Genetic Characterization of Enterovirus A71 Circulating in Africa

Fernandez-Garcia, Maria Dolores; Volle, Romain; Joffret, Marie-Line; Sadeuh-Mba, Serge Alain; Gouandjika‐Vasilache, Ionela; Kébé, Ousmane; Wiley, Michael R.; Majumdar, Manasi; Simon‐Lorière, Etienne; Sakuntabhai, Anavaj; Palacios, Gustavo; Martı́n, Javier; Delpeyroux, Françis; Ndiaye, Kader; Bessaud, Maël

doi:10.3201/eid2404.171783

Cited by 17 publications

(22 citation statements)

References 14 publications

(25 reference statements)

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“…The fact that severe complications associated with EV-A71 infections mostly occur in countries of the Asia-Pacific region is intriguing as EV-A71 appears to be widely circulating in other areas of the world. New genogroups have been recently described in India [ 31 ] and Africa [ 34 ], and also now in Pakistan, as we show here. It will be worth investigating further the differences in clinical severity induced by EV-A71 infections in different geographical regions.…”

Section: Discussionsupporting

confidence: 77%

Environmental Surveillance Reveals Complex Enterovirus Circulation Patterns in Human Populations

Majumdar

Sharif

Klapsa

et al. 2018

Open Forum Infectious Diseases

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BackgroundEnteroviruses are common human pathogens occasionally associated with severe disease, notoriously paralytic poliomyelitis caused by poliovirus. Other enterovirus serotypes such as enterovirus A71 and D68 have been linked to severe neurological syndromes. New enterovirus serotypes continue to emerge, some believed to be derived from nonhuman primates. However, little is known about the circulation patterns of many enterovirus serotypes and, in particular, the detailed enterovirus composition of sewage samples.MethodsWe used a next-generation sequencing approach analyzing reverse transcriptase polymerase chain reaction products synthesized directly from sewage concentrates.ResultsWe determined whole-capsid genome sequences of multiple enterovirus strains from all 4 A to D species present in environmental samples from the United Kingdom, Senegal, and Pakistan.ConclusionsOur results indicate complex enterovirus circulation patterns in human populations with differences in serotype composition between samples and evidence of sustained and widespread circulation of many enterovirus serotypes. Our analyses revealed known and divergent enterovirus strains, some of public health relevance and genetically linked to clinical isolates. Enteroviruses identified in sewage included vaccine-derived poliovirus and enterovirus D-68 stains, new enterovirus A71 and coxsackievirus A16 genogroups indigenous to Pakistan, and many strains from rarely reported serotypes. We show how this approach can be used for the early detection of emerging pathogens and to improve our understanding of enterovirus circulation in humans.

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Section: Discussionsupporting

confidence: 77%

Environmental Surveillance Reveals Complex Enterovirus Circulation Patterns in Human Populations

Majumdar

Sharif

Klapsa

et al. 2018

Open Forum Infectious Diseases

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“…Contigs were queried against the ViPR database 59 retrieved in march 2019 using DIAMOND 60 . In addition to contigs matching EVA-71 (7345 (0.02%) reads mapped to this virus), whose sequence was previously obtained 13 , two large contigs corresponded to HePVs sequences. Using the sequence from the top DIAMOND hits (ADA79690, ANJ01603) as reference, HePVs contigs were assembled into a full-length HePV scaffold with missing sections (gaps).…”

Section: Sample Collection and Virus Isolationmentioning

confidence: 87%

“…It has been successfully used to identify or characterize full-genomes of new HPeVs like a HPeV1 variant 35 , type 4 31 , types 5 and 6 32 , type 7 36 , type 16 26 , type 17 37 , types 18 and 19 38 or to detect HPeVs in clinical specimens 25,26,[39][40][41] . Thanks to NGS, we were able to detect a mixed infection of HPeV15 and EV-A71 when using this technique to characterize the full genome sequence of EV-A71 13 . Several studies have reported HPeVs in mixed infections.…”

Section: Discussionmentioning

confidence: 99%

Identification and molecular characterization of the first complete genome sequence of Human Parechovirus type 15

