Genetic and phenotypic characterization of recently discovered enterovirus D type 111

International audienceMembers of the species Enterovirus D (EV-D) remain poorly studied. The two first EV-D types (EV-D68 and EV-D70) have regularly caused outbreaks in humans since their discovery five decades ago but have been neglected until the recent occurrence of severe respiratory diseases due to EV-D68. The three other known EV-D types (EV-D94, EV-D111 and EV-D120) were discovered in the 2000s-2010s in Africa and have never been observed elsewhere. One strain of EV-D111 and all known EV-D120s were detected in stool samples of wild non-human primates, suggesting that these viruses could be zoonotic viruses. To date, EV-D111s are only known through partial genetic sequences of the few strains that have been identified so far. In an attempt to bring new pieces to the puzzle, we genetically characterized four EV-D111 strains (among the seven that have been reported until now). We observed that the EV-D111 strains from human samples and the unique simian EV-D111 strain were not phylogenetically distinct, thus suggesting a recent zoonotic transmission. We also discovered evidences of probable intertypic genetic recombination events between EV-D111s and EV-D94s. As recombination can only happen in co-infected cells, this suggests that EV-D94s and EV-D111s share common replication sites in the infected hosts. These sites could be located in the gut since the phenotypic analysis we performed showed that, contrary to EV-D68s and like EV-D94s, EV-D111s are resistant to acid pHs. We also found that EV-D111s induce strong cytopathic effects on L20B cells, a cell line routinely used to specifically detect polioviruses. An active circulation of EV-D111s among humans could then induce a high number of false-positive detection of polioviruses, which could be particularly problematic in Central Africa, where EV-D111 circulates and which is a key region for poliovirus eradication

Characterization of Enteroviruses from Non-Human Primates in Cameroon Revealed Virus Types Widespread in Humans along with Candidate New Types and Species.

International audienceEnteroviruses (EVs) infecting African Non-Human Primates (NHP) are still poorly documented. This study was designed to characterize the genetic diversity of EVs in both captive and wild NHP in Cameroon and to compare this diversity with that found in humans.Stool specimens were collected in April 2008 in NHP housed in sanctuaries in Yaounde and neighborhoods. Moreover, stool specimens collected from wild NHP from June 2006 to October 2008 in the southern rain forest of Cameroon were considered. RNAs purified directly from stool samples were screened for EVs using a sensitive RT-nested PCR targeting the VP1 capsid coding gene whose nucleotide sequence was used for molecular typing.Captive chimpanzees (Pan troglodytes) and gorillas (Gorilla gorilla) were primarily infected by EV types already reported in humans in Cameroon and elsewhere: Coxsackievirus A13 and A24, Echovirus 15 and 29, and EV-B82. Moreover EV-A119, a novel virus type recently described in humans in central and west Africa, was also found in a captive Chimpanzee. EV-A76 which is a widespread virus in humans was identified in wild chimpanzees, thus suggesting its adaptation and parallel circulation in human and NHP populations in Cameroon. Interestingly, some EVs harbored by wild NHP were genetically distinct from all existing types and were thus assigned as new types. One chimpanzee-derived virus was tentatively assigned as EV-J121 in the EV-J species. In addition, two EVs from wild monkeys provisionally registered as EV-122 and EV-123 were found to belong to a candidate new species. Overall, this study indicates that the genetic diversity of EVs in NHP is more important than previously known and could be the source of future new emerging human viral diseases

Detection and genetic diversity of parechoviruses in children with acute flaccid paralysis in Cameroon.

Human Parechoviruses (HPeVs) have rarely been considered in the virological investigation of Acute Flacid Paralysis (AFP) cases in Africa, where enteric infections are very common. This study investigated the prevalence and genetic diversity of HPeV in 200 children aged ≤ 15 years with AFP in Cameroon from 2018 to 2019. HPeVs were detected in their faecal RNA using 5'-untranslated real-time RT-PCR. Detected HPeVs were typed by phylogenetic comparison with homologous sequences from homotypic reference strains. Overall, HPeV RNA was detected in 11.0% (22/200) of the 200 stool samples tested. Twelve HPeVs were successfully sequenced and reliably assigned to HPeV-A1, A4, A5, A10, A14, A15, A17 and A18 genotypes. Phylogenetic analyses revealed a high genetic variability among the studied HPeVs, as well as between the studied HPeVs and their previously reported counterparts from Cameroon in 2014. These findings suggest that different HPeV genotypes co-circulate in Cameroon without documented epidemics

HIV-infected children living in Central Africa have low persistence of antibodies to vaccines used in the Expanded Program on Immunization.

