27%) from 13 districts turned to be positive on RT-qPCR. SARs-COV-2 RNA positive samples from areas with COVID 19 patients and quarantine center strengthen the findings and use of wastewater surveillance in future. Furthermore, sequence data of partial ORF 1a generated from COVID 19 patient quarantine center drainage sample also reinforce our findings that SARs-CoV-2 can be detected in wastewater. This study finding indicates that SARs-CoV-2 detection through wastewater surveillance has an epidemiologic potential that can be used as supplementary system to monitor viral tracking and circulation in cities with lower COVID-19 testing capacity or heavily populated areas where door-to-door tracing may not be possible. However, attention is needed on virus concentration and detection assay to increase the sensitivity. Development of highly sensitive assay will be an indicator for virus monitoring and to provide early warning signs.
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Affiliation(s)
- Salmaan Sharif
- National Institute of Health, Islamabad, Pakistan
- * E-mail:
| | - Aamer Ikram
- National Institute of Health, Islamabad, Pakistan
| | | | | | | | - Yasir Arshad
- National Institute of Health, Islamabad, Pakistan
| | - Jamal Ahmed
- World Health Organization, Islamabad, Pakistan
| | | | - Lubna Rehman
- National Institute of Health, Islamabad, Pakistan
| | | | | | - Johar Ali
- National Institute of Health, Islamabad, Pakistan
| | - Mehar Angez
- National Institute of Health, Islamabad, Pakistan
| | | | - Ribqa Akthar
- National Institute of Health, Islamabad, Pakistan
| | | | | | | | | | | | - Abdul Ahad
- National Institute of Health, Islamabad, Pakistan
| | - Nazish Badar
- National Institute of Health, Islamabad, Pakistan
| | - Massab Umair
- National Institute of Health, Islamabad, Pakistan
| | - Sana Tamim
- National Institute of Health, Islamabad, Pakistan
| | - Asiya Ashraf
- National Institute of Health, Islamabad, Pakistan
| | - Faheem Tahir
- National Institute of Health, Islamabad, Pakistan
| | - Nida Ali
- World Health Organization, Islamabad, Pakistan
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Umair M, Ikram A, Salman M, Alam MM, Badar N, Rehman Z, Tamim S, Khurshid A, Ahad A, Ahmad H, Ullah S. Importation of SARS-CoV-2 Variant B.1.1.7 in Pakistan. J Med Virol 2021; 93:2623-2625. [PMID: 33570181 PMCID: PMC8013196 DOI: 10.1002/jmv.26869] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/15/2022]
Affiliation(s)
- Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Aamer Ikram
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | | | - Nazish Badar
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Zaira Rehman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Sana Tamim
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Adnan Khurshid
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Abdul Ahad
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Hamza Ahmad
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Samee Ullah
- Department of Virology, National Institute of Health, Islamabad, Pakistan
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Tamim S, Heylen E, Zeller M, Ranst MV, Matthijnssens J, Salman M, Aamir UB, Sharif S, Ikram A, Hasan F. Phylogenetic analysis of open reading frame of 11 gene segments of novel human-bovine reassortant RVA G6P[1] strain in Pakistan. J Med Virol 2020; 92:3179-3186. [PMID: 31696948 DOI: 10.1002/jmv.25625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/30/2019] [Indexed: 11/05/2022]
Abstract
Multiple Rotavirus A (RVA) strains are linked with gastrointestinal infections in children that fall in age bracket of 0 to 60 months. However, the problem is augmented with emergence of unique strains that reassort with RVA strains of animal origin. The study describes the sequence analysis of a rare G6P[1] rotavirus strain isolated from a less than 1 year old child, during rotavirus surveillance in Rawalpindi district, Pakistan in 2010. Extracted RNA from fecal specimen was subjected to high throughput RT-PCR for structural and nonstructural gene segments. The complete rotavirus genome of one isolate RVA/Human-wt/PAK/PAK99/2010/G6P[1] was sequenced for phylogenetic analysis to elucidate the evolutionary linkages and origin. Full genome examination of novel strain RVA/Human-wt/PAK/PAK99/2010/G6P[1] revealed the unique genotype assemblage: G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H1. The evolutionary analyses of VP7, VP4, NSP1 and NSP3 gene segments revealed that PAK99 clustered with bovine, or cattle-like rotavirus strains from other closely related species, in the genotypes G6, P[1], A3 and T6 respectively. Gene segments VP6, VP1, VP2, VP3, NSP2 and NSP4 all possessed the DS-1-like bovine genotype 2 and bovine (-like) RVA strains instead of RVA strains having human origin. However, the NSP5 gene was found to cluster closely with contemporary human Wa-like rotavirus strains of H1 genotype. This is the first report on bovine-human (Wa-like reassortant) genotype constellation of G6P[1] strain from a human case in Pakistan (and the second description worldwide). Our results emphasize the significance of incessant monitoring of circulating RVA strains in humans and animals for better understanding of RV evolution.
