Emergence of SARS-CoV-2 Delta Variant, Benin, May-July 2021.

Severe acute respiratory syndrome coronavirus 2 Delta variant epidemiology in Africa is unknown. We found Delta variant was introduced in Benin during April-May 2021 and became predominant within 2 months, after which a steep increase in reported coronavirus disease incidence occurred. Benin might require increased nonpharmaceutical interventions and vaccination coverage.

Limited Specificity of Serologic Tests for SARS-CoV-2 Antibody Detection, Benin.

We used commercially available ELISAs to test 68 samples from coronavirus disease cases and prepandemic controls from Benin. We noted <25% false-positive results among controls, likely due to unspecific immune responses elicited by acute malaria. Serologic tests must be carefully evaluated to assess coronavirus disease spread and immunity in tropical regions.

Mutations Associated with SARS-CoV-2 Variants of Concern, Benin, Early 2021.

Intense transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Africa might promote emergence of variants. We describe 10 SARS-CoV-2 lineages in Benin during early 2021 that harbored mutations associated with variants of concern. Benin-derived SARS-CoV-2 strains were more efficiently neutralized by antibodies derived from vaccinees than patients, warranting accelerated vaccination in Africa.

Development of rice farming: a cause of the emergence of multiple insecticide resistance in populations of Anopheles gambiae s.l and its impact on human health in Malanville, Bénin.

Aim: The rise in rice production in the district of Malanville, Northen Benin, is a present concern, as it has resulted in the widespread usage of pesticides for crop protection. This could impact human health but also life cycle of Anopheles gambiae, the main vector of malaria. Methods: Therefore, insecticide susceptibility bioassays were carried out on populations of An. gambiae s.l aged to 3-5 days old (two from areas where insecticide is highly used and other two areas of low insecticide use) and subjected to insecticide-impregnated papers (Permethrin 0.75%; deltamethrin 0.05%; DDT 4% and bendiocarb 0.1%) following WHO protocol. Polymerase Chain Reactions (PCRs) were used for the detection of Acethlylcholinestrase (Ace-1) and the knock down resistance (kdr) L1014F mutations in An. gambiae populations. Finally, indirect bioassays were conducted for the investigating on the factors affecting the life cycle of An. gambiae due to the use of pesticides. Results: An. gambiae from the four sites were resistant to DDT (6 to 8% and 10 to 14% respectively from areas of high and low dose), pyrethroids (22 to 26% and 30 to 36% for permethrin, from areas of high and low dose respectively and 66 to 70% and 72 to 80% for deltamethrin, from high and low dose) but susceptible to carbamate. The kdr L1014F mutation was detected in An. gambiae populations (0.88 to 0.90 and 0.84 to 0.88 from high and low dose, respectively). The ace-1 was detected at low frequencies (<0.002). Bioassays on the impacts of the use of pesticides in the life cycle of An. gambiae showed that soil substrates with pesticides residues have a negative impact on the life cycle eggs of An. gambiae. Conclusion: These findings confirmed the negative impacts of pesticides use in rice farming and its impacts on the life cycle of An. gambiae.

Genetic diversity and wing geometric morphometrics among four populations of Aedes aegypti (Diptera: Culicidae) from Benin.

BACKGROUND: The impact of the arbovirus vector Aedes aegypti is of major concern for global public health as the viruses that it transmits affect millions of people each year worldwide. Originating in Africa, Ae. aegypti has now spread throughout much of the world. While the genetic makeup of Ae. aegypti in the New World has been extensively studied, there is limited knowledge on its genetic diversity in Africa, particularly at a microgeographical level. METHODS: We investigated mitochondrial cytochrome oxidase I of four Ae. aegypti populations from Benin and employed wing morphometric analyses as a cost-effective and reliable tool to explore population structure. Our sampling encompassed various areas of Benin, from the southern to the northern borders of the country, and included urban, semi-urban, and sylvatic sites. RESULTS: We observed a notable level of genetic diversity (haplotype diversity of 0.8333) and nucleotide diversity (0.00421986), and identified seven distinct haplotypes. Sylvatic and semi-urban sites exhibited a greater number of haplotypes compared to urban sites. Utilizing 18 wing landmarks, we calculated the centroid size, which revealed significant variation among the three landscape types. However, principal component analysis, employed to assess wing shape variation, did not demonstrate significant differences between populations based on landscape type. CONCLUSIONS: Our findings indicate substantial genetic and morphological diversity among Ae. aegypti populations in Benin, and provide insight into important biological characteristics of these populations with respect to their potential to transmit viruses. To the best of our knowledge, this is the first study undertaken in Africa to integrate genetics with morphology to analyse the population structure of the major arbovirus vector Ae. aegypti.

First Detection of the Invasive Mosquito Vector Aedes albopictus (Diptera: Culicidae) in Benin, West Africa, 2021.

