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Nabakooza G, Galiwango R, Frost SDW, Kateete DP, Kitayimbwa JM. Molecular Epidemiology and Evolutionary Dynamics of Human Influenza Type-A Viruses in Africa: A Systematic Review. Microorganisms 2022; 10:900. [PMID: 35630344 PMCID: PMC9145646 DOI: 10.3390/microorganisms10050900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023] Open
Abstract
Genomic characterization of circulating influenza type-A viruses (IAVs) directs the selection of appropriate vaccine formulations and early detection of potentially pandemic virus strains. However, longitudinal data on the genomic evolution and transmission of IAVs in Africa are scarce, limiting Africa's benefits from potential influenza control strategies. We searched seven databases: African Journals Online, Embase, Global Health, Google Scholar, PubMed, Scopus, and Web of Science according to the PRISMA guidelines for studies that sequenced and/or genomically characterized Africa IAVs. Our review highlights the emergence and diversification of IAVs in Africa since 1993. Circulating strains continuously acquired new amino acid substitutions at the major antigenic and potential N-linked glycosylation sites in their hemagglutinin proteins, which dramatically affected vaccine protectiveness. Africa IAVs phylogenetically mixed with global strains forming strong temporal and geographical evolution structures. Phylogeographic analyses confirmed that viral migration into Africa from abroad, especially South Asia, Europe, and North America, and extensive local viral mixing sustained the genomic diversity, antigenic drift, and persistence of IAVs in Africa. However, the role of reassortment and zoonosis remains unknown. Interestingly, we observed substitutions and clades and persistent viral lineages unique to Africa. Therefore, Africa's contribution to the global influenza ecology may be understated. Our results were geographically biased, with data from 63% (34/54) of African countries. Thus, there is a need to expand influenza surveillance across Africa and prioritize routine whole-genome sequencing and genomic analysis to detect new strains early for effective viral control.
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Affiliation(s)
- Grace Nabakooza
- Department of Immunology and Molecular Biology, Makerere University, Old Mulago Hill Road, P.O. Box 7072, Kampala 256, Uganda;
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda; (R.G.); (J.M.K.)
| | - Ronald Galiwango
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda; (R.G.); (J.M.K.)
- Centre for Computational Biology, Uganda Christian University, Plot 67-173, Bishop Tucker Road, P.O. Box 4, Mukono 256, Uganda
- African Center of Excellence in Bioinformatics and Data Intensive Sciences, Infectious Diseases Institute, Makerere University, Kampala 256, Uganda
| | - Simon D. W. Frost
- Microsoft Research, Redmond, 14820 NE 36th Street, Washington, DC 98052, USA;
- London School of Hygiene & Tropical Medicine (LSHTM), University of London, Keppel Street, Bloomsbury, London WC1E7HT, UK
| | - David P. Kateete
- Department of Immunology and Molecular Biology, Makerere University, Old Mulago Hill Road, P.O. Box 7072, Kampala 256, Uganda;
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda; (R.G.); (J.M.K.)
| | - John M. Kitayimbwa
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda; (R.G.); (J.M.K.)
- Centre for Computational Biology, Uganda Christian University, Plot 67-173, Bishop Tucker Road, P.O. Box 4, Mukono 256, Uganda
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Danilenko AV, Kolosova NP, Shvalov AN, Ilyicheva TN, Svyatchenko SV, Durymanov AG, Bulanovich JA, Goncharova NI, Susloparov IM, Marchenko VY, Tregubchak TV, Gavrilova EV, Maksyutov RA, Ryzhikov AB. Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. PLoS One 2021; 16:e0251019. [PMID: 33914831 PMCID: PMC8084186 DOI: 10.1371/journal.pone.0251019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
Outbreaks of influenza, which is a contagious respiratory disease, occur throughout the world annually, affecting millions of people with many fatal cases. The D222G/N mutations in the hemagglutinin (HA) gene of A(H1N1)pdm09 are associated with severe and fatal human influenza cases. These mutations lead to increased virus replication in the lower respiratory tract (LRT) and may result in life-threatening pneumonia. Targeted NGS analysis revealed the presence of mutations in major and minor variants in 57% of fatal cases, with the proportion of viral variants with mutations varying from 1% to 98% in each individual sample in the epidemic season 2018-2019 in Russia. Co-occurrence of the mutations D222G and D222N was detected in a substantial number of the studied fatal cases (41%). The D222G/N mutations were detected at a low frequency (less than 1%) in the rest of the studied samples from fatal and nonfatal cases of influenza. The presence of HA D222Y/V/A mutations was detected in a few fatal cases. The high rate of occurrence of HA D222G/N mutations in A(H1N1)pdm09 viruses, their increased ability to replicate in the LRT and their association with fatal outcomes points to the importance of monitoring the mutations in circulating A(H1N1)pdm09 viruses for the evaluation of their epidemiological significance and for the consideration of disease prevention and treatment options.