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Affiliation(s)
- Sana Tamim
- Public Health Laboratories, Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan
| | - Elisabeth Heylen
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium
| | | | - Muhammad Salman
- Public Health Laboratories, Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan
| | - Uzma Bashir Aamir
- IHP unit Health Emergencies, WHO Country Office, Islamabad, Pakistan
| | - Salman Sharif
- Public Health Laboratories, Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan
| | - Aamer Ikram
- Public Health Laboratories, Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan
| | - Fariha Hasan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
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Tamim S, Matthijnssens J, Heylen E, Zeller M, Van Ranst M, Salman M, Hasan F. Evidence of zoonotic transmission of VP6 and NSP4 genes into human species A rotaviruses isolated in Pakistan in 2010. Arch Virol 2019; 164:1781-1791. [PMID: 31079214 DOI: 10.1007/s00705-019-04271-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/30/2019] [Indexed: 10/26/2022]
Abstract
Introduction of animal group A rotavirus (RVA) gene segments into the human RVA population is a major factor shaping the genetic landscape of human RVA strains. The VP6 and NSP4 genes of 74 G/P-genotyped RVA isolates collected in Rawalpindi during 2010 were analyzed, revealing the presence of VP6 genotypes I1 (60.8%) and I2 (39.2%) and NSP4 genotypes E1 (60.8%), E2 (28.3%) and E-untypable (10.8%) among the circulating human RVA strains. The typical human RVA combinations I1E1 and I2E2 were found in 59.4% and 24.3% of the cases, respectively, whereas 5.4% of the RVA strains were reassortants, i.e., either I1E2 or I2E1. The phylogeny of the NSP4 gene showed that one G2P[4] and two G1P[6] RVA strains clustered with porcine E1 RVA strains or RVA strains that were considered to be (partially) of porcine origin. In addition, the NSP4 gene segment of the unusual human G6P[1] RVA strains clustered closely with bovine E2 RVA strains, further strengthening the hypothesis of an interspecies transmission event. The study further demonstrates the role of genomic re-assortment and the involvement of interspecies transmission in the evolution of human RVA strains. The VP6 and NSP4 nucleotide sequences analyzed in the study received the GenBank accession numbers KC846908- KC846971 and KC846972-KC847037, respectively.
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Affiliation(s)
- Sana Tamim
- Public Health Laboratories Division, Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan.
