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. 2017 Sep 12;14(1):175.
doi: 10.1186/s12985-017-0846-x.

Non-polio enteroviruses in faeces of children diagnosed with acute flaccid paralysis in Nigeria

T O C Faleye  1   2 , M O Adewumi  2 , M O Japhet  3   4 , O M David  1 , A O Oluyege  1 , J A Adeniji  2   5 , O Famurewa  1   6
Affiliations

Non-polio enteroviruses in faeces of children diagnosed with acute flaccid paralysis in Nigeria

T O C Faleye et al. Virol J. .

Abstract

Background: The need to investigate the contribution of non-polio enteroviruses to acute flaccid paralysis (AFP) cannot be over emphasized as we move towards a poliovirus free world. Hence, we aim to identify non-polio enteroviruses recovered from the faeces of children diagnosed with AFP in Nigeria.

Methods: Ninety-six isolates, (95 unidentified and one previously confirmed Sabin poliovirus 3) recovered on RD cell culture from the stool of children <15 years old diagnosed with AFP in 2014 were analyzed. All isolates were subjected to RNA extraction, cDNA synthesis and three different PCR reactions (one panenterovirus 5'-UTR and two different VP1 amplification assays). VP1 amplicons were then sequenced and isolates identified.

Results: 92.71% (89/96) of the isolates were detected by at least one of the three assays as an enterovirus. Precisely, 79.17% (76/96), 6.25% (6/96), 7.30% (7/96) and 7.30% (7/96) of the isolates were positive for both, positive and negative, negative and positive, as well as negative for both the 5'-UTR and VP1 assays, respectively. In this study, sixty-nine (69) of the 83 VP1 amplicons sequenced were identified as 27 different enterovirus types. The most commonly detected were CV-B3 (10 isolates) and EV-B75 (5 isolates). Specifically, one, twenty-four and two of the enterovirus types identified in this study belong to EV-A, EV-B and EV-C respectively.

Conclusions: This study reports the circulating strains of 27 non-polio enterovirus types in Nigerian children with AFP in 2014 and Nigerian strains of CV-B2, CV-B4, E17, EV-B80, EV-B73, EV-B97, EV-B93, EV-C99 and EV-A120 were reported for the first time. Furthermore, it shows that being positive for the 5'-UTR assay should not be the basis for subjecting isolates to the VP1 assays.

Keywords: AFP; Enteroviruses; Nigeria; Non-polio enteroviruses; VP1 analysis.

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Conflict of interest statement

Ethics approval and consent to participate

Enterovirus isolates were analysed in this study. The stool samples from which these isolates were recovered were collected in accordance with the national ethical guidelines as part of the National AFP surveillance programme in Nigeria and sent to the WHO National Polio Laboratory in Ibadan, Nigeria to ascertain whether poliovirus is the etiologic agent of the diagnosed AFP using the WHO algorithm. The isolates analyzed in this study were subsequently anonymized for further studies before use in this study. Thus, this article does not contain any studies with human participants performed by any of the authors. In addition, no information that can be used to associate the isolates analyzed in this study to any individual is included in this manuscript.

Consent for publication

Not applicable.

Competing interests

The authors declare that no conflict of interests exist.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
The algorithm used in this study. A depicts the 5′-UTR assay. B and C show the two VP1 assays. While B has only one stage of PCR, C has two consecutive stages (snPCR) of PCR
Fig. 2
Fig. 2
Phylogram of genetic relationship between VP1 nucleotide sequences of CV-B3 isolates. The phylogenetic tree is based on an alignment of the partial VP1 sequences. The CV-B3 sequences recovered in Nigeria in 2002 and the strains newly described in this study are indicated within sub-Saharan Africa (SSA). The strains indicated with black triangl represent CV-B3 strains from Niger; a country in west-Africa that shares a border with Northern-Nigeria
Fig. 3
Fig. 3
Phylogram of genetic relationship between VP1 nucleotide sequences of EV-B75 isolates. The phylogenetic tree is based on an alignment of the partial VP1 sequences. The newly sequenced strains are indicated with black diamond while other strains from west-Africa are indicated with black triangle. The GenBank accession numbers and strain of the isolates are indicated in the tree. Bootstrap values are indicated if >50%. SEA represents South-East Asia
Fig. 4
Fig. 4
Phylogram of genetic relationship between VP1 nucleotide sequences of E19 isolates. The phylogenetic tree is based on an alignment of the partial VP1 sequences. The newly sequenced strains are indicated with black diamond while other strains from west-Africa are indicated with black triangle. The GenBank accession numbers and strain of the isolates are indicated in the tree. Bootstrap values are indicated if >50%. SEA represents South-East Asia
Fig. 5
Fig. 5
Phylogram of genetic relationship between VP1 nucleotide sequences of E7 isolates. The phylogenetic tree is based on an alignment of the partial VP1 sequences. The newly sequenced strains are indicated with black diamond while other strains from west-Africa within the Global cluster are indicated with black triangle. The GenBank accession numbers and strain of the isolates are indicated in the tree. Bootstrap values are indicated if >50%
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