Genetic Diversity of Human Enterovirus 68 Strains Isolated in Kenya Using the Hypervariable 3′- End of VP1 Gene

Opanda, Silvanos; Wamunyokoli, Fred; Khamadi, Samoel; Coldren, Rodney L.; Bulimo, Wallace

doi:10.1371/journal.pone.0102866

Cited by 36 publications

(34 citation statements)

References 36 publications

(60 reference statements)

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“…Our phylogenetic analyses are notable in that they suggest a relatively complex molecular evolution of EV-D68 during the 2014 outbreak. Before this outbreak, EV-D68 was rarely reported and was associated with mild respiratory illness, although small outbreaks had been documented since 2005 (15,16,(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33). Previous studies showed that the A, B, and C clades circulated or cocirculated during different time periods in different geographic regions (15,16,18,19,(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)59).…”

Section: Discussionmentioning

confidence: 99%

“…time were associated with acute respiratory infections, ranging from mild upper respiratory tract illness and asthma to severe bronchitis and pneumonia, with the exception of four isolated cases associated with neurological syndromes, notably, acute flaccid myelitis (AFM), in which viruses were isolated from the cerebrospinal fluid or nasopharyngeal swabs (12,31,34). The 2014 outbreak of EV-D68 was the largest outbreak recorded in North America, with more than 1,153 confirmed EV-D68 cases in 49 U.S. states and the District of Columbia (35).…”

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confidence: 99%

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Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States

Tan

Hassan

Schuster

et al. 2016

J Virol

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In August 2014, an outbreak of enterovirus D68 (EV-D68) occurred in North America, causing severe respiratory disease in children. Due to a lack of complete genome sequence data, there is only a limited understanding of the molecular evolution and epidemiology of EV-D68 during this outbreak, and it is uncertain whether the differing clinical manifestations of EV-D68 infection are associated with specific viral lineages. We developed a high-throughput complete genome sequencing pipeline for EV-D68 that produced a total of 59 complete genomes from respiratory samples with a 95% success rate, including 57 genomes from Kansas City, MO, collected during the 2014 outbreak. With these data in hand, we performed phylogenetic analyses of complete genome and VP1 capsid protein sequences. Notably, we observed considerable genetic diversity among EV-D68 isolates in Kansas City, manifest as phylogenetically distinct lineages, indicative of multiple introductions of this virus into the city. In addition, we identified an intersubclade recombination event within EV-D68, the first recombinant in this virus reported to date. Finally, we found no significant association between EV-D68 genetic variation, either lineages or individual mutations, and a variety of demographic and clinical variables, suggesting that host factors likely play a major role in determining disease severity. Overall, our study revealed the complex pattern of viral evolution within a single geographic locality during a single outbreak, which has implications for the design of effective intervention and prevention strategies. IMPORTANCEUntil recently, EV-D68 was considered to be an uncommon human pathogen, associated with mild respiratory illness. However, in 2014 EV-D68 was responsible for more than 1,000 disease cases in North America, including severe respiratory illness in children and acute flaccid myelitis, raising concerns about its potential impact on public health. Despite the emergence of EV-D68, a lack of full-length genome sequences means that little is known about the molecular evolution of this virus within a single geographic locality during a single outbreak. Here, we doubled the number of publicly available complete genome sequences of EV-D68 by performing high-throughput next-generation sequencing, characterized the evolutionary history of this outbreak in detail, identified a recombination event, and investigated whether there was any correlation between the demographic and clinical characteristics of the patients and the viral variant that infected them. Overall, these results will help inform the design of intervention strategies for EV-D68.

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confidence: 99%

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Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States

Tan

Hassan

Schuster

et al. 2016

J Virol

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“…Given the diversity of laboratory tests utilized, it is important to verify the ability of laboratory-developed tests (LDTs) and commercially available NAATs to accurately detect emerging pathogens (9)(10)(11)(12)(13)(14). This study compared the analytical sensitivities of LDTs and commercial NAATs used in hospital-based and provincial public health laboratories across Canada for the detection of EV-D68.…”

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confidence: 99%

“…This study was initiated and completed prior to the identification of multiple lineages within North America (4,(12)(13)(14). It is possible that the performance characteristics of molecular assays differ with genetic differences between the currently circulating lineages of EV-D68, and studies are under way to investigate this possibility.…”

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confidence: 99%

Detection of Enterovirus D68 in Canadian Laboratories

Hatchette

Drews

Grudeski³

et al. 2015

J Clin Microbiol

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“…(4)(5)(6)(7)(8)(9)(10)(11)(12). A large outbreak in the United States and Canada in 2014 affected many more than the 1,100 laboratory-confirmed cases (13).…”

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Prevalence and Phylogenetic Characterization of Enterovirus D68 in Pediatric Patients with Acute Respiratory Tract Infection in Thailand

et al. 2016

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SUMMARY: Enterovirus D68 (EV-D68) is associated with severe lower respiratory tract infection and neurological abnormalities including acute myelitis and cranial nerve dysfunction. To determine whether an increased incidence of EV-D68 occurs in Southeast Asia, we retrospectively tested specimens collected from Thai pediatric patients who were less than 5 years of age and presented with acute respiratory tract infections between 2012 and 2014. Reverse transcription-polymerase chain reaction and nucleotide sequencing of the 5 ? -UTR/VP2 region were used to identify EV-D68. We also examined the epidemiological pattern of EV-D68 since 2009, when it was first identified in Thailand, and compiled records of clinical manifestations in children with confirmed EV-D68 infection. From 837 samples, 5 samples (0.6z) tested positive for EV-D68. All patients presented with viral pneumonia and required hospitalization. Phylogenetic analysis of the VP4/VP2 regions revealed that EV-D68 strains circulating in Thailand between 2012 and 2014 were closely related to strains reported in Japan, United Kingdom, China, and France. Continued surveillance of probable EV-D68-associated severe respiratory tract infection and the development of a rapid diagnostic test for EV-D68 are essential in supporting awareness and facilitating disease prevention and control.Enterovirus D68 (EV-D68) is a subtype of Enterovirus enterovirus D within the family Picornaviridae. It was first isolated in the United States in 1962 from respiratory specimens obtained from 4 pediatric patients with pneumonia and bronchiolitis (1). Since then, EV-D68 infections have occurred in small numbers and accounted for only 26 reports among enteroviruses detected in the United States during the 36-year surveillance period from 1970-2005 (2). Between 2008-2010, clusters of EV-D68 emerged in the Philippines, Japan, the Netherlands, and the United States (3). EV-D68 infections have

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Genetic Diversity of Human Enterovirus 68 Strains Isolated in Kenya Using the Hypervariable 3′- End of VP1 Gene

Cited by 36 publications

References 36 publications

Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States

Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States

Detection of Enterovirus D68 in Canadian Laboratories

Prevalence and Phylogenetic Characterization of Enterovirus D68 in Pediatric Patients with Acute Respiratory Tract Infection in Thailand

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