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Rega Institute, Herestraat 49 box 1040, 3000, Leuven, Belgium
| | - Elisabeth Heylen
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium
| | - Muhammad Salman
- Public Health Laboratories Division, Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan
| | - Fariha Hasan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
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Zeller M, Heylen E, Tamim S, McAllen JK, Kirkness EF, Akopov A, De Coster S, Van Ranst M, Matthijnssens J. Comparative analysis of the Rotarix™ vaccine strain and G1P[8] rotaviruses detected before and after vaccine introduction in Belgium. PeerJ 2017; 5:e2733. [PMID: 28070453 PMCID: PMC5214804 DOI: 10.7717/peerj.2733] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 10/28/2016] [Indexed: 02/04/2023] Open
Abstract
G1P[8] rotaviruses are responsible for the majority of human rotavirus infections worldwide. The effect of universal mass vaccination with rotavirus vaccines on circulating G1P[8] rotaviruses is still poorly understood. Therefore we analyzed the complete genomes of the Rotarix™ vaccine strain, and 70 G1P[8] rotaviruses, detected between 1999 and 2010 in Belgium (36 before and 34 after vaccine introduction) to investigate the impact of rotavirus vaccine introduction on circulating G1P[8] strains. All rotaviruses possessed a complete Wa-like genotype constellation, but frequent intra-genogroup reassortments were observed as well as multiple different cluster constellations circulating in a single season. In addition, identical cluster constellations were found to circulate persistently over multiple seasons. The Rotarix™ vaccine strain possessed a unique cluster constellation that was not present in currently circulating G1P[8] strains. At the nucleotide level, the VP6, VP2 and NSP2 gene segments of Rotarix™ were relatively distantly related to any Belgian G1P[8] strain, but other gene segments of Rotarix™ were found in clusters also containing circulating Belgian strains. At the amino acid level, the genetic distance between Rotarix™ and circulating Belgian strains was considerably lower, except for NSP1. When we compared the Belgian G1P[8] strains collected before and after vaccine introduction a reduction in the proportion of strains that were found in the same cluster as the Rotarix™ vaccine strain was observed for most gene segments. The reduction in the proportion of strains belonging to the same cluster may be the result of the vaccine introduction, although natural fluctuations cannot be ruled out.
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Affiliation(s)
- Mark Zeller
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven , Leuven , Belgium
| | - Elisabeth Heylen
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven , Leuven , Belgium
| | - Sana Tamim
- Department of Microbiology, Quaid-i-Azam University , Islamabad , Pakistan
| | | | | | - Asmik Akopov
- The J. Craig Venter Institute , Rockville , MD , USA
| | - Sarah De Coster
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven , Leuven , Belgium
| | - Marc Van Ranst
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven , Leuven , Belgium
| | - Jelle Matthijnssens
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven , Leuven , Belgium
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Zeller M, Heylen E, Damanka S, Pietsch C, Donato C, Tamura T, Kulkarni R, Arora R, Cunliffe N, Maunula L, Potgieter C, Tamim S, Coster SD, Zhirakovskaya E, Bdour S, O'Shea H, Kirkwood CD, Seheri M, Nyaga MM, Mphahlele J, Chitambar SD, Dagan R, Armah G, Tikunova N, Van Ranst M, Matthijnssens J. Emerging OP354-Like P[8] Rotaviruses Have Rapidly Dispersed from Asia to Other Continents. Mol Biol Evol 2015; 32:2060-71. [PMID: 25858434 DOI: 10.1093/molbev/msv088] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The majority of human group A rotaviruses possess the P[8] VP4 genotype. Recently, a genetically distinct subtype of the P[8] genotype, also known as OP354-like P[8] or lineage P[8]-4, emerged in several countries. However, it is unclear for how long the OP354-like P[8] gene has been circulating in humans and how it has spread. In a global collaborative effort 98 (near-)complete OP354-like P[8] VP4 sequences were obtained and used for phylogeographic analysis to determine the viral migration patterns. During the sampling period, 1988-2012, we found that South and East Asia acted as a source from which strains with the OP354-like P[8] gene were seeded to Africa, Europe, and North America. The time to the most recent common ancestor (TMRCA) of all OP354-like P[8] genes was estimated at 1987. However, most OP354-like P[8] strains were found in three main clusters with TMRCAs estimated between 1996 and 2001. The VP7 gene segment of OP354-like P[8] strains showed evidence of frequent reassortment, even in localized epidemics, suggesting that OP354-like P[8] genes behave in a similar manner on the evolutionary level as other P[8] subtypes. The results of this study suggest that OP354-like P[8] strains have been able to disperse globally in a relatively short time period. This, in combination with a relatively large genetic distance to other P[8] subtypes, might result in a lower vaccine effectiveness, underscoring the need for a continued surveillance of OP354-like P[8] strains, especially in countries where rotavirus vaccination programs are in place.
