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Siafakas N, Anastassopoulou C, Lafazani M, Chronopoulou G, Rizos E, Pournaras S, Tsakris A. Predominance of Recombinant Norovirus Strains in Greece, 2016-2018. Microorganisms 2023; 11:2885. [PMID: 38138029 PMCID: PMC10745620 DOI: 10.3390/microorganisms11122885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
GII.4 noroviruses have caused the overwhelming majority of norovirus-related gastroenteritis cases during the past two decades. However, a trend towards the emergence of new genotypes and novel GII.4 variants provided the impetus to explore further the changing patterns in norovirus epidemiology during the present study. Genotyping of 60 norovirus strains detected during a period of 33 months (January 2016-October 2018) was performed on the basis of the capsid VP1-coding ORF2 gene sequence. All norovirus strains detected were classified into seven genotypes, six of which belonged to genogroup GII. GII.2 was the dominant genotype till February 2017, whereas GII.4 prevailed thereafter. Most of the GII.4 strains were of the Sydney_2012 variant, whereas five strains could not be classified. Further recombination analysis at the ORF1/ORF2 gene junction revealed that 23 out of 24 strains were recombinant, thereby showcasing the significant role of genetic recombination in norovirus evolution and epidemiology. Continuous genomic surveillance and molecular characterization are essential for tracking norovirus evolution, which could contribute to the elucidation of new aspects of virus-host interactions that potentially affect host morbidity and epidemiology.
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Affiliation(s)
- Nikolaos Siafakas
- Clinical Microbiology Laboratory, ATTIKON University Hospital, 12462 Athens, Greece; (M.L.); (S.P.)
| | - Cleo Anastassopoulou
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.A.); (A.T.)
| | - Maria Lafazani
- Clinical Microbiology Laboratory, ATTIKON University Hospital, 12462 Athens, Greece; (M.L.); (S.P.)
| | - Genovefa Chronopoulou
- Biopathology Department, Athens Medical Center, 5-7 Distomou Str., 15125 Marousi, Greece;
| | - Emmanouil Rizos
- 2nd Department of Psychiatry, ATTIKON University Hospital, 12462 Athens, Greece;
| | - Spyridon Pournaras
- Clinical Microbiology Laboratory, ATTIKON University Hospital, 12462 Athens, Greece; (M.L.); (S.P.)
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.A.); (A.T.)
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Norovirus waterborne outbreak in Chalkidiki, Greece, 2015: detection of GI.P2_GI.2 and GII.P16_GII.13 unusual strains. Epidemiol Infect 2020; 147:e227. [PMID: 31364530 PMCID: PMC6625189 DOI: 10.1017/s0950268819000852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Noroviruses, along with rotaviruses, are among the leading causes of gastroenteritis worldwide and novel strains are periodically emerging. In August 2015, an unusual increase of gastroenteritis cases occurred in a touristic district in Kassandra peninsula, Chalkidiki, Northern Greece. Seven stool specimens from cases were tested positive for norovirus. Molecular investigation and phylogenetic analysis identified that there was co-circulation of norovirus GI.P2_GI.2 and the recombinant strain GII.P16_GII.13. A 1:1 case–control study conducted and showed that tap water consumption significantly associated with developing symptoms of gastroenteritis (odds ratio = 36.9, P = 0.018). The results of the epidemiological investigation, the co-circulation of two different norovirus strains, the information of a pipeline breakage at the water supply system before the onset of cases, and reports on flooded wells and sewage overflow, indicated the possibility of water contamination by sewage during the pipeline breakage leading to a large outbreak with a peak at 10 August and a possible secondary person-to-person transmission after the 16th of August. Norovirus GI.P2_GI.2 strains are rarely reported in Europe, while it is the first time that infection from the recombinant strain GII.P16_GII.13 is recorded in Greece.
