Genomic Characterization of a Coxsackievirus A20 Strain Recovered from a Child with Acute Flaccid Paralysis in Nigeria

Faleye, Temitope Oluwasegun Cephas; Adewumi, Moses Olubusuyi; O, Olayinka; Adeniji, Johnson Adekunle

doi:10.1128/mra.00849-19

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(2 citation statements)

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“…Most cVDPVs detected to date have recombinant genomes typically composed of a P1 region (encoding capsid proteins) derived from parental OPV and P2–P3 regions (encoding non-structural proteins) derived from non-vaccine viruses, most likely NPEV-C strains ( Kew et al., 2005 ; Combelas et al., 2011 ). The NPEV-C sequences found in the P2–P3 regions of previously described pathogenic cVDPVs are CVA17, CVA20, CVA11, and CVA13 ( Rakoto-Andrianarivelo et al., 2007 ; Faleye et al., 2019 ). In our study, we similarly observed that strain SPA866 may be a vaccine/non-vaccine recombinant given that P2–P3 regions showed high divergences (18.8% and 17%, respectively) with Sabin 2, suggesting that the putative non-OPV sequence of SPA866 was derived from co-circulating NPEV-C.…”

Section: Discussionmentioning

confidence: 93%

“…Future whole-genome sequencing of co-circulating human NPEV-C strains from West African countries, such as Senegal, Guinea, and Mauritania, will provide a clearer picture of the contribution of recombinants to the emergence of West African VDPVs. Vaccine/non-vaccine breakpoints in the genomes of recombinant VDPVs are usually located at the end of the 2A- or 2B-coding sequences, although they may also be found close to the vaccine/non-vaccine junction or in the P3 region ( Rakoto-Andrianarivelo et al., 2007 ; Bessaud et al., 2016 ; Faleye et al., 2019 ; Joffret et al., 2021 ). Here we show that the likely site of recombination of strain SPA866 is in the 2A region, which is in accordance with previous studies describing breakpoints in the genomes of recombinant VDPVs type-2 from Madagascar, Nigeria, and the Central African Republic located at this position ( Rakoto-Andrianarivelo et al., 2007 ; Faleye et al., 2019 ; Joffret et al., 2021 ).…”

Section: Discussionmentioning

confidence: 99%

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Metagenomic sequencing, molecular characterization, and Bayesian phylogenetics of imported type 2 vaccine-derived poliovirus, Spain, 2021

Fernández-García

Faye

Díez-Fuertes

et al. 2023

Front. Cell. Infect. Microbiol.

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IntroductionIn 2021, a type 2 vaccine-derived poliovirus (VDPV2) was isolated from the stool of a patient with acute flaccid paralysis (AFP) admitted to Spain from Senegal. A virological investigation was conducted to characterize and trace the origin of VDPV2.MethodsWe used an unbiased metagenomic approach for the whole-genome sequencing of VDPV2 from the stool (pre-treated with chloroform) and from the poliovirus-positive supernatant. Phylogenetic analyses and molecular epidemiological analyses relying on the Bayesian Markov Chain Monte Carlo methodology were used to determine the geographical origin and estimate the date of the initiating dose of the oral poliovirus vaccine for the imported VDPV2.ResultsWe obtained a high percentage of viral reads per total reads mapped to the poliovirus genome (69.5% for pre-treated stool and 75.8% for isolate) with a great depth of sequencing coverage (5,931 and 11,581, respectively) and complete genome coverage (100%). The two key attenuating mutations in the Sabin 2 strain had reverted (A481G in the 5’UTR and Ile143Thr in VP1). In addition, the genome had a recombinant structure between type-2 poliovirus and an unidentified non-polio enterovirus-C (NPEV-C) strain with a crossover point in the protease-2A genomic region. VP1 phylogenetic analysis revealed that this strain is closely related to VDPV2 strains circulating in Senegal in 2021. According to Bayesian phylogenetics, the most recent common ancestor of the imported VDPV2 could date back 2.6 years (95% HPD: 1.7–3.7) in Senegal. We suggest that all VDPV2s circulating in 2020–21 in Senegal, Guinea, Gambia, and Mauritania have an ancestral origin in Senegal estimated around 2015. All 50 stool samples from healthy case contacts collected in Spain (n = 25) and Senegal (n = 25) and four wastewater samples collected in Spain were poliovirus negative.DiscussionBy using a whole-genome sequencing protocol with unbiased metagenomics from the clinical sample and viral isolate with high sequence coverage, efficiency, and throughput, we confirmed the classification of VDPV as a circulating type. The close genomic linkage with strains from Senegal was consistent with their classification as imported. Given the scarce number of complete genome sequences for NPEV-C in public databases, this protocol could help expand poliovirus and NPEV-C sequencing capacity worldwide.

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Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Metagenomic sequencing, molecular characterization, and Bayesian phylogenetics of imported type 2 vaccine-derived poliovirus, Spain, 2021

Fernández-García

Faye

Díez-Fuertes

et al. 2023

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

show abstract

Genomic Characterization of a Coxsackievirus A20 Strain Recovered from a Child with Acute Flaccid Paralysis in Nigeria

Abstract: In light of recurrent outbreaks of circulating vaccine-derived poliovirus 2 (cVDPV2) in Nigeria, we describe the genome sequence of a coxsackievirus A20 strain (CVA20).

Cited by 1 publication

References 8 publications

Metagenomic sequencing, molecular characterization, and Bayesian phylogenetics of imported type 2 vaccine-derived poliovirus, Spain, 2021

Metagenomic sequencing, molecular characterization, and Bayesian phylogenetics of imported type 2 vaccine-derived poliovirus, Spain, 2021

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