Molecular characterization of enteroviruses in patients with acute respiratory infection and influenza-like illness in the Central African Republic revealed mainly polioviruses and other enteric enterovirus types

Enteroviruses (EVs) that infect humans cause a broad range of pathologies, notably neurological, respiratory, cutaneous and enteric diseases, leading to morbidity and mortality, especially in young children. These pathologies particularly affect countries in Asia and Sub-Saharan Africa. In the last decades, some EVs with a marked respiratory tropism have emerged as a source of acute respiratory illnesses: EV-D68 has been associated with outbreaks of severe respiratory distress and acute myelitis since 2014, while several respiratory genotypes belonging to the species Enterovirus coxsackiepol were discovered in the 2010s. Very little is known about the latter, and no data exist on their circulation or clinical impact in the Central African Republic. In an attempt to bridge this gap, a retrospective study was carried out on nasopharyngeal samples collected as part of influenza surveillance at five sentinel sites in the Central African Republic in 2019. A total of 178 samples negative for influenza viruses were pooled and screened for the detection of EVs (rhinoviruses excluded). A positive result was obtained for 17 out of 20 pools. Genomic amplification was attempted by using generic primers against EVs (rhinoviruses excluded), and the virus genomes were partly sequenced by Illumina technology. A total of 46 contigs covered the VP1 region. The corresponding viruses belonged to several virus types of three species: E. coxsackiepol (14/26, 58.3%), Enterovirus betacoxsackie (9/26, 34.6%) and Enterovirus alphacoxsackie (3/26, 11.5%). Unexpectedly, no respiratory virus types (such as EV-D68, EV-C104, EV-C105, EV-C109, EV-C117 or EV-C118) were detected. Of note, polioviruses from vaccine origin were detected in eight pools (40.0%), supporting the notion that respiratory specimens may serve as a source for poliovirus re-introduction after eradication. In conclusion, we did not detect any respiratory EVs, a finding that most likely reflects a low baseline prevalence of these viruses during inter-epidemic periods. Moreover, we confirmed that several EV types, whose primary replication site is the gastrointestinal tract, are also capable of replicating in the oropharynx, polioviruses included, which constitutes a concern for mitigating the risk of poliovirus re-introduction in the post-eradication era.