Molecular Characterization of Norovirus Strains Isolated from Older Children and Adults in Impoverished Communities of Vhembe District, South Africa.

BACKGROUND: Human norovirus (NoV) is an etiological agent associated with acute gastroenteritis (AGE) in both children and adults worldwide. However, very few studies have been reported on the prevalence and genetic diversity of NoV strains in children older than 5 years of age and adults with little or inadequate water and sanitation conditions. OBJECTIVES: The aim of this study was assessing the prevalence of the human norovirus in older children and adults suffering with diarrhoea from rural communities in the Vhembe district, Limpopo province. METHODS: Between August 2017 and October 2018, stool samples were collected from outpatients suffering from AGE and screened for NoV strains using the RIDA©GENE norovirus I and II real-time one-step RT-PCR. RNA extracts of NoV-positive samples were subjected to RT-PCR amplification and nucleotide sequencing to genotype the positive NoV strains. RESULTS: Out of 80 collected stool samples, 13 (16%) were tested positive for norovirus. Genogroup GII was identified in 6/13 (46%) samples and genogroup GI in 7/13 (54%) samples. The sequence analyses showed multiple genotypes including GII.Pg, GII.1, GII.2, GII.4, and GI.3. Phylogenetic analysis revealed the relatedness of NoV genotypes identified with other strains reported globally. CONCLUSION: Continued systematic surveillance to evaluate norovirus association with diarrhoea is needed to assist with epidemiological surveillance and disease burden in people of all the age groups.

Enteric pathogen co-infections in the paediatric population from rural communities in the Vhembe District, South Africa

Background. Enteric pathogens co-infections are a serious health risk in children under the age of 5 years.Objective. The study aimed to determine the prevalence of diarrhoea-causing pathogens in children suffering from diarrhoea in rural communities of the Vhembe District.Methods. A cross-sectional study was conducted from July 2014 to June 2015. Diarrhoeal stool specimens (N=237) were collected from children attending primary healthcare facilities in rural communities of the Vhembe District. Stools were screened for enteric viral adenovirus 40/41, rotavirus and norovirus pathogens by means of enzyme immuno-assay (EIA) and enteric bacterial Escherichia coli spp.(diarrhoeagenic pathotypes), Shigella spp., Salmonella spp. and Vibrio spp. pathogens by means of multiplex polymerase chain reaction.Results. A total of 59.1% (140/237) were positive for at least one or more enteric pathogens.Enterotoxigenic E. coli (ETEC) (27.9%),enteroaggregative E. coli (EAEC) (26.8%) and atypical enteropathogenic E. coli (EPEC) (17.9%) were frequently detected in children less than 2 years of age. Bacterial-bacteria co-infections were detected in 24.5% (n=58) and bacterial-viral co-infections in 14.3% (n=34) of the stool specimens.Conclusion. The findings indicated that enteric pathogen co-infections are major causes of diarrhoea in children less than 2 years of age in the Vhembe District

Complete coding regions of the prototypes enterovirus B93 and C95: phylogenetic analyses of the P1 and P3 regions of EV-B and EV-C strains.

Complete coding regions were sequenced for two new enterovirus genomes: EV-B93 previously identified by VP1 sequencing, derived from a child with acute flaccid paralysis in the Democratic Republic of Congo; and EV-C95 from a French soldier with acute gastroenteritis in Djibouti. The EV-B93 P1 had more than 30% nucleotide divergence from other EV-B types, with highest similarity to E-15 and EV-B80. The P1 nucleotide sequence of EV-C95 was most similar, 71%, to CV-A21. Complete coding regions for the new enteroviruses were compared with those of 135 EV-B and 176 EV-C strains representing all types available in GenBank. When strains from the same outbreak or strains isolated during the same year in the same geographical region were excluded, 27 of the 58 EV-B, and 16 of the 23 EV-C types were represented by more than one sequence. However, for EV-B the P3 sequences formed three clades mainly according to origin or time of isolation, irrespective of type, while for EV-C the P3 sequences segregated mainly according to disease manifestation, with most strains causing paralysis, including polioviruses, forming one clade, and strains causing respiratory illness forming another. There was no intermixing of types between these two clades, apart from two EV-C96 strains. The EV-B P3 sequences had lower inter-clade and higher intra-clade variability as compared to the EV-C sequences, which may explain why inter-clade recombinations are more frequent in EV-B. Further analysis of more isolates may shed light on the role of recombinations in the evolution of EV-B in geographical context.

Characterization of human rotavirus recovered from children with acute diarrhea in Kinshasa, Democratic Republic Of Congo.

