Large-scale genomic analysis reveals recurrent patterns of intertypic recombination in human enteroviruses

Nikolaidis, Marios; Mimouli, Kalliopi; Kyriakopoulou, Zaharoula; Tsimpidis, Michail; Tsakogiannis, D.; Markoulatos, Panayotis; Amoutzias, Grigoris D.

doi:10.1016/j.virol.2018.10.006

Cited by 40 publications

(47 citation statements)

References 80 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Recombination plays a crucial role in the evolution of enterovirus (Simmonds and Welch 2006). The hot spots for enterovirus recombination are often located in the 2A/2B genomic regions (Nikolaidis et al 2018). Because the analyzed sequences are predominantly represented by partial VP1 genomic region, some circulating enterovirus recombinants may be missed by this and other studies.…”

Section: Discussionmentioning

confidence: 99%

National Epidemiology and Evolutionary History of Four Hand, Foot and Mouth Disease-Related Enteroviruses in China from 2008 to 2016

Wan

et al. 2019

Virol. Sin.

View full text Add to dashboard Cite

Hand, foot and mouth disease (HFMD) is a major public health concern in China. The most predominant enteroviruses that cause HFMD have traditionally been attributed to enterovirus A71 (EVA71) and coxsackievirus A16 (CVA16). Since its first large outbreak in 2008, the dominant HFMD pathogens are constantly changing. In 2013 and 2015, CVA6 exceeded both EVA71 and CVA16 to become the leading cause of HFMD in some provinces. However, there still lacks a comprehensive overview on the molecular epidemiology and evolution of HFMD-related enteroviruses at the national level. In this study, we performed systematic epidemiological analyses of HFMD-related enteroviruses using the data of 64 published papers that met the inclusion criteria, and conducted phylogenetic analyses based on 12,080 partial VP1 sequences identified in China before 31st June 2018. We found that EVA71 prevalence has decreased sharply but other enteroviruses have increased rapidly from 2008 to 2016 and that one subtype of each enterovirus is represented during the epidemic. In addition, four genotypes EVA71_C4, CVA16_B1, CVA6_D and CVA10_C are the most predominant enterovirus strains and collectively they cause over 90% of all HFMD cases in China according to the phylogenetic trees using representative partial VP1 sequences. These four major enterovirus genotypes have different geographical distributions, and they may cocirculate with other genotypes and serotypes. These results suggest that more molecular epidemiological studies should be performed on several enteroviruses simultaneously, and such information should have implications for virological surveillance, disease management, vaccine development and policy-making on the prevention and control of HFMD.

show abstract

Section: Discussionmentioning

confidence: 99%

National Epidemiology and Evolutionary History of Four Hand, Foot and Mouth Disease-Related Enteroviruses in China from 2008 to 2016

Wan

et al. 2019

Virol. Sin.

View full text Add to dashboard Cite

show abstract

“…In our study, we used the CVB3 H3 Woodruff variant, which presented high susceptibility for myocardial cells in vitro and lacked tropism for heart in vivo [9]. Interestingly, CVB3 may recombine with other Enterovirus B viruses, like Echo-6, Echo-16, Echo-30, Echo-25, and CVB5 [55]. Thus, in a clinical setting, although the virus may be identified as CVB3, based on the VP1 sequence, it is still possible that the recombinant sequence of a patient may have different properties and the cellular response may be different.…”

Section: Discussionmentioning

confidence: 99%

Coxsackievirus B3 Infection of Human Neural Progenitor Cells Results in Distinct Expression Patterns of Innate Immune Genes

