ABSTRACT
Human parechoviruses (HPeV) circulate worldwide, causing a broad variety of symptoms, preferentially in early childhood. We report here the nearly complete genome sequence of a novel HPeV type, consisting of 7,062 nucleotides and encoding 2,179 amino acids. M36/CI/2014 was taxonomically classified as HPeV-17 by the picornavirus study group.
ABSTRACT
INTRODUCTION: Gastrointestinal infections caused by viruses, bacteria, and parasites are endemic in most developing countries due to inadequate provision of safe water supplies, sanitation, and hygiene. To investigate the enteric pathogens infecting people living in Côte d'Ivoire, the Luminex Gastrointestinal Pathogen Panel (xTAG GPP) assay was used to analyze 34 human fecal samples. This study represents the first application of this technology to samples from a sub-Saharan African country. METHODOLOGY: Thirty-four stool samples from asymptomatic and symptomatic patients, 1-15 years of age, were analyzed by xTAG GPP. The Luminex assay represents a qualitative bead-based multiplexed molecular diagnostic test able to identify concurrently 15 enteric pathogens, including bacteria, viruses, and parasites. RESULTS: Overall, 22 out of 34 (64.7%) fecal specimens were detected to be positive by xTAG GPP. Sixteen were from asymptomatic subjects, and 10 patients (45.4%) showed co-infections. G. duodenalis was detected in 15 patients, in both mono- and co-infections, representing the most frequent pathogen, followed by enterotoxigenic Escherichia coli (ETEC) LT/ST. Four norovirus isolates were also detected and assigned to genogroups I and II. CONCLUSIONS: Considering the burden of enteric infections in developing countries, particularly among children, and the high rate of co-infections in asymptomatic subjects, this study shows the need for diagnostic tools such as xTAG GPP to improve diagnosis and treatment of these infections in endemic areas.
Subject(s)
Feces/microbiology , Gastroenteritis/epidemiology , Adolescent , Campylobacter/isolation & purification , Child , Child, Preschool , Cote d'Ivoire/epidemiology , Escherichia coli O157/isolation & purification , Female , Gastroenteritis/microbiology , Gastroenteritis/parasitology , Gastroenteritis/virology , Giardia/isolation & purification , Humans , Infant , Male , Norovirus/isolation & purification , Polymerase Chain Reaction , Reagent Kits, Diagnostic , Reproducibility of Results , Sensitivity and SpecificityABSTRACT
BACKGROUND: Human enteroviruses (EVs) and parechoviruses (HPeVs) belong to the family Picornaviridae. Although most EV and HPeV infections remain asymptomatic, both pathogens can cause a wide spectrum of clinical manifestations ranging from respiratory or gastrointestinal symptoms to myocarditis, neonatal sepsis, and infections of the central nervous system. OBJECTIVES: Aim of the present study was to investigate the spectrum of EVs and HPeVs in apparently healthy adults and children living in the South of Côte d'Ivoire. STUDY DESIGN: The study included 105 stool samples obtained from healthy individuals aged 0-53 years between June 2013 and December 2014 in the Sud-Como region of Côte d'Ivoire. After collection and shipment to Germany, the samples were analyzed by real-time PCR for the presence of EVs and HPeVs RNA. Molecular typing and virus isolation of all samples were performed.''é RESULTS: Out of 105 samples, 24 (22.8%) were EV positive and six (5.2%) were HPeV positive. Twenty-one EV positive samples could be characterized with serotypes belonging to EV group A-C, while three could not be further specified. Interestingly, several rarely described serotypes were identified, e.g., EV-C99, EV-B93, EV-C116, and EV-A119. Typing of HPeV positive samples resulted in HPeV-1 and -5 detections, while one isolate could not be assigned to the known HPeV types. CONCLUSIONS: This study showed a large variety of EV strains in healthy people in the South of Côte d'Ivoire and provided the first available data about HPeV infections in a sub-Saharan African country.
Subject(s)
Carrier State/epidemiology , Carrier State/virology , Enterovirus Infections/virology , Enterovirus/isolation & purification , Parechovirus/isolation & purification , Picornaviridae Infections/virology , Adolescent , Adult , Child , Child, Preschool , Cote d'Ivoire/epidemiology , Enterovirus/classification , Enterovirus/genetics , Enterovirus Infections/epidemiology , Feces/virology , Female , Genotype , Humans , Infant , Male , Middle Aged , Molecular Epidemiology , Molecular Typing , Parechovirus/classification , Parechovirus/genetics , Picornaviridae Infections/epidemiology , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction , Young AdultABSTRACT
Giardia duodenalis genotypes and Cryptosporidium species were studied in humans and free-ranging animals living in closed enclaves in Côte d'Ivoire. Three hundred and seven stool samples were tested from humans, and 47 from freely roaming domestic animals (dogs, goats, ducks, chickens). Molecular characterization of the isolates was performed by sequence analysis of a portion of the SSU-rDNA for Giardia and the COWP gene for Cryptosporidium, and a ß-giardin SYBR-green real-time PCR was also used to confirm the assignment of Giardia isolates to Assemblages. In humans, genotyping of Giardia assigned many of the sequences (43/56 by the SSU-rDNA gene, and 36/61 by the ß-giardin gene) to Assemblage B. The animal species harboured only zoonotic Assemblages A and B, except for dogs, in which host specific Assemblages C and D were also detected. Cryptosporidium meleagridis, C. parvum and C. hominis were detected in humans, while among the animals only chickens were found positive for oocysts, identified as C. meleagridis and C. parvum. The results provide further evidence about the role of free-ranging domestic animals living closely with humans in the environmental dissemination and potential transmission of these anthropozoonotic pathogens to humans.
