Enterovirus surveillance reveals proposed new serotypes and provides new insight into enterovirus 5′-untranslated region evolution

Smura, Teemu; Blomqvist, Soile; Paananen, Anja; Vuorinen, Tytti; Sobotová, Zdenka; Buboviča, Veronika; Ivanova, Olga E.; Hovi, Tapani; Roivainen, Merja

doi:10.1099/vir.0.82866-0

Cited by 67 publications

(68 citation statements)

References 43 publications

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“…5). The observed recombination product between different HEV species is consistent with previous reports that interspecies recombination involving the 5Ј UTR can occur in enteroviruses, as reported by Smura et al, who describe an enterovirus genome closely related to HEV-A types except for the 5Ј UTR region, which clusters with HEV-C and -D sequences (41). The recombination evidence in EV109 is similar to the recombination event reported by Tapparel et al in EV104 (44).…”

Section: Discussionsupporting

confidence: 80%

“…Intraspecies recombination events occur frequently in enteroviruses, especially within the nonstructural coding region, but interspecies exchanges involving the 5Ј UTR have also been observed (3,8,15,26,33,38,39,41). A phylogenetic tree constructed using enterovirus 5Ј UTR sequences (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…All known enterovirus 5Ј UTR sequences, however, cluster into two groups containing either HEV-A and -B sequences or HEV-C and -D sequences. Recent findings have described enterovirus genomes with a coding region that clusters with one species and a 5Ј UTR that clusters with a different species, suggesting possible interspecies recombination events (41,44). Understanding the recombination-driven evolution of HEV-C viruses is of particular public health concern due to the viruses' ability to recombine with vaccine poliovirus, resulting in circulating, highly neurovirulent vaccine-derived polioviruses (17,21,34).…”

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confidence: 99%

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Human Enterovirus 109: a Novel Interspecies Recombinant Enterovirus Isolated from a Case of Acute Pediatric Respiratory Illness in Nicaragua

Yozwiak

Skewes-Cox²,

Gordon

et al. 2010

J Virol

119

102

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Enteroviruses (Picornaviridae family) are a common cause of human illness worldwide and are associated with diverse clinical syndromes, including asymptomatic infection, respiratory illness, gastroenteritis, and meningitis. In this study, we report the identification and complete genome sequence of a novel enterovirus isolated from a case of acute respiratory illness in a Nicaraguan child. Unbiased deep sequencing of nucleic acids from a nose and throat swab sample enabled rapid recovery of the full-genome sequence. Phylogenetic analysis revealed that human enterovirus 109 (EV109) is most closely related to serotypes of human enterovirus species C (HEV-C) in all genomic regions except the 5 untranslated region (5 UTR). Bootstrap analysis indicates that the 5 UTR of EV109 is likely the product of an interspecies recombination event between ancestral members of the HEV-A and HEV-C groups. Overall, the EV109 coding region shares 67 to 72% nucleotide sequence identity with its nearest relatives. EV109 isolates were detected in 5/310 (1.6%) of nose and throat swab samples collected from children in a pediatric cohort study of influenza-like illness in Managua, Nicaragua, between June 2007 and June 2008. Further experimentation is required to more fully characterize the pathogenic role, disease associations, and global distribution of EV109.

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Section: Discussionsupporting

confidence: 80%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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Human Enterovirus 109: a Novel Interspecies Recombinant Enterovirus Isolated from a Case of Acute Pediatric Respiratory Illness in Nicaragua

Yozwiak

Skewes-Cox²,

Gordon

et al. 2010

J Virol

119

102

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“…As previously discussed (9,33,37), there is further recombination between coding regions and 5=UTRs and 3=UTRs within human and simian enteroviruses. Sequence relationships in the 5=UTR and 3=UTR are distinct, although both regions show different propensities for species mergers and splits.…”

Section: Genome Configurationsmentioning

confidence: 73%

High Rates of Infection with Novel Enterovirus Variants in Wild Populations of Mandrills and Other Old World Monkey Species

