Identification and molecular characterization of non-polio enteroviruses from children with acute flaccid paralysis in West Africa, 2013-2014

Abstract

Besides polioviruses, non-polio enteroviruses (NPEVs) may also be associated with acute flaccid paralysis (AFP). Because poliomyelitis is on the verge of eradication, more attention should be paid to study NPEVs from non-polio AFP cases and their epidemic patterns. In West African countries the epidemiology of NPEVs remains largely unexplored. We investigated the genetic diversity, frequency, circulation patterns, and molecular epidemiology of NPEVs in seven West African countries by analyzing retrospectively a panel of 3195 stool samples from children with AFP collected through routine poliomyelitis surveillance activities between 2013 and 2014. VP1 sequencing and typing on 201 isolates revealed 39 NPEV types corresponding to EV-A (6.9%), EV-B (90.5%), EV-C (2%) and EV-D (0.5%) species. Echoviruses were isolated most frequently with 138 cases (68.6%), followed by coxsackievirus group B with 35 cases (17.4%). No single NPEV type was remarkably dominant. Interestingly, several rarely described types with limited detection worldwide were identified (EVA76, EVA119, EVB75, EVB77, EVB97, EVC99, CVA20, CVA21 and EVD94). This study demonstrates the extensive diversity and diverse circulation patterns of NPEVs from AFP surveillance and highlights the need to formulate effective long-term strategies to monitor NPEV circulations in West Africa.

Figure 1

Monthly distribution of NPEV isolates from AFP cases, West Africa, 2013–2014.

Figure 2

Phylogenetic analysis of 14 EV-A, 182 EV-B, 4 EV-C and 1 EV-D study strains and 43 international reference strains performed on ~400 bp-sized nucleotide sequence data set within the 5′-VP1 region. Phylogenetic trees were inferred with a Neighbor Joining algorithm that applied Kimura 2-parameter model after excluding gaps from the alignments. The reliability of the tree topologies was estimated by bootstrap analysis with 1000 replicates. Scale is shown at the bottom as substitutions per site. Evolutionary analyses were conducted with MEGA5 software. Study strains are indicated with black triangles. Study strains are indicated by the GenBank accession number, country, year of isolation and the internal laboratory code that corresponds to the serial number of the AFP case. Numbers in brackets indicate the number of study strains in the sub-cluster. SEN Senegal; MAU Mauritania; GAM Gambia; GUI Guinea Conakry; GUB Guinea Bissau; NIG Niger.

Figure 3

Phylogenetic analysis based on the VP1 nucleotide sequences (400 bp in length) of the 16 E13 study strains and a representative global set of 64 strains from GenBank database belonging to E13 type. Strains reported in this study are shown with black triangles. Cluster 2 (n = 52 strains) is compressed for clarity. Study strains are indicated by the GenBank accession number, laboratory code, country and year of isolation. Scale is shown at the bottom as substitutions per site.

Figure 4

Phylogenetic analysis based on the VP1 nucleotide sequences (407 bp in length) of the 15 E6 study strains and a representative global set of 58 strains from GenBank database belonging to E6 type. Strains reported in this study are shown with black triangles. Study strains are indicated by the GenBank accession number, laboratory code, country and year of isolation. Scale is shown at the bottom as substitutions per site.