Background: The re-emergence of yellow fever poses a serious public health risk to unimmunized communities in the tropical regions of Africa and South America and unvaccinated travelers visiting these regions. This risk is further accentuated by the likely spread of the virus to areas with potential for yellow fever transmission such as in Asia, Europe, and North America. To mitigate this risk, surveillance of yellow fever is pivotal. We performed an analysis of laboratory-based surveillance of yellow fever suspected cases in Cameroon during 2010–2020 to characterize the epidemiology of yellow fever cases and define health districts at high risk. Method: We reviewed IgM capture ELISA and plaque reduction neutralization test (PRNT) test results of all suspected yellow fever patients analyzed at Centre Pasteur of Cameroon, the national yellow fever testing laboratory, during 2010–2020. Results: Of the 20,261 yellow fever suspected patient’s samples that were tested, yellow fever IgM antibodies were detected in 360 patients representing an annual average of 33 cases/year. A major increase in YF IgM positive cases was observed in 2015 and in 2016 followed by a decrease in cases to below pre-2015 levels. The majority of the 2015 cases occurred during the latter part of the year while those in 2016, occurred between February and May. This trend may be due to an increase in transmission that began in late 2015 and continued to early 2016 or due to two separate transmission events. In 2016, where the highest number of cases were detected, 60 health districts in the 10 regions of Cameroon were affected with the Littoral, Northwest and, Far North regions being the most affected. After 2016, the number of detected yellow fever IgM positive cases dropped. Conclusion: Our study shows that yellow fever transmission continues to persist and seems to be occurring all over Cameroon with all 10 regions under surveillance reporting a case. Preventive measures such as mass vaccination campaigns and routine childhood immunizations are urgently needed to increase population immunity. The diagnostic limitations in our analysis highlight the need to strengthen laboratory capacity and improve case investigations.

Transmission of wild polioviruses (WPVs) and vaccine-derived polioviruses (VDPVs) have been interrupted in Cameroon since July 2014. Subsequently, Cameroon withdrew Sabin type 2 from routine immunization in April 2016. This study aimed to investigate the detection rates and overtime distribution of the types of PVs recovered from urban sewage in Cameroon. From January 2016 to December 2017, 517 sewage specimens originating from Yaounde (325 specimens) and Douala (192 specimens) were analyzed. No WPVs and VDPVs were isolated in this study. In contrast, vaccine strains of poliovirus were detected throughout the study period. Isolates Sabin types 1 and 3 were sporadically detected whereas Sabin 2 was found only from January to May 2016 both in Yaounde and Douala. The absence of Sabin 2 in sewage specimens since June 2016 indicates its rapid disappearance after withdrawal from routine immunization in April 2016. This study provides substantial support to the observation that WPV and VDPVs have been successfully eliminated in Cameroon. However, it remains essential to maintain and extend high quality environmental surveillance as long as WPV reservoirs and VDPV outbreaks are detected in Africa.

To date, data on animal enteroviruses (EVs) are scarce, especially in Central Africa. The aim of this study was to characterize EVs among pigs and goats in Cameroon and the Central African Republic (CAR). A total of 226 pig and goat faecal samples collected in two previous studies carried out in Cameroon and CAR were pooled and screened with molecular assays targeting EV-Es, EV-Fs and EV-Gs. EV genomes were amplified by RT-PCR and their sequences were obtained by Illumina sequencing and de novo assembly. Based on the capsid sequences, 27 EV-G sequences were identified and assigned to 11 virus types, while no EV-E or EV-F was observed. Phylogenetic analysis revealed that the EV-Gs detected in Central Africa do not form specific clusters compared to EV-Gs previously reported in other continents. This suggests a worldwide circulation of EV-Gs, which is likely due to the massive international trade of live animals. One human EV, EV-C99, which belongs to the species Enterovirus C, was detected in pigs. This is the third detection of such an event in a similar context, reinforcing the hypothesis that some EV-Cs could be infecting pigs. Our work provides new data on the genetic diversity of EVs circulating among domestic animals in Central Africa.

To date, 15 species have been described within the genus Enterovirus. Previous studies suggested the existence of another species comprising strains isolated from the stool specimens of non-human primates (NHPs) in Central Africa. Moreover, numerous full-length or partial genomic sequences of NHP enteroviruses (EVs) can be found in GenBank without being properly classified. To our knowledge, no comprehensive synthesis of NHP EV data exists, leaving genetic relationships between strains across independent studies unclear. To address these gaps, we sequenced the complete genome of four NHP EVs from our stool collection and conducted an extensive search of NHP EV sequences in GenBank to perform a comprehensive phylogenetic analysis. Our analyses revealed two new species tentatively named Enterovirus mbel and Enterovirus noa , which contain at least 6 and 2 virus types, respectively. We also identified new virus types within the known species EV-J. Phylogenetic analyses strongly suggest interspecies recombination events between NHP EVs in the non-structural region of the genome, challenging the long-held view that recombination is confined within narrowly defined subsets of EVs belonging to the same species. We also performed the first comprehensive comparative analysis of full length human and NHP EV genomes, focusing on GC content, dinucleotide frequencies and codon-usage bias. GC content emerged as the most robust host-associated marker: all NHP-associated virus types within species E. alphacoxsackie and E. betacoxsackie displayed GC % below 47 %, whereas human-derived virus types exhibited GC % above 47 %. Dinucleotide frequency, Effective Number of Codons (ENC) and Relative Synonymous Codon Usage highlighted distinct codon-bias clusters that mirror the phylogenetic relationships between EVs but only partially correlate with their respective hosts of origin. This work enhances our understanding of EVs circulating in NHPs and paves the way for future research aiming at understanding the mechanisms underlying host-adaptation among EVs.