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Molecular epidemiology of noroviruses in children in South Greece, 2013‐2015. J Med Virol 2018; 90:1703-1711. [DOI: 10.1002/jmv.25251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/16/2018] [Indexed: 12/21/2022]
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Ludwig-Begall LF, Mauroy A, Thiry E. Norovirus recombinants: recurrent in the field, recalcitrant in the lab - a scoping review of recombination and recombinant types of noroviruses. J Gen Virol 2018; 99:970-988. [PMID: 29906257 DOI: 10.1099/jgv.0.001103] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Noroviruses are recognized as the major global cause of sporadic and epidemic non-bacterial gastroenteritis in humans. Molecular mechanisms driving norovirus evolution are the accumulation of point mutations and recombination. Intragenotypic recombination has long been postulated to be a driving force of GII.4 noroviruses, the predominant genotype circulating in humans for over two decades. Increasingly, emergence and re-emergence of different intragenotype recombinants have been reported. The number and types of norovirus recombinants remained undefined until the 2007 Journal of General Virology research article 'Norovirus recombination' reported an assembly of 20 hitherto unclassified intergenotypic norovirus recombinant types. In the intervening decade, a host of novel recombinants has been analysed. New recombination breakpoints have been described, in vitro and in vivo studies supplement in silico analyses, and advances have been made in analysing factors driving norovirus recombination. This work presents a timely overview of these data and focuses on important aspects of norovirus recombination and its role in norovirus molecular evolution. An overview of intergenogroup, intergenotype, intragenotype and 'obligatory' norovirus recombinants as detected via in silico methods in the field is provided, enlarging the scope of intergenotypic recombinant types to 80 in total, and notably including three intergenogroup recombinants. A recap of advances made studying norovirus recombination in the laboratory is given. Putative drivers and constraints of norovirus recombination are discussed and the potential link between recombination and norovirus zoonosis risk is examined.
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Affiliation(s)
- Louisa F Ludwig-Begall
- 1Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, B-4000 Liège, Belgium
| | - Axel Mauroy
- 2Staff direction for risk assessment, Control Policy, Federal Agency for the Safety of the Food Chain, Blv du Jardin Botanique 55, 1000 Brussels, Belgium
| | - Etienne Thiry
- 1Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, B-4000 Liège, Belgium
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Tsimpidis M, Bachoumis G, Mimouli K, Kyriakopoulou Z, Robertson DL, Markoulatos P, Amoutzias GD. T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes. BMC Bioinformatics 2017; 18:13. [PMID: 28056784 PMCID: PMC5216575 DOI: 10.1186/s12859-016-1420-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/10/2016] [Indexed: 12/22/2022] Open
Abstract
Background Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequence fragments and detect candidate recombination events that may later be further analyzed with more sensitive and specialized methods. Results T-RECs, a Windows based graphical tool, employs pairwise alignment of sliding windows and can perform (i) genotyping, (ii) clustering of new genomes, (iii) detect recent recombination events among different evolutionary lineages, (iv) manual inspection of detected recombination events by similarity plots and (v) annotation of genomic regions. Conclusions T-RECs is very effective, as demonstrated by an analysis of 555 Norovirus complete genomes and 2500 sequence fragments, where a recombination hotspot was identified at the ORF1-ORF2 junction.
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Affiliation(s)
- Michail Tsimpidis
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece
| | - Georgios Bachoumis
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece
| | - Kalliopi Mimouli
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece
| | - Zaharoula Kyriakopoulou
- Department of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece
| | | | - Panayotis Markoulatos
- Department of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece
| | - Grigoris D Amoutzias
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece.
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Ayukekbong JA, Mesumbe HN, Oyero OG, Lindh M, Bergström T. Role of noroviruses as aetiological agents of diarrhoea in developing countries. J Gen Virol 2015; 96:1983-1999. [PMID: 26002299 DOI: 10.1099/vir.0.000194] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Diarrhoea is considered to be the second leading cause of death due to infections among children < 5 years of age worldwide that may be caused by bacteria, parasites, viruses and non-infectious agents. The major causative agents of diarrhoea in developing countries may vary from those in developed countries. Noroviruses are considered to be the most common cause of acute diarrhoea in both children and adults in industrialized countries. On the other hand, there is a lack of comprehensive epidemiological evidence from developing countries that norovirus is a major cause of diarrhoea. In these regions, asymptomatic norovirus infections are very common, and similar detection rates have been observed in patients with diarrhoea and asymptomatic persons. This review summarizes the current knowledge of norovirus infection in developing countries and seeks to position infections with noroviruses among those of other enteropathogens in terms of disease burden in these regions.
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Affiliation(s)
- James Ayukepi Ayukekbong
- Section for Clinical Research, Redeem Biomedical System, Buea, Cameroon
- Department of Infectious Diseases/Section of Clinical Virology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | | | - Olufunmilayo G Oyero
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Nigeria
| | - Magnus Lindh
- Department of Infectious Diseases/Section of Clinical Virology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Tomas Bergström
- Department of Infectious Diseases/Section of Clinical Virology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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