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Affiliation(s)
- Alexey V. Danilenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Natalia P. Kolosova
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Alexander N. Shvalov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Tatyana N. Ilyicheva
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Svetlana V. Svyatchenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Alexander G. Durymanov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Julia A. Bulanovich
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Natalia I. Goncharova
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Ivan M. Susloparov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Vasiliy Y. Marchenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Tatyana V. Tregubchak
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Elena V. Gavrilova
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Rinat A. Maksyutov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Alexander B. Ryzhikov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
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Bhoye D, Behera AK, Cherian SS. A molecular modelling approach to understand the effect of co-evolutionary mutations (V344M, I354L) identified in the PB2 subunit of influenza A 2009 pandemic H1N1 virus on m7GTP ligand binding. J Gen Virol 2016; 97:1785-1796. [PMID: 27154164 DOI: 10.1099/jgv.0.000500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The cap binding domain of the polymerase basic 2 (PB2) subunit of influenza polymerases plays a critical role in mediating the 'cap-snatching' mechanism by binding the 5' cap of host pre-mRNAs during viral mRNA transcription. Monitoring variations in the PB2 protein is thus vital for evaluating the pathogenic potential of the virus. Based on selection pressure analysis of PB2 gene sequences of the pandemic H1N1 (pH1N1) viruses of the period 2009-2014, we identified a site, 344V/M, in the vicinity of the cap binding pocket showing evidence of adaptive evolution and another co-evolving residue, 354I/L, in close vicinity. Modelling of the three-dimensional structure of the pH1N1 PB2 cap binding domain, docking of the pre-mRNA cap analogue m7GTP and molecular dynamics simulation studies of the docked complexes performed for four PB2 variants observed showed that the complex possessing V344M with I354L possessed better ligand binding affinity due to additional hydrogen bond contacts between m7GTP and the key residues His432 and Arg355 that was attributed to a displacement of the 424 loop and a flip of the side chain of Arg355, respectively. The co-evolutionary mutations identified (V344M, I354L) were found to be established in the PB2 gene of the pH1N1 viral population over the period 2010-2014. The study demonstrates the molecular basis for the enhanced m7GTP ligand binding affinity with the 344M-354L synergistic combination in PB2. Furthermore, the insight gained into understanding the molecular mechanism of cap binding in pH1N1 viruses may be useful for designing novel drugs targeting the PB2 cap binding domain.
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Affiliation(s)
- Dipali Bhoye
- Bioinformatics and Data Management Group, National Institute of Virology, Pune 411001, Maharashtra, India
| | - Abhisek Kumar Behera
- Bioinformatics and Data Management Group, National Institute of Virology, Pune 411001, Maharashtra, India
| | - Sarah S Cherian
- Bioinformatics and Data Management Group, National Institute of Virology, Pune 411001, Maharashtra, India
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Matos-Patrón A, Byrd-Leotis L, Steinhauer DA, Barclay WS, Ayora-Talavera G. Amino acid substitution D222N from fatal influenza infection affects receptor-binding properties of the influenza A(H1N1)pdm09 virus. Virology 2015; 484:15-21. [DOI: 10.1016/j.virol.2015.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 03/15/2015] [Accepted: 05/12/2015] [Indexed: 12/12/2022]
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Goka EA, Vallely PJ, Mutton KJ, Klapper PE. Mutations associated with severity of the pandemic influenza A(H1N1)pdm09 in humans: a systematic review and meta-analysis of epidemiological evidence. Arch Virol 2014; 159:3167-83. [PMID: 25078388 DOI: 10.1007/s00705-014-2179-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/12/2014] [Indexed: 10/25/2022]
Abstract
Mutations in the haemagglutinin (HA), non-structural protein 1 (NS1) and polymerase basic protein 2 (PB2) of influenza viruses have been associated with virulence. This study investigated the association between mutations in these genes in influenza A(H1N1)pdm09 virus and the risk of severe or fatal disease. Searches were conducted on the MEDLINE, EMBASE and Web of Science electronic databases and the reference lists of published studies. The PRISMA and STROBE guidelines were followed in assessing the quality of studies and writing-up. Eighteen (18) studies, from all continents, were included in the systematic review (recruiting patients 0 - 77 years old). The mutation D222G was associated with a significant increase in severe disease (pooled RD: 11 %, 95 % CI: 3.0 % - 18.0 %, p = 0.004) and the risk of fatality (RD: 23 %, 95 % CI: 14.0 %-31.0 %, p = < 0.0001). No association was observed between the mutations HA-D222N, D222E, PB2-E627K and NS1-T123V and severe/fatal disease. The results suggest that no virus quasispecies bearing virulence-conferring mutations in the HA, PB2 and NS1 predominated. However issues of sampling bias, and bias due to uncontrolled confounders such as comorbidities, and viral and bacterial coinfection, should be born in mind. Influenza A viruses should continue to be monitored for the occurrence of virulence-conferring mutations in HA, PB2 and NS1. There are suggestions that respiratory virus coinfections also affect virus virulence. Studies investigating the role of genetic mutations on disease outcome should make efforts to also investigate the role of respiratory virus coinfections.
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Affiliation(s)
- E A Goka
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, 1st Floor Stopford building, Oxford Road, Manchester, M13 9PL, UK,
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