Nguyen

Harvala

Ngole

et al. 2014

J Virol

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Enteroviruses (EVs) are a genetically and antigenically diverse group of viruses infecting humans. A mostly distinct set of EV variants have additionally been documented to infect wild apes and several, primarily captive, Old World monkey (OWM) species. To investigate the prevalence and genetic characteristics of EVs infecting OWMs in the wild, fecal samples from mandrills (Mandrillus sphinx) and other species collected in remote regions of southern Cameroon were screened for EV RNA. Remarkably high rates of EV positivity were detected in M. sphinx (100 of 102 screened), Cercocebus torquatus (7/7), and Cercopithecus cephus (2/4), with high viral loads indicative of active infection. Genetic characterization in VP4/VP2 and VP1 regions allowed EV variants to be assigned to simian species H (EV-H) and EV-J (including one or more new types), while seven matched simian EV-B variants, SA5 and EV110 (chimpanzee). Sequences from the remaining 70 formed a new genetic group distinct in VP4/2 and VP1 region from all currently recognized human or simian EV species. Complete genome sequences were obtained from three to determine their species assignment. In common with EV-J and the EV-A A13 isolate, new group sequences were chimeric, being most closely related to EV-A in capsid genes and to EV-B in the nonstructural gene region. Further recombination events created different groupings in 5= and 3= untranslated regions. While clearly a distinct EV group, the hybrid nature of new variants prevented their unambiguous classification as either members of a new species or as divergent members of EV-A using current International Committee on Taxonomy of Viruses (ICTV) assignment criteria. IMPORTANCEThis study is the first large-scale investigation of the frequency of infection and diversity of enteroviruses (EVs) infecting monkeys (primarily mandrills) in the wild. Our findings demonstrate extremely high frequencies of active infection (95%) among mandrills and other Old World monkey species inhabiting remote regions of Cameroon without human contact. EV variants detected were distinct from those infecting human populations, comprising members of enterovirus species B, J, and H and a large novel group of viruses most closely related to species A in the P1 region. The viral sequences obtained contribute substantially to our growing understanding of the genetic diversity of EVs and the existence of interspecies chimerism that characterizes the novel variants in the current study, as well as in previously characterized species A and J viruses infecting monkeys. The latter findings will contribute to future development of consensus criteria for species assignments in enteroviruses and other picornavirus genera.

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“…One cluster includes PV, HEV-C, and HEV-D species. HEV-A and HEV-B constitute the other cluster [13,14].…”

Section: Lamp Primer Designmentioning

confidence: 99%

Development of Loop-Mediated Isothermal Amplification (LAMP) for Universal Detection of Enteroviruses

et al. 2013

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Enteroviruses are found in most environments and cause several diseases in humans. Loop-mediated isothermal amplification (LAMP) was adapted and evaluated for the rapid detection of enteroviruses. Based on the highly conserved 5 0 untranslated region (5 0 -UTR) of the human enteroviruses (HEVs), particularly human enterovirus A (HEV-A) and HEV-B, a set of universal primers was designed. The LAMP amplification was carried out under isothermal conditions at 61°C, depending on the template concentration results were obtained within 45-90 min. The detection limits were found to be 10 1 copies of cloned enterovirus 71 fragments, more sensitive than conventional PCR. Nine water samples collected from drinking water sources during three seasons and 19 stool specimens collected from HFMD patients were analyzed. By using the LAMP assay, the majority of samples was tested positive, 9/9 (100 %) and 18/19 (94.7 %), respectively. LAMP is a practical method for the rapid detection of enteroviruses in environmental and clinical samples.

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Enterovirus surveillance reveals proposed new serotypes and provides new insight into enterovirus 5′-untranslated region evolution

Cited by 67 publications

References 43 publications

Human Enterovirus 109: a Novel Interspecies Recombinant Enterovirus Isolated from a Case of Acute Pediatric Respiratory Illness in Nicaragua

Human Enterovirus 109: a Novel Interspecies Recombinant Enterovirus Isolated from a Case of Acute Pediatric Respiratory Illness in Nicaragua

High Rates of Infection with Novel Enterovirus Variants in Wild Populations of Mandrills and Other Old World Monkey Species

Development of Loop-Mediated Isothermal Amplification (LAMP) for Universal Detection of Enteroviruses

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