Gim

Lee

et al. 2020

Viruses

View full text Add to dashboard Cite

Coxsackievirus B3 (CVB3), a member of Picornaviridae family, is an important human pathogen that causes a wide range of diseases, including myocarditis, pancreatitis, and meningitis. Although CVB3 has been well demonstrated to target murine neural progenitor cells (NPCs), gene expression profiles of CVB3-infected human NPCs (hNPCs) has not been fully explored. To characterize the molecular signatures and complexity of CVB3-mediated host cellular responses in hNPCs, we performed QuantSeq 3′ mRNA sequencing. Increased expression levels of viral RNA sensors (RIG-I, MDA5) and interferon-stimulated genes, such as IFN-β, IP-10, ISG15, OAS1, OAS2, Mx2, were detected in response to CVB3 infection, while IFN-γ expression level was significantly downregulated in hNPCs. Consistent with the gene expression profile, CVB3 infection led to enhanced secretion of inflammatory cytokines and chemokines, such as interleukin-6 (IL-6), interleukin-8 (IL-8), and monocyte chemoattractant protein-1 (MCP-1). Furthermore, we show that type I interferon (IFN) treatment in hNPCs leads to significant attenuation of CVB3 RNA copy numbers, whereas, type II IFN (IFN-γ) treatment enhances CVB3 replication and upregulates suppressor of cytokine signaling 1/3 (SOCS) expression levels. Taken together, our results demonstrate the distinct molecular patterns of cellular responses to CVB3 infection in hNPCs and the pro-viral function of IFN-γ via the modulation of SOCS expression.

show abstract

“…It can involve replicative or non-replicative mechanisms [ 2 , 3 ] and potentially serves functions that include the purging of deleterious mutations and the creation of advantageous novel genetic combinations to evade host immunity, gain resistance to antiviral agents, alter virulence and expand the host range [ 1 , 4 , 5 ]. Molecular epidemiological studies, for example, of circulating enteroviruses, have shown that recombination is a frequent occurrence in picornaviruses (e.g., [ 6 , 7 , 8 ]), and analysis of viral metagenomic data has emphasized the importance of recombination in the acquisition of novel sequences and, consequently, in the evolution of viruses [ 9 , 10 ]. In contrast to nucleotide substitution, which only allows gradual searching through evolutionary fitness space, recombination can lead to large shifts that can create beneficial genetic diversity but may also disrupt favorable combinations of co-adapted alleles [ 1 , 11 ].…”

Section: Recombination As a Motive Force In Viral Evolutionmentioning

confidence: 99%

Dissemination of Internal Ribosomal Entry Sites (IRES) Between Viruses by Horizontal Gene Transfer

Arhab

Bulakhov

Pestova

et al. 2020

Viruses

View full text Add to dashboard Cite

Members of Picornaviridae and of the Hepacivirus, Pegivirus and Pestivirus genera of Flaviviridae all contain an internal ribosomal entry site (IRES) in the 5′-untranslated region (5′UTR) of their genomes. Each class of IRES has a conserved structure and promotes 5′-end-independent initiation of translation by a different mechanism. Picornavirus 5′UTRs, including the IRES, evolve independently of other parts of the genome and can move between genomes, most commonly by intratypic recombination. We review accumulating evidence that IRESs are genetic entities that can also move between members of different genera and even between families. Type IV IRESs, first identified in the Hepacivirus genus, have subsequently been identified in over 25 genera of Picornaviridae, juxtaposed against diverse coding sequences. In several genera, members have either type IV IRES or an IRES of type I, II or III. Similarly, in the genus Pegivirus, members contain either a type IV IRES or an unrelated type; both classes of IRES also occur in members of the genus Hepacivirus. IRESs utilize different mechanisms, have different factor requirements and contain determinants of viral growth, pathogenesis and cell type specificity. Their dissemination between viruses by horizontal gene transfer has unexpectedly emerged as an important facet of viral evolution.

show abstract

Large-scale genomic analysis reveals recurrent patterns of intertypic recombination in human enteroviruses

Cited by 40 publications

References 80 publications

National Epidemiology and Evolutionary History of Four Hand, Foot and Mouth Disease-Related Enteroviruses in China from 2008 to 2016

National Epidemiology and Evolutionary History of Four Hand, Foot and Mouth Disease-Related Enteroviruses in China from 2008 to 2016

Coxsackievirus B3 Infection of Human Neural Progenitor Cells Results in Distinct Expression Patterns of Innate Immune Genes

Dissemination of Internal Ribosomal Entry Sites (IRES) Between Viruses by Horizontal Gene Transfer

Contact Info

Product

Resources

About