Aedes albopictus (Skuse) is native to Southeast Asia and has colonized tropical and temperate regions worldwide in the last three to four decades. In Africa, data on its distribution is incomplete. Most studies having focused on the abundance, competition to other species, and phylogenetics of this vector are from the central African region. Here, we report the first detection of Ae. albopictus in Benin, West Africa. A total of 13 specimens were collected during the study period in 2021. The phylogenetic analysis of a cytochrome oxidase c subunit I gene fragment revealed a close relationship to populations from tropical India. Because of its close geographical proximity to areas where it has been found, it is assumed that the species was introduced several years before and is currently widely distributed in Benin. Additional studies are needed to explore its distribution, expansion range, and competitive effects on native species.

An Observational Laboratory-Based Assessment of SARS-CoV-2 Molecular Diagnostics in Benin, Western Africa.

Information on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread in Africa is limited by insufficient diagnostic capacity. Here, we assessed the coronavirus disease (COVID-19)-related diagnostic workload during the onset of the pandemic in the central laboratory of Benin, Western Africa; characterized 12 SARS-CoV-2 genomes from returning travelers; and validated the Da An RT-PCR-based diagnostic kit that is widely used across Africa. We found a 15-fold increase in the monthly laboratory workload due to COVID-19, dealt with at the cost of routine activities. Genomic surveillance showed near-simultaneous introduction of distinct SARS-CoV-2 lineages termed A.4 and B.1, including the D614G spike protein variant potentially associated with higher transmissibility from travelers from six different European and African countries during March-April 2020. We decoded the target regions within the ORF1ab and N genes of the Da An dual-target kit by MinION-based amplicon sequencing. Despite relatively high similarity between SARS-CoV-2 and endemic human coronaviruses (HCoVs) within the ORF1ab target domain, no cross-detection of high-titered cell culture supernatants of HCoVs was observed, suggesting high analytical specificity. The Da An kit was highly sensitive, detecting 3.2 to 9.0 copies of target-specific in vitro transcripts/reaction. Although discrepant test results were observed in low-titered clinical samples, clinical sensitivity of the Da An kit was at least comparable to that of commercial kits from affluent settings. In sum, virologic diagnostics are achievable in a resource-limited setting, but unprecedented pressure resulting from COVID-19-related diagnostics requires rapid and sustainable support of national and supranational stakeholders addressing limited laboratory capacity.IMPORTANCE Months after the start of the COVID-19 pandemic, case numbers from Africa are surprisingly low, potentially because the number of SARS-CoV-2 tests performed in Africa is lower than in other regions. Here, we show an overload of COVID-19-related diagnostics in the central laboratory of Benin, Western Africa, with a stagnating average number of positive samples irrespective of daily sample counts. SARS-CoV-2 genomic surveillance confirmed a high genomic diversity in Benin introduced by travelers returning from Europe and other African countries, including early circulation of the D614G spike mutation associated with potentially higher transmissibility. We validated a widely used RT-PCR kit donated by the Chinese Jack Ma Foundation and confirmed high analytical specificity and clinical sensitivity equivalent to tests used in affluent settings. Our assessment shows that although achievable in an African setting, the burden from COVID-19-related diagnostics on national reference laboratories is very high.

Antimicrobial resistance and toxigenic profiles of bacteria isolated from tropical shrimps (Farfantepenaeus notialis and Penaeus monodon) in Cameroun.

OBJECTIVE: Post-harvest shrimp losses are a big problem due to the proliferation of spoilage bacteria. Presence and multiplication of these bacteria promotes the emergence of food-borne diseases. This study was carried out to characterize some spoilage bacteria from tropical brackish water shrimps and black tiger shrimps stored in ambient temperature (25 °C). RESULTS: 22 isolates of Bacillus spp; 09 isolates of Coagulase Negative Staphylococci (CNS) and 04 isolates of enterobacteria such as Pantoea spp (01); Serratia plymutica (01) and Serratia rubidaea (02) have been identified. Resistance and virulence genes were then detected. All isolates expressed resistance to at least three of antibiotics tested. 03 isolates of enterobacteria were susceptible to cetfazidim and amoxicillin-clavulanic acid. Bacillus spp showed total susceptibility to cefixim, ertapenem and cetfazidim. Staphylococci were susceptible to clindamycin. Pantoea spp was resistant to all antibiotics but exhibited intermediate susceptibility to amoxicillin-clavulanic acid. 04 isolates of Staphylococci were positive to mecA resistances genes. All the enterobacteria harbor no tetracycline resistance genes. All the isolates of Bacillus exhibited the presence of enterotoxin genes. Also, a high prevalence of 21 isolates to hemolytic enterotoxins was noted. 17 isolates from them kept ability to cell-lyse factor production like sphingomyelinase activities. The majority of Bacillus isolates identified by the present study poses a potential risk of food poisoning due to the prevalence of toxin genes found.