Between July and October of 2003, 2004, and 2005, outbreaks of acute gastroenteritis occurred among children <5 years of age in Kinshasa, Democratic Republic of the Congo. Stool specimens (67 in 2003, 108 in 2004, and 116 in 2005) were collected and screened for rotaviruses using either latex agglutination (Diarlex LAA; Orion Diagnostics) or enzyme immunoassay (IDEIA; DakoCytomation). The molecular characteristics of the rotavirus strains were then determined. Group A rotavirus was detected in 195 (76%) of 258 stool specimens. Polyacrylamide gel electrophoresis was used to observe the 11 rotavirus double-stranded RNA segments in 83% of the 195 rotavirus-positive specimens. Six rotavirus group A electropherotypic patterns were noted, predominantly within the short classic pattern (111 [69%]) and the long pattern (37 [23%]). Mixed patterns were noted in the 14 remaining specimens (9%). Of the 29 samples subjected to subgrouping VP6 enzyme immunoassay, subgroup I predominated. Some of the specimens collected in 2003 (n = 26), 2004 (n = 38), and 2005 (n = 52) were analyzed by reverse-transcription polymerase chain reaction, which showed that t G8P[6] and G8P[8] strains predominated in 2003, and G1P[6] strains with short electropherotypic patterns predominated in 2004 and 2005. The emergence in Kinshasa of G8 serotypes, unusually associated with the P[6] genotype, as well as uncommon G1 rotavirus strains showing a short RNA pattern, is significant in relation to the introduction of a rotavirus vaccine and underscores the need for continued rotavirus serotype surveillance in the Democratic Republic of the Congo.

[Virological surveillance of acute flaccid paralysis in Democratic Republic of Congo from 1997-2001]. / Surveillance virologique des paralysies flasques aiguës en République démocratique du Congo (RDC) 1997-2001.

The purpose of this report is to describe the results of virological surveillance of acute flaccid paralysis (AFP) in Democratic Republic of Congo (DRC), a war-torn country. A total of 3658 stool samples were collected from patients with AFP in provinces under government control and processed as recommended by WHO. The number of specimens tested increased from 32 in 1997 to 2471 in 2001 as the national epidemiologic surveillance program for AFP improved. The national reference laboratory accredited in 1999 was appraised on the basis of the annual rate of non-polio enterovirus isolation which rose from 10% in 1999 to 20% in 2001 and by the percentage of lab results reported within 28 days which rose from 50% in 1999 to over the 80% threshold required by WHO in 2001. From 1997 to 2001, 68 strains of wild poliovirus were isolated including 52 type 1 strains, one type 2 strain and 15 type 3 strains. Most cases of poliomyelitis (81%) reported between 1997 and 2001 involved children aged 0 to 5 years. Only 12% of cases involved children aged 6 to 14 years and 3% involved young adults. Sixty-seven percent of the 45 poliomyelitis patients with documented vaccine status had received 0 to 3 doses of oral poliovirus vaccine (OPV). Fifteen children (33%) developed the disease despite having received more than 4 required doses of OPV. Since 1997 three provinces of DRC, ie., Bas-Congo, Kinshasa city and Nord-Kivu, have been free of wild poliovirus. In 2001 wild poliovirus circulation had been stopped throughout the country thanks to implementation of routine immunization and especially of the national immunization days (NIDs) program.

Surveillance virologique des paralysies flasques aiguës en Republique Démocratique du Congo (RDC) 1997-2001

Lesauteursrap p o rtent les résultatsde l'analyse de la surveillance viro l ogiquedespara lysies flasques aiguës (PFA )en République Démocratique du Congo (RDC),pays longtemps ravagé par des conflits armés. Au total,3658 échantillons deselles de cas de PFA en provenance des provinces sous contrôle gouvernemental,ont été analysés selon les méthodes recom-mandées par l'OMS. L' a m é l i o ration de la surveillance épidémiologique des PFA s'est traduite par l'accroissement sensible dunombre d'échantillons traités qui est passé de 32 en 1997 à 2471 en 2001. Les performances du laboratoire national de réfé-rence accrédité en 1999,ontétéappréciées par le taux annuel d'isolement desentérov i rusnon poliov i rus qui estpassé de10%en 1999 à 20% en 2001,et par le rendu des résultats qui est passé de 50% en 1999 pour dépasser en 2001 le seuil de 80% exigépar l'OMS. De 1997 à 2001,68 souches de poliovirus sauvages ont été isolées dont 52 souches de type 1,une souche de type 2et 15de type 3. Quat re-vingt un pour cent des casdepoliomyélitesurve nus entre 1997 et 2001ontétéobservés chezdes enfa n t sâgés de 0 à 5 ans. Seulement 12% ont été détectés chez des enfants âgés de 6 à 14 ans contre 3% chez de jeunes adolescents.Soixante-sept pour cent des 45 sujets atteints de poliomyélite et dont l'état vaccinal était connu,avaient reçu 0 à 3 doses devaccinanti-poliomyélitiqueoral. Parcontre15sujets(33%) bien qu'ayant reçuplusde4 dosesrequises deva c c i n ,avaient quandmême développélamaladie. Depuis1997,t roisprovinces dela RDC sontexemptesde poliov i russauvage :la ville deKinshasa,leBas-Congoet leNord - K ivu. En 2001,lacirc u l ation depoliov i russauvage aétéinterrompuesurtoutel'étenduedupaysgr â c eaux activités de vaccination de routine et surtout à l'organisation des journées nationales de vaccination