Circulation and Molecular Epidemiology of Enteroviruses in Paralyzed, Immunodeficient and Healthy Individuals in Tunisia, a Country with a Polio-Free Status for Decades
Abstract
:1. Introduction
2. Material and Methods
2.1. Studied Population and Sampling
2.2. Enterovirus Detection from Stool Samples
2.3. Identification of Viral Isolates
2.3.1. Typing of Nonpolio enteroviruses
2.3.2. Typing of Polioviruses and Identification of VDPVs
3. Results
3.1. Nonpolio Enterovirus Detection
3.2. Poliovirus Detection
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Number of Individuals per Year (Stool Samples) | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Clinical Status | Total Studied Individuals (Stool Samples) | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | 2017 |
Paralytic cases | 607 (1296) | 49 (109) | 60 (129) | 42 (85) | 58 (126) | 48 (101) | 56 (123) | 41 (86) | 43 (91) | 61 (126) | 87 (184) | 62 (136) |
Healthy contacts | 825 (825) | 154 (154) | 96 (96) | 60 (60) | 65 (65) | 34 (34) | 85 (85) | 30 (30) | 60 (60) | 80 (80) | 61 (61) | 100 (100) |
Immunodeficients | 290 (614) | 14 (22) | 18 (36) | 53 (118) | 61 (138) | 20 (61) | 23 (50) | 19 (37) | 41 (83) | 21 (35) | 11 (20) | 9 (14) |
TOTAL | 1722 (2735) | 217 (285) | 174 (261) | 155 (263) | 184 (329) | 102 (196) | 164 (258) | 90 (153) | 144 (234) | 162 (241) | 104 (265) | 171 (250) |
Species | Types | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | 2017 | Total |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A | CV-A2 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 2 |
CV-A4 | 0 | 0 | 0 | 0 | 3 | 0 | 1 | 1 | 1 | 0 | 2 | 8 | |
CV-A6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 2 | |
CV-A8 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 0 | 3 | |
CV-A10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 3 | 4 | |
CV-A16 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 2 | 5 | |
EV-A71 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 2 | 0 | 4 | |
EV-A76 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | |
B | CV-B2 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 3 |
CV-B4 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 1 | 4 | |
CVB5 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | |
E2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | |
E3 | 3 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 6 | |
E4 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | |
E6 | 0 | 0 | 5 | 4 | 10 | 0 | 0 | 0 | 3 | 0 | 0 | 22 | |
E7 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 3 | 1 | 5 | |
E9 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | |
E11 | 1 | 3 | 0 | 7 | 0 | 0 | 2 | 0 | 0 | 0 | 2 | 15 | |
E13 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 4 | |
E14 | 0 | 0 | 4 | 11 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 18 | |
E16 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | |
E20 | 0 | 0 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 0 | 0 | 5 | |
E21 | 1 | 5 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 8 | |
E24 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | |
E25 | 0 | 0 | 0 | 0 | 2 | 2 | 0 | 0 | 4 | 0 | 0 | 8 | |
E30 | 0 | 0 | 0 | 5 | 2 | 1 | 0 | 2 | 0 | 0 | 1 | 11 | |
C | CV-A21 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 3 |
CV-A24 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | |
Total | 6 | 12 | 18 | 30 | 22 | 14 | 3 | 11 | 11 | 16 | 12 | 155 | |
Positivity Rate | 2.1 | 4.6 | 6.8 | 9.1 | 11.2 | 5.4 | 2.0 | 4.7 | 4.6 | 6.0 | 4.8 |
N° of Stool Samples | N° of Positive Polioviruses Per Clinical Status Per Year | Total N° | Positivity Rate | |||
---|---|---|---|---|---|---|
PV1 | PV2 | PV3 | ||||
AFP * | 1296 | 7 | 4 | 8 | 19 | 1.5 |