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Affiliation(s)
- Mark Zeller
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Elisabeth Heylen
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Susan Damanka
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | | | - Celeste Donato
- Enteric Virus Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Tsutomu Tamura
- Department of Virology, Niigata Prefectural Institute of Public Health and Environmental Sciences, Niigata, Japan
| | - Ruta Kulkarni
- Enteric Viruses Group, National Institute of Virology, Pune, Maharashtra, India
| | - Ritu Arora
- Enteric Viruses Group, National Institute of Virology, Pune, Maharashtra, India
| | - Nigel Cunliffe
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Leena Maunula
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Christiaan Potgieter
- Department of Biochemistry, Centre for Human Metabonomics, North-West University, Potchefstroom, South Africa Deltamune (Pty) Ltd, Lyttelton, Centurion, South Africa
| | - Sana Tamim
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sarah De Coster
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Elena Zhirakovskaya
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Salwa Bdour
- Department of Biological Sciences, Faculty of Science, The University of Jordan, Amman, Jordan
| | - Helen O'Shea
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - Carl D Kirkwood
- Enteric Virus Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Mapaseka Seheri
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Martin Monene Nyaga
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Jeffrey Mphahlele
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Shobha D Chitambar
- Enteric Viruses Group, National Institute of Virology, Pune, Maharashtra, India
| | - Ron Dagan
- Soroka University Medical Center and the Faculty of Health Sciences, Ben-Gurion University of Negev, Beer Sheva, Israel
| | - George Armah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Nina Tikunova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Marc Van Ranst
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
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10
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Chishti MS, Bhatti A, Tamim S, Lee K, McDonald ML, Leal SM, Ahmad W. Splice-site mutations in the TRIC gene underlie autosomal recessive nonsyndromic hearing impairment in Pakistani families. J Hum Genet 2007; 53:101-105. [PMID: 18084694 DOI: 10.1007/s10038-007-0209-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2007] [Accepted: 10/01/2007] [Indexed: 11/29/2022]
Abstract
Hereditary hearing impairment (HI) displays extensive genetic heterogeneity. To date, 67 autosomal recessive nonsyndromic hearing impairment (ARNSHI) loci have been mapped, and 24 genes have been identified. This report describes three large consanguineous ARNSHI Pakistani families, all of which display linkage to marker loci located in the genetic interval of DFNB49 locus on chromosome 5q13. Recently, Riazuddin et al. (Am J Hum Genet 2006; 79:1040-1051) reported that variants within the TRIC gene, which encodes tricellulin, are responsible for HI due to DFNB49. TRIC gene sequencing in these three families led to the identification of a novel mutation (IVS4+1G> A) in one family and the discovery of a previously described mutation (IVS4+2T> C) in two families. It is estimated that 1.06% (95% confidence interval 0.02-3.06%) of families with ARNSHI in Pakistan manifest HI due to mutations in the TRIC gene.
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Affiliation(s)
- Muhammad S Chishti
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Attya Bhatti
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Sana Tamim
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Kwanghyuk Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Alkek Building N1619.01, Houston, TX, 77030, USA
| | - Merry-Lynn McDonald
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Alkek Building N1619.01, Houston, TX, 77030, USA
| | - Suzanne M Leal
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Alkek Building N1619.01, Houston, TX, 77030, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan.
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11
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Huber C, Pons O, Hendel H, Haumont P, Jacquemin L, Tamim S, Zagury JF. Genomic studies in AIDS: problems and answers. Development of a statistical model integrating both longitudinal cohort studies and transversal observations of extreme cases. Biomed Pharmacother 2003; 57:25-33. [PMID: 12642034 DOI: 10.1016/s0753-3322(02)00335-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Genomic studies developed to understand HIV-1 infection and pathogenesis have often lead to conflicting results. This is linked to various factors, including differences in cohort design and selection, the numbers of patients involved, the influence of population substructure, the ethnic origins of the participants, and phenotypic definition. These difficulties in the interpretation of results are examined through published studies on the role of polymorphisms in HLA and the chemokine receptors genes in AIDS. Our analysis suggests that the use of haplotypes will strengthen the results obtained in a given cohort, and meta-analysis including multiple cohorts to gather large-enough numbers of patients should also allow clarification of the genetic associations observed. A P-value of 0.001 appears to be a good compromise for significance on candidate genes in a genetic study. Due to the generally limited size of available cohorts, results will have to be validated in other cohorts. We developed a model to fit transversal case studies (extreme case-control studies) with longitudinal cohorts (all-stages patients) for observations on two gene polymorphisms of CCR5 and NQO1. Interestingly, we observe a protective effect for the CCR5-Delta32 mutant allele in 95% of the simulations based on that model when using a population of 600 subjects; however, when using populations of 250 subjects we find a significant protection in only 59% of the simulations. Our model gives thus an explanation for the discrepancies observed in the various genomic studies published in AIDS on CCR5-Delta32 and other gene polymorphisms: they result from statistical fluctuations due to a lack of power. The sizes of most seroconverter cohorts presently available seem thus insufficient since they include less than a few hundred subjects. This result underlines the power and usefulness of the transversal studies involving extreme patients and their complementarity to longitudinal studies involving seroconverter cohorts. The transposition approach of extreme case-control data into longitudinal analysis should prove useful not only in AIDS but also in other diseases induced by chronic exposure to a foreign agent or with chronic clinical manifestations.
