Assana Cissé

Background: The burden of viral co‐infections among COVID‐19 patients is underexplored in low‐resource settings such as Burkina Faso. This study aimed to determine the prevalence and associated factors of respiratory viral co‐infections among laboratory‐confirmed COVID‐19 patients. Methods: A cross‐sectional study was conducted from January 1 to December 31, 2023, across 13 sentinel sites in Burkina Faso. Patients presenting with influenza‐like illness or severe acute respiratory infection had nasopharyngeal and/or oropharyngeal swabs collected and tested for SARS‐CoV‐2 and other respiratory viruses using multiplex real‐time RT‐PCR. Descriptive statistics, univariate, and multivariate logistic regression analyses were performed to identify predictors of viral co‐infections. Results: Among 201 SARS‐CoV‐2‐positive patients enrolled (median age: 1 year; interquartile range: 0.5–7). Co‐infections was identified in 48.8% (95% CI: 41.8–55.6) of cases and a single co‐infections was detected in 33.8% (95% CI: 27.5–40.6) of patients. Human rhinovirus (17.9%), adenovirus (14.4%), respiratory syncytial virus (11.4%), and influenza A/B (9.9%) were most frequently detected. In multivariate analysis, children aged 6 months to 14 years had higher odds of co‐infection (aOR 2.7; 95% CI: 1.2–5.9; p = 0.013). Fever (aOR 2.6; 95% CI: 1.3–5.5; p = 0.008) and hospitalization (aOR 4.3; 95% CI: 1.6–12.0; p = 0.005) were also independently associated with co‐infection. Conclusion: Viral co‐infections were frequent among SARS‐CoV‐2 positive patients, particularly in children and hospitalized individuals. Strengthening multiplex diagnostic capacity and integrated respiratory virus surveillance in resource‐limited settings may improve clinical management and inform public health response strategies.

Background: Influenza is a major cause of acute respiratory infections worldwide. In tropical regions such as Sub‐Saharan Africa, influenza circulates year‐round with irregular peaks, yet genomic data guiding prevention strategies remain limited. This study characterized the genetic diversity and seasonal dynamics of influenza A(H1N1)pdm09 and A(H3N2) viruses circulating in Burkina Faso in 2024. Methods: A cross‐sectional study was conducted from January to December 2024, including seven sentinel surveillance sites. Patients presenting with influenza‐like illness or severe acute respiratory illness were enrolled. Respiratory specimens were tested by real‐time RT‐PCR. Influenza‐positive samples with a cycle threshold ≤ 30 underwent whole‐genome sequencing using Oxford Nanopore and Illumina platforms. Phylogenetic analyses and clade assignment were performed using MEGA Version 12. Results: Out of 2951 samples tested, 6.74% were positive for influenza viruses. Females had higher odds of influenza positivity than males (OR = 1.48; 95% CI: 1.11–1.98). A significantly higher risk of positivity was observed in the age groups of 5–15 years (OR = 1.67; 95% CI: 1.07–2.52; p = 0.02) and 25–50 years (OR = 2.54; 95% CI: 1.53–4.03; p < 0.001). Influenza A(H3N2) peaked in July, while A(H1N1)pdm09 peaked in October. Phylogenetic analysis of 43 genomes revealed co‐circulation of multiple clades within both subtypes. Conclusion: Influenza A viruses circulating in Burkina Faso in 2024 showed substantial genetic diversity, underscoring the need for continuous genomic surveillance to inform vaccine strain selection and public health strategies in tropical Africa.

Influenza and COVID-19 remain major public health concerns due to their high morbidity, mortality, and epidemic potential. The COVID-19 pandemic notably disrupted health and economic systems worldwide in 2020. Despite reduced global attention, these pathogens continue to circulate, and emerging disease resurgence remains a constant threat, emphasizing the importance of ongoing epidemiological and virological surveillance. This study aimed to describe year-long surveillance of SARS-CoV-2 and influenza viruses in post-pandemic Burkina Faso. A prospective cross-sectional survey was conducted from January to December 2023 in sentinel surveillance sites across four regions. Patients with influenza-like illness (ILI), severe acute respiratory infection (SARI), and their contacts were recruited. Nasopharyngeal or oropharyngeal swabs were collected and tested for influenza and SARS-CoV-2 using real-time RT-PCR. Socio-demographic and clinical data were obtained from medical records or interviews. Among 3,311 samples, 11.41% tested positive for influenza and 6.07% for SARS-CoV-2. Influenza A viruses predominated (90.21%), followed by type B (7.79%). Of all participants, 68.4% were ILI and 31.6% SARI cases. Influenza A was more common among ILI patients. Two influenza waves were observed, during the dry/cold season (February–March) and the end of the rainy season (October). Children were most affected by influenza, while SARS-CoV-2 was more frequent among adolescents and adults. Influenza and SARS-CoV-2 were significantly present in ILI and SARI cases. Targeted vaccination for high-risk groups and during peak influenza seasons could enhance prevention and reduce disease burden.

Background: Despite the availability of vaccines against SARS‑CoV‑2, mortality due to COVID-19 continues to increase, with nearly 7 million deaths reported globally. Continued analysis of the evolution and genomic diversity can provide necessary information to timely inform public health responses. We report the dynamics of SARS‑CoV‑2 lineages in Burkina Faso between August 2021 and September 2022.Methodology: A total of 188 patients, whose nasopharyngeal and/or oropharyngeal swabs tested positive for SARS-CoV-2 by RT-PCR at the National Influenza Reference Laboratory (NIRL) of the Institut de Recherche en Sciences de la Santé (IRSS) in Burkina Faso, were sequenced, and the whole genomes of the virus annotated and screened for mutations using the ARTIC protocol and Oxford Nanopore Technology. Subsequently, different SARS-CoV-2 lineages were assigned using NextClade. The socio-demographic characteristics of the study participants were collected. Descriptive statistics on the data were conducted using R software version 4.3.2. Comparisons were made using the Chi-square test for qualitative variables, and statistical significance was set at p<0.05.Results: Majority of the 188 COVID-19 positive cases lived in urban areas (85.1%), travelling from high-risk transmission zones. Of 134 SARS-CoV-2 genomes successfully sequenced and submitted to the NextClade database, the Delta (50.7%, n=68) and Omicron (42.5%, n=57) variants were predominant. The most frequent lineages detected were B.1.617.2 (20.1%, n=27), BA.1.13 (17.2%, n=23), and AY.133 (14.2%, n=19). Temporal trend showed that the pandemic was driven by the Delta variant which was progressively replaced by the Omicron variant of SARS-CoV-2.Conclusion: Although heterogeneity was seemingly not important during the study period, the Delta variant which was the most predominant variant in the country, was progressively replaced by the Omicron variant. Continuous genomic surveillance might be necessary to timely detect the virulent variants.

Tialla D, et al. J Vet Sci. 2022 Feb;23(3):e33. https://doi.org/10.4142/jvs.21235