Healthy contacts | 825 | 4 | 3 | 4 | 11 | 1.3 |
Patients with PIDs ** | 614 | 14 | 16 | 12 | 42 | 6.8 |
Total | 2735 | 25 | 23 | 24 | 72 | 2.6 |
2007 | 285 | 0 | 6 | 0 | 6 | 2.1 |
2008 | 261 | 1 | 1 | 2 | 4 | 1.5 |
2009 | 263 | 5 | 3 | 2 | 10 | 3.8 |
2010 | 329 | 6 | 2 | 4 | 12 | 3.6 |
2011 | 196 | 0 | 2 | 1 | 3 | 1.5 |
2012 | 258 | 1 | 5 | 2 | 8 | 3.1 |
2013 | 153 | 5 | 0 | 0 | 5 | 3.3 |
2014 | 234 | 3 | 4 | 3 | 10 | 4.3 |
2015 | 241 | 1 | 0 | 3 | 4 | 1.7 |
2016 | 265 | 0 | 0 | 4 | 4 | 1.5 |
2017 | 250 | 3 | 0 | 3 | 6 | 2.4 |
Total | 2735 | 25 | 23 | 24 | 72 | 2.6 |
Serotype | Isolated Strains | N° of mutations in the Entire VP1 Region | Synonymous Mutations | Nonsynonymous Mutations | Amino Acid Changes | N° of Mixed Bases | Position(s) of Mixed Base(s) | Final N° of Nucleotide Changes |
---|---|---|---|---|---|---|---|---|
Type 1 | PV1 *-S326-PIDs +-TUN-09 | 5 | C2722U, G2740A | G2749A, A2775G, A2795G | Ile90Met, Lys99Arg, Thr106Ala | 7 | C2544Y a, G2701R b, U2731W c, C2752Y, U2872Y, C3088Y, G3376R | 12 |
PV1-S358-PIDs-TUN-09 | 14 | G2678A, C2722U, G2740A, C2761U, U2767C, U2872C, U3154C, G3292A, G3371A, G3376A | C2544U, G2749A, A2775G, A2795G | Thr22Met, Ile90Met, Lys99Arg, Thr106Ala, | 0 | 14 | ||
PV1-S047-PIDs-TUN-10 | 11 | U2569C, C2722U, G2740A, U2872C, C3144U, G3292A, G3376A | C2544U, G2749A, A2775G, A2795G | Thr22Met, Ile90Met, Lys99Arg, Thr106Ala, | 0 | 11 | ||
PV1-S200-PIDs-TUN-13 | 6 | U2779C, C2968U, A3033U, U3352C | A2747U, G2776U | Ile90Leu, Lys99Asn | 5 | G2620R, U2626Y, G2957R, A3079Y, U3169Y | 11 | |
Type 2 | PV2-S177-PIDs-TUN-14 | 9 | G2502A, A2518G, C2560U, A2628G, A2718G, C2787U, A2992G, G3093A, U3111C | 0 | 9 | |||
PV2-S293-PIDs-TUN-07 | 3 | G3048A | C2540U, U2909C | Pro20Leu, Ile143Thr | 6 | U2499Y, G2625R, C2706Y, A2838R, G2892R, A3375R | 8 | |
PV2-S294-PIDs-TUN-07 | 3 | G3048A | C2540U, U2909C | Pro20Leu, Ile143Thr | 6 | U2499Y, G2625R, C2706Y, A2838R, G2892R, A3375R | 10 | |
PV2-S297-PIDs-TUN-07 | 5 | U2523C, C2595U, G2694A, U2814A | U2909C | Ile143Thr | 1 | A3122R | 6 | |
PV2-S001-PIDs-TUN-08 | 4 | G2892A, G3048A | C2540U, U2909C | Pro20Leu, Ile143Thr | 4 | U2499Y, G2625R, C2706Y, A3375R | 8 | |
Type 3 | PV3-S335-AFP |-TUN-16 | 2 | C2637U, U2790C | Ala54Val, Met105Thr | 8 | U2503W, A2716R, U2876Y, G2888K d, A2897R, A3017R, G3107K, A3232R | 10 | |
PV3-S011-AFP-TUN-17 | 10 | U2860C, U3205A, U3364C | C2637U, U2790C, G2888U, A2897G, A3017G, A3111G, G3334U | Ala54Val, Met105Thr, Ala137Ser, Ala138Ser, Ile181Val, Lys212Arg, Arg286Ser | 1 | G2866R | 11 |
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Chouikha, A.; Rezig, D.; Driss, N.; Abdelkhalek, I.; Ben Yahia, A.; Touzi, H.; Meddeb, Z.; Ben Farhat, E.; Yahyaoui, M.; Triki, H. Circulation and Molecular Epidemiology of Enteroviruses in Paralyzed, Immunodeficient and Healthy Individuals in Tunisia, a Country with a Polio-Free Status for Decades. Viruses 2021, 13, 380. https://doi.org/10.3390/v13030380
Chouikha A, Rezig D, Driss N, Abdelkhalek I, Ben Yahia A, Touzi H, Meddeb Z, Ben Farhat E, Yahyaoui M, Triki H. Circulation and Molecular Epidemiology of Enteroviruses in Paralyzed, Immunodeficient and Healthy Individuals in Tunisia, a Country with a Polio-Free Status for Decades. Viruses. 2021; 13(3):380. https://doi.org/10.3390/v13030380
Chicago/Turabian StyleChouikha, Anissa, Dorra Rezig, Nadia Driss, Ichrak Abdelkhalek, Ahlem Ben Yahia, Henda Touzi, Zina Meddeb, Essia Ben Farhat, Mahrez Yahyaoui, and Henda Triki. 2021. "Circulation and Molecular Epidemiology of Enteroviruses in Paralyzed, Immunodeficient and Healthy Individuals in Tunisia, a Country with a Polio-Free Status for Decades" Viruses 13, no. 3: 380. https://doi.org/10.3390/v13030380