Table 2.
Frequency of different enterovirus types detected in stool specimens of AFP cases, 2013-2014, based on partial VP1 gene sequences. SEN Senegal; MAU Mauritania; GAM Gambia; GUB Guinea Bissau; GUI Guinea Conakry; NIG Niger.
| Species | Type | N° of isolates | % of total | nt homologies (aa) between prototype strain and isolates (%)* | GenBank accession numbers | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SEN | MAU | GAM | GUB | GUI | NIG | Total | |||||||||||
| Isolation Year# | |||||||||||||||||
| 13 | 14 | 13 | 14 | 13 | 14 | 13 | 14 | 13 | 14 | 13 | 14 | 13 + 14 | |||||
| A | Coxsackievirus A2 | 1 | 1 | 0.5 | 80.7 (93.6) | KY433790 | |||||||||||
| Coxsackievirus A4 | 1 | 1 | 1 | 3 | 1.5 | 84.3–86 (96.3) | KY433787; KY433789; KY433793 | ||||||||||
| Coxsackievirus A6 | 1 | 1 | 0.5 | 83.8 (94.7) | KY433795 | ||||||||||||
| Coxsackievirus A14 | 1 | 1 | 2 | 1 | 82–83.5 (98.5) | KY433792; KY433794 | |||||||||||
| Coxsackievirus A16 | 1 | 1 | 0.5 | 75.3 (88.4) | KY433791 | ||||||||||||
| Enterovirus A71 | 1 | 1 | 1 | 1 | 4 | 2 | 80.6–82.4 (93.6–94.9) | KT818793-96 | |||||||||
| Enterovirus A76 | 1 | 1 | 1 | 84.6 (99.2) | KY433796 | ||||||||||||
| Enterovirus A119 | 1 | 1 | 0.5 | 93.8 (97.3) | KY433788 | ||||||||||||
| Subtotal | 3 | 1 | 1 | 5 | 4 | 14 | 6.9 | ||||||||||
| B | Coxsackievirus B2 | 1 | 2 | 1 | 1 | 1 | 6 | 3 | 84.6–86.4 (98.5–99.2) | KY433600-05 | |||||||
| Coxsackievirus B3 | 2 | 2 | 1 | 77.4–77.7 (96.1) | KY433718-19 | ||||||||||||
| Coxsackievirus B4 | 1 | 3 | 1 | 2 | 2 | 1 | 10 | 5 | 80.6–82.3 (99.3) | KY433737-46 | |||||||
| Coxsackievirus B5 | 2 | 1 | 2 | 1 | 3 | 2 | 11 | 5.5 | 75.5–81.4 (93.3–95.5) | KY433747-57 | |||||||
| Coxsackievirus B6 | 4 | 2 | 6 | 3 | 77.3–79.1 (96.2–97) | KY433606-11 | |||||||||||
| Echovirus 1 | 6 | 2 | 1 | 9 | 4.5 | 70.8–81.1 (88.1–97) | KY433612-14; KY433697-702 | ||||||||||
| Echovirus 2 | 1 | 1 | 2 | 1 | 78.6–80.2 (93.9–94.7) | KY433728; KY433730 | |||||||||||
| Echovirus 3 | 1 | 1 | 1 | 2 | 3 | 1 | 9 | 4.5 | 78.6–82.7 (93.9–99.3) | KY433758-66 | |||||||
| Echovirus 6 | 3 | 1 | 1 | 1 | 7 | 2 | 15 | 7.5 | 74.4–77.6 (90.3–93.3) | KY433767-78; KY433703-05 | |||||||
| Echovirus 7 | 2 | 2 | 1 | 1 | 3 | 1 | 10 | 5 | 74.4–78.9 (90–91.6) | KY433615-22; KY433706-07 | |||||||
| Echovirus 11 | 3 | 4 | 2 | 3 | 12 | 6 | 76.7–82.9 (86.9–96.3) | KY433623-29; KY433708-12 | |||||||||
| Echovirus 12 | 1 | 1 | 2 | 1 | 5 | 2.5 | 79.4–81.4 (97.7–99.2) | KY433630-34 | |||||||||
| Echovirus 13 | 5 | 1 | 4 | 6 | 16 | 8 | 70.1–78.9 (84.1–92.4) | KY433635-45; KY433713-17 | |||||||||
| Echovirus 14 | 1 | 1 | 2 | 1 | 79.5 (96.3–97.1) | KY433726; KY433733 | |||||||||||
| Echovirus 18 | 1 | 2 | 3 | 1.5 | 83.9–85.2 (97.7–98.5) | KY433734-36 | |||||||||||
| Echovirus 19 | 3 | 1 | 2 | 1 | 7 | 3.4 | 77.8–79.8 (84.6–89.7) | KY433646-52 | |||||||||
| Echovirus 20 | 4 | 1 | 1 | 1 | 1 | 1 | 9 | 4.5 | 78.8–82.5 (93.3–97) | KY433653-61 | |||||||
| Echovirus 24 | 1 | 1 | 1 | 1 | 1 | 3 | 1 | 9 | 4.5 | 76.8–78.6 (96.2–97) | KY433662-70 | ||||||
| Echovirus 25 | 2 | 1 | 1 | 1 | 5 | 2.5 | 79.1–80.3 (93.3–94.8) | KY433720-24 | |||||||||
| Echovirus 27 | 1 | 1 | 0.5 | 78 (88) | KY433729 | ||||||||||||
| Echovirus 29 | 4 | 1 | 2 | 1 | 8 | 4.3 | 76–78.5 (91–94) | KY433779-86 | |||||||||
| Echovirus 30 | 2 | 1 | 1 | 1 | 2 | 7 | 3.4 | 80.7–83.2 (94.8–97) | KY433671-77 | ||||||||
| Echovirus 32 | 1 | 1 | 1 | 3 | 1.5 | 79.1–79.8 (93.3–94.8) | KY433727; KY433731-32 | ||||||||||
| Echovirus 33 | 1 | 1 | 1 | 3 | 6 | 3 | 77.6–79.1 (95.5–97) | KY433678-83 | |||||||||
| Enterovirus B75 | 1 | 2 | 1 | 1 | 5 | 2.5 | 84.5–87.9 (97–98.5) | KY433684-88 | |||||||||
| Enterovirus B77 | 1 | 1 | 0.5 | 80.6 (92.7) | KY433725 | ||||||||||||
| Enterovirus B97 | 1 | 1 | 1 | 3 | 1.5 | 88.1–87.4 (96.9–99.2) | KY433689-91 | ||||||||||
| Subtotal | 49 | 18 | 7 | 5 | 31 | 72 | 182 | 90.5 | |||||||||
| C | Coxsackievirus A20 | 1 | 1 | 2 | 1 | 76–79.8 (86.5–94) | KY433692-93 | ||||||||||
| Coxsackievirus A21 | 1 | 1 | 0.5 | 74.7 (99) | KY433695 | ||||||||||||
| Enterovirus C99 | 1 | 1 | 0.5 | 81.7 (79.7) | KY433694 | ||||||||||||
| Subtotal | 2 | 2 | 4 | 2 | |||||||||||||
| D | Enterovirus D94 | 1 | 1 | 0.5 | 81.6 (94.5) | KY433696 | |||||||||||
| Subtotal | 1 | 1 | 0.5 | ||||||||||||||
| Total | 54 | 19 | 7 | 6 | 36 | 79 | 201 | 100 | |||||||||
*Homology was calculated using the ~400 bp length of the 5′ end of VP1.
#Year code: 13 for 2013; 14 for 2014