Fernandez-Garcia

Simon‐Lorière

Kébé

et al. 2020

Sci Rep

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Using a metagenomics approach, we have determined the first full-length genome sequence of a human parechovirus type 15 (HPeV15) strain, isolated from a child with acute flaccid paralysis and co-infected with EV-A71. HPeV15 is a rarely reported type. To date, no full-length genome sequence of HPeV15 is available in the GenBank database, where only limited VP1 sequences of this virus are available. Pairwise comparisons of the complete VP1 nucleotide and deduced amino acid sequences revealed that the study strain belongs to type 15 as it displayed 79.6% nucleotide and 93.4% amino acid identity with the HPeV15 prototype strain. Comparative analysis of available genomic regions and phylogenetic analysis using the P2 and P3 coding regions revealed low nucleotide identity to HPeV reference genomes. Phylogenetic and similarity plot analyses showed that genomic recombination events might have occurred in the UTRs and nonstructural region during HPeV15 evolution. The study strain has high similarity features with different variants of HPeV3 suggesting intertypic recombination. Our data contributes to the scarce data available on HPeVs in Africa and provides valuable information for future studies that aim to understand the evolutionary history, molecular epidemiology or biological and pathogenic properties of HPeV15. Human parechoviruses (HPeVs) are non-enveloped viruses that belong to one of the four species of genus Parechovirus within the Picornaviridae family. HPeV positive-sense single-stranded RNA genome is about 7300 bases in length, flanked by 5′ and 3′ untranslated regions (UTRs). The genome encodes a polyprotein which is cleaved by the viral protease (3 C) to produce the mature structural (VP0, VP3 and VP1) and nonstructural (2A-C, 3A-D) proteins 1. HPeVs can be transmitted through the fecal-oral and respiratory routes 1,2. HPeV infections are common throughout the world and most often cause asymptomatic or mild gastrointestinal or respiratory symptoms 1,2. However, syndromes such as encephalitis, aseptic meningitis, acute flaccid paralysis (AFP), sepsis and myocarditis have been increasingly recognized in primary HPeV infection in neonates and infants 2. After EVs, HPeVs are considered the second most common cause of central nervous system (CNS) viral infections 2. However, HPeV infections are currently underdiagnosed given that routine diagnostic assays are generally lacking in clinical settings 1,3. Following HPeV intestinal replication, infectious viruses are shed in feces where viruses can be detected by PCR and virus isolation 3. However, HPeVs are known for poor adaptation to cell cultivation systems and not all types replicate in cell lines routinely used for enterovirus (EV) detection 4,5. Because specific types could be missed or underdiagnosed using viral isolation, molecular identification methods are highly recommended for the routine detection of HPeVs in clinical samples 3,4. To date, 19 different HPeV types (HPeV1 to 19) have been described based on sequence similarity within their VP1 capsid pro...

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“…Isolates E55 and 328 from Tunisia (2014) and Algeria (2013), respectively, were consistently assigned to the subgenogroup C2. Both isolates were related to strains isolated in France during the same year but were relatively distant from strains reported in Mauretania, Senegal, and Guinea ( Fernandez-Garcia et al, 2018 ) ( Figure 6C ). Isolates S14 (2011) and E30 (2014) from Tunisia were consistently assigned to the subgenogroup C4, along with isolates collected in France in 2012 ( Figure 6D ).…”

Section: Resultsmentioning

confidence: 59%

“…Other EV-A71 sequences available in sequences databanks were also selected to include representative of the different EV-A71 genogroups (A-G) ( Figure 6A). EV-A71 isolates found in sub-Saharan countries (n = 5) were assigned to the genogroup E and the subgenogroup C2 (Fernandez-Garcia et al, 2018). EV-A71 isolates found in Madagascar (n = 1) was assigned to the subgenogroup C4.…”

Section: Application Of the Real-time Rt-pcr Assay In The Surveillancmentioning

confidence: 99%

Development of a New Internally Controlled One-Step Real-Time RT-PCR for the Molecular Detection of Enterovirus A71 in Africa and Madagascar

et al. 2020

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Enterovirus A71 (EV-A71) is a leading cause of hand-foot-and-mouth disease (HFMD) and can be associated with severe neurological complications. EV-A71 strains can be classified into seven genogroups, A-H, on the basis of the VP1 capsid protein gene sequence. Genogroup A includes the prototype strain; genogroups B and C are responsible of major outbreaks worldwide, but little is known about the others, particularly genogroups E and F, which have been recently identified in Africa and Madagascar, respectively. The circulation of EV-A71 in the African region is poorly known and probably underestimated. A rapid and specific assay for detecting all genogroups of EV-A71 is required. In this study, we developed a real-time RT-PCR assay with a competitive internal control (IC). The primers and TaqMan probe specifically target the genomic region encoding the VP1 capsid protein. Diverse EV-A71 RNAs were successfully amplified from the genogroups A, B, C, D, E, and F, with similar sensitivity and robust reproducibility. Neither cross reaction with other EVs nor major interference with the competitive IC was detected. Experimentally spiked stool and plasma specimens provided consistent and reproducible results, and validated the usefulness of the IC for demonstrating the presence of PCR inhibitors in samples. The analysis in an African laboratories network of 1889 untyped enterovirus isolates detected 15 EV-A71 of different genogroups. This specific real-time RT-PCR assay provides a robust and sensitive method for the detection of EV-A71 in biological specimens and for the epidemiological monitoring of EV-A71 including its recently discovered genogroups.

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Genetic Characterization of Enterovirus A71 Circulating in Africa

Cited by 17 publications

References 14 publications

Environmental Surveillance Reveals Complex Enterovirus Circulation Patterns in Human Populations

Environmental Surveillance Reveals Complex Enterovirus Circulation Patterns in Human Populations

Identification and molecular characterization of the first complete genome sequence of Human Parechovirus type 15

Development of a New Internally Controlled One-Step Real-Time RT-PCR for the Molecular Detection of Enterovirus A71 in Africa and Madagascar

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