High genetic diversity of Newcastle disease virus in poultry in West and Central Africa: cocirculation of genotype XIV and newly defined genotypes XVII and XVIII.

Despite rampant Newcastle disease virus (NDV) outbreaks in Africa for decades, the information about the genetic characteristics of the virulent strains circulating in West and Central Africa is still scarce. In this study, 96 complete NDV fusion gene sequences were obtained from poultry sampled in Cameroon, Central African Republic, Côte d'Ivoire, and Nigeria between 2006 and 2011. Based on rational criteria recently proposed for the classification of NDV strains into classes, genotypes, and subgenotypes, we revisited the classification of virulent strains, in particular those from West and Central Africa, leading to their grouping into genotype XIV and newly defined genotypes XVII and XVIII, each with two subgenotypes. Phylogenetic analyses revealed that several (sub)genotypes are found in almost every country. In Cameroon, most strains were related to vaccine strains, but a single genotype XVII strain was also found. Only three highly similar genotype XVII strains were detected in Central African Republic. Subgenotypes XVIIa, XVIIIa, and XVIIIb cocirculated in Côte d'Ivoire, while subgenotypes XIVa, XIVb, XVIIa, XVIIb, and XVIIIb were found in Nigeria. While these genotypes are so far geographically restricted, local and international trade of domestic and exotic birds may lead to their spread beyond West and Central Africa. A high genetic diversity, mutations in important neutralizing epitopes paired with suboptimal vaccination, various levels of clinical responses of poultry and wild birds to virulent strains, strains with new cleavage sites, and other genetic modifications found in these genotypes tend to undermine and complicate NDV management in Africa.

Epidemiology of chicken anemia virus in Central African Republic and Cameroon.

BACKGROUND: Although chicken anemia virus (CAV) has been detected on all continents, little is known about this virus in sub-Saharan Africa. This study aimed to detect and characterize CAV for the first time in Central African Republic and in Cameroon. RESULTS: An overall flock seroprevalence of 36.7% was found in Central African Republic during the 2008-2010 period. Virus prevalences were 34.2% (2008), 14.3% (2009) and 10.4% (2010) in Central African Republic and 39% (2007) and 34.9% (2009) in Cameroon. CAV DNA was found in cloacal swabs of 76.9% of seropositive chickens, suggesting that these animals excreted the virus despite antibodies. On the basis of VP1 sequences, most of the strains in Central African Republic and Cameroon belonged to 9 distinct phylogenetic clusters at the nucleotide level and were not intermixed with strains from other continent. Several cases of mixed infections in flocks and individual chickens were identified. CONCLUSIONS: Our results suggest multiple introductions of CAV in each country that later spread and diverged locally. Mixed genotype infections together with the observation of CAV DNA in cloacal samples despite antibodies suggest a suboptimal protection by antibodies or virus persistence.

Epidemiology and genetic characterization of respiratory syncytial virus in children with acute respiratory infections: Findings from the influenza sentinel surveillance network in Central African Republic, 2015 to 2018.

BACKGROUND AND AIMS: Respiratory syncytial virus (RSV) is one of the main viral pathogens causing acute respiratory infections in children under 5 years of age but has seldom been studied in Central African Republic (CAF). Taking advantage of the national influenza surveillance network in CAF, this study aimed at providing the first insights into RSV prevalence and seasonality over 4 years of surveillance and the clinical manifestations of RSV in this population in CAF. METHODS: A total of 3903 children under 5 years matching the influenza-like illness (ILI, 68.5%) or severe acute respiratory infection (SARI, 31.5%) case definitions were recruited from January 2015 to December 2018. The presence of RSV viral RNA in nasopharyngeal samples was assessed by RT-PCR, followed by RSV-A and RSV-B typing and Sanger sequencing on a subset of samples. Phylogenetic analyses were carried on partial G protein sequences. Associations between RSV and demographic or clinical manifestations were investigated by statistical analyses. RESULTS: RSV prevalence was significantly higher in infants <6 months (13.4%), in hospitalized children (13.3% vs 5.5%) and in male patients (9.5% vs 6.4%). An overall prevalence of RSV of 8.0% in the period of 2015 to 2018 was shown, with significant annual (6.4%-10.6%) and seasonal (12.7% in rainy season vs 3.0% in dry season) fluctuations. While RSV seasons in 2015, 2016, and 2018 were relatively similar, 2017 showed deviations from the overall patterns with significantly higher RSV circulation and an outbreak peak 3 to 5 months earlier. Concomitant circulation of RSV-A and RSV-B with an alternating predominance of RSV-A and RSV-B strains and temporal RSV-A genotype replacement from NA1 to ON1 was observed. CONCLUSION: This study represents the first in-depth epidemiological analysis of RSV in CAF and provides first insights into RSV genetic diversity and seasonality in the country.