International audienceBACKGROUND: The Expanded Program on Immunization (EPI) is the most cost-effective measures to control vaccine-preventable diseases. Currently, the EPI schedule is similar for HIV-infected children; the introduction of antiretroviral therapy (ART) should considerably prolong their life expectancy. METHODS AND PRINCIPAL FINDINGS: To evaluate the persistence of antibodies to the EPI vaccines in HIV-infected and HIV-exposed uninfected children who previously received these vaccines in routine clinical practice, we conducted a cross-sectional study of children, aged 18 to 36 months, born to HIV-infected mothers and living in Central Africa. We tested blood samples for antibodies to the combined diphtheria, tetanus, and whole-cell pertussis (DTwP), the measles and the oral polio (OPV) vaccines. We enrolled 51 HIV-infected children of whom 33 were receiving ART, and 78 HIV-uninfected children born to HIV-infected women. A lower proportion of HIV-infected children than uninfected children had antibodies to the tested antigens with the exception of the OPV types 1 and 2. This difference was substantial for the measles vaccine (20% of the HIV-infected children and 56% of the HIV-exposed uninfected children, p<0.0001). We observed a high risk of low antibody levels for all EPI vaccines, except OPV types 1 and 2, in HIV-infected children with severe immunodeficiency (CD4(+) T cells <25%). CONCLUSIONS AND SIGNIFICANCE: Children were examined at a time when their antibody concentrations to EPI vaccines would have still not undergone significant decay. However, we showed that the antibody concentrations were lowered in HIV-infected children. Moreover, antibody concentration after a single dose of the measles vaccine was substantially lower than expected, particularly low in HIV-infected children with low CD4(+) T cell counts. This study supports the need for a second dose of the measles vaccine and for a booster dose of the DTwP and OPV vaccines to maintain the antibody concentrations in HIV-infected and HIV-exposed uninfected children

Phylogenetic relationships among <i>Enterovirus C</i> strains from human and non-human primates.

<p>The NJ tree is based on the alignment of the full-length VP1 sequences. Studied viruses from apes are highlighted in bold red with host names indicated in brackets while human-derived isolates from Cameroon are specified in bold blue. Prototype strains are indicated by triangles (▴). For clarity, type and lineage-specific clusters containing exclusively human isolates have been collapsed. The scale is shown at the bottom as substitutions per site. Viral isolates belonging to enterovirus species commented in the text are gathered in grey-shaded boxes.</p

Global description of the primates samples and overall PCR, isolation and VP1 sequencing results.

a<p>, ND, not done; n/a, not applicable.</p>b<p>, Overall 12 VP1 amplicons showed very low signal insufficient for sequencing reactions. However, 11 of the corresponding viruses could be sequenced in the 5′UTR region while the remaining one was refractory to 5′UTR amplification but showed a divergent 3D^pol sequence (GenBank n° KF648605 and KF648607).</p>c<p>, Includes one sample with a mixture of CV-A13 and an EV-A.</p>d<p>, Includes one sample with a mixture of EV-A71 and EV-B82.</p

VP1 sequence relationships between the newly sequenced EV-J121 and other currently recognized EV-J strains.

<p>VP1 sequence relationships between the newly sequenced EV-J121 and other currently recognized EV-J strains.</p

Phylogenetic relationships among the candidate new enterovirus types and species and other known human and animal enteroviruses.

<p>Studied viruses from non-human primates are highlighted in bold red with host names indicated in brackets. For clarity most species clusters have been collapsed. The scale is shown at the bottom as substitutions per site.</p

Phylogenetic relationships among the 5′UTR, VP1 and 3D^pol sequences of enteroviruses from human and non-human primates.

<p>Only non species C enteroviruses were considered in these trees. The 5′UTR, VP1 and 3D^pol trees were based on the alignments of partial sequences (positions according to EV-A71 strain BrCr numbering: 193–430 for 5′UTR, 2615–2903 for VP1 and 6034–6377 for 3D^pol regions). Only non species C enteroviruses whose partial or complete VP1 sequences could be generated were considered in this comparative analysis. Prototypes strains originating from non-human primates (▴) or humans (Δ) are indicated. All other non-human primates strains from previous studies are distinguished by black circles (•) and those from this study are color-coded according to virus types. Non-human primates-derived viruses characterized in this study are further highlighted by yellow stars whereas green stars specify viruses previously identified in Cameroon either from humans or non-human primates.</p