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Affiliation(s)
- C Huber
- UFR Biomédicale, Université Paris V, INSERM U472, IFR69, 45, rue des Saints-Pères, 75006, Paris, France
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12
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Douabin-Gicquel V, Soriano N, Ferran H, Wojcik F, Palierne E, Tamim S, Jovelin T, McKie AT, Le Gall JY, David V, Mosser J. Identification of 96 single nucleotide polymorphisms in eight genes involved in iron metabolism: efficiency of bioinformatic extraction compared with a systematic sequencing approach. Hum Genet 2001; 109:393-401. [PMID: 11702220 DOI: 10.1007/s004390100599] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2001] [Accepted: 07/31/2001] [Indexed: 11/28/2022]
Abstract
Single nucleotide polymorphisms (SNPs) can significantly contribute to the characterization of the genes predisposing to iron overloads or deficiencies. We report an SNP survey of coding and non-coding regions of eight genes involved in iron metabolism, by two successive methods. First, we made use of the public domain sequence data, by using assembled expressed sequence tags, non-redundant sequences, and SNP database screening. We extracted 77 potential SNPs of which only 31 could be further validated by sequencing DNA from 44 unrelated multi-ethnic individuals. Our results indicate that a bioinformatic approach may be effective only in those cases where candidate SNPs are extracted from two different data sources or in cases of experimentally confirmed SNPs. Second, additional systematic sequencing of DNA from 24 unrelated Breton subjects increased the number of SNPs over a total length of 86 kb to 96. The average distance between the SNPs and minor allele frequencies were higher than reported by others authors; this discrepancy may reflect the nature of the genes studied and the ethnic homogeneity of our test population.
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Affiliation(s)
- V Douabin-Gicquel
- Département de Biochimie et Biologie Moléculaire, et UMR6061 CNRS, Faculté de Médecine, 2 Avenue du Pr Léon Bernard CS34317, 35043 Rennes cédex, France
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13
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Tamim S, Lauret MG, Drouet M, Sabbah A. [Level of histamine in supernatants from the basophil activation test: applications to hymenoptera allergy and drug allergy--preliminary study]. Allerg Immunol (Paris) 1999; 31:35-44. [PMID: 10219425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Histamine Release technic consists in calculating histamine liberated by blood cells in touch with an allergen. To this day, this method is only used in Hymenoptera venom allergy diagnosis. The principle of this study is to measure histamine released by activated basophils in surnageons of Basophil Activation Test (BAT) for different allergens: Hymenoptera venoms: Bee, White Faced Hornet, Vespula Wasp. Drugs: Cefaperos, Clamoxyl, Alfatil, Rapifen, Diprivan, Nesdonal, Mivacron. A threshold of positivity (amplification factor in comparison with the control) is determined for these two classes of allergens: 45 for Hymenoptera venoms and 9 for drugs. These results, compared to the other diagnosis technics (Histamine Release, Basophil Activation Test, Prick Tests) discloses very high correlation rates in each case. This method seems to be a reliable method for Hymenoptera venom allergy diagnosis and for drugs allergy diagnosis too. However, this study is based on a few number of patients, so a significant statistic conclusion can't be expressed but it opens an interesting way of research.
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Affiliation(s)
- S Tamim
- Laboratoire d'Immuno-Allergologie-C.H.U., Angers, France
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