Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern—particularly Alpha, Beta, Delta, and Omicron—on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Background: The transmission patterns and genetic diversity of dengue virus (DENV) circulating in Africa remain poorly understood. Circulation of the DENV serotype 1 (DENV1) in Angola was detected in 2013, while DENV serotype 2 (DENV2) was detected in 2018. Here, we report results from molecular and genomic investigations conducted at the Ministry of Health national reference laboratory (INIS) in Angola on suspected dengue cases detected between January 2017 and February 2019. Methods: A total of 401 serum samples from dengue suspected cases were collected in 13 of the 18 provinces in Angola. Of those, 351 samples had complete data for demographic and epidemiological analysis, including age, gender, province, type of residence, clinical symptoms, as well as dates of onset of symptoms and sample collection. RNA was extracted from residual samples and tested for DENV-RNA using two distinct real time RT-PCR protocols. On-site whole genome nanopore sequencing was performed on RT-PCR+ samples. Bayesian coalescent models were used to estimate date and origin of outbreak emergence, as well as population growth rates. Results: Molecular screening showed that 66 out of 351 (19%) suspected cases were DENV-RNA positive across 5 provinces in Angola. DENV RT-PCR+ cases were detected more frequently in urban sites compared to rural sites. Of the DENV RT-PCR+ cases most were collected within 6 days of symptom onset. 93% of infections were confirmed by serotype-specific RT-PCR as DENV2 and 1 case (1.4%) was confirmed as DENV1. Six CHIKV RT-PCR+ cases were also detected during the study period, including 1 co-infection of CHIKV with DENV1. Most cases (87%) were detected in Luanda during the rainy season between April and October. Symptoms associated with severe dengue were observed in 11 patients, including 2 with a fatal outcome. On-site nanopore genome sequencing followed by genetic analysis revealed an introduction of DENV2 Cosmopolitan genotype (also known as DENV2-II genotype) possibly from India in or around October 2015, at least 1 year before its detection in the country. Coalescent models suggest relatively moderately rapid epidemic growth rates and doubling times, and a moderate expansion of DENV2 in Angola during the studied period. Conclusion: This study describes genomic, epidemiological and demographic characteristic of predominately urban transmission of DENV2 in Angola. We also find co-circulation of DENV2 with DENV1 and CHIKV and report several RT-PCR confirmed severe dengue cases in the country. Increasing dengue awareness in healthcare professional, expanding the monitorization of arboviral epidemics across the country, identifying most common mosquito breeding sites in urban settings, implementing innovative vector control interventions and dengue vaccination campaigns could help to reduce vector presence and DENV transmission in Angola.

Co‐epidemics happening simultaneously can generate a burden on healthcare systems. The co‐occurrence of SARS‐CoV‐2 with vector‐borne diseases (VBD), such as malaria and dengue in resource‐limited settings represents an additional challenge to the healthcare systems. Herein, we assessed the coinfection rate between SARS‐CoV‐2 and VBD to highlight the need to carry out an accurate diagnosis and promote timely measures for these infections in Luanda, the capital city of Angola. This was a cross‐sectional study conducted with 105 subjects tested for the SARS‐CoV‐2 and VBD with a rapid detection test in April 2021. The participants tested positive for SARS‐CoV‐2 (3.80%), malaria (13.3%), and dengue (27.6%). Low odds related to testing positivity to SARS‐CoV‐2 or VBD were observed in participants above or equal to 40 years (odds ratio [OR]: 0.60, p = 0.536), while higher odds were observed in male (OR: 1.44, p = 0.392) and urbanized areas (OR: 3.78, p = 0.223). The overall co‐infection rate between SARS‐CoV‐2 and VBD was 11.4%. Our findings showed a coinfection between SARS‐CoV‐2 with malaria and dengue, which could indicate the need to integrate the screening for VBD in the SARS‐CoV‐2 testing algorithm and the adjustment of treatment protocols. Further studies are warranted to better elucidate the relationship between COVID‐19 and VBD in Angola.

This study aimed to investigate the characteristics related to SARS-CoV-2 in Luanda, Angola. A total of 622 individuals were screened for SARS-CoV-2 from January to September 2020. Chi-square and logistic regression were used to identify the relationship between sociodemographic characteristics and SARS-CoV-2. Of the 622 tested, 14.3% tested positive. The infection rate was the same for both genders (14.3%). Individuals ≥40 years old, from non-urbanized areas, and healthcare professionals had a higher frequency of infection. The risk of infection was very high in individuals ≥60 years old (AOR: 23.3, 95% CI: 4.83–112), in women (AOR: 1.24, 95% CI: 0.76–2.04), in Luanda (AOR: 7.40, 95% CI: 1.64–33.4), and healthcare professionals (AOR: 1.27, 95% CI: 0.60–2.71), whereas a low risk was observed in individuals from urbanized areas (AOR: 0.44, 95% CI: 0.26–0.75). Our results suggest that Angolan authorities should implement a greater effort in non-urbanized areas and among healthcare professionals since when these individuals presented any indication for a COVID-19 test, such as fever/cough/myalgia, they were more likely to test positive for SARS-CoV-2 than having some other cause for symptoms.

Background: Despite the guidelines provided by the World Health Organization for the treatment of malaria, treatment failure occurs in many hospitalized patients. Objective: Evaluate whether blood cell count parameters may serve as predictors for malaria treatment. Methodology: A cross-sectional study with a quantitative approach. Results: Of the 219 patients, 21.5% showed failure to antimalarial treatment, Patient with 21 and 40 years (72.6%), male (53.4%), from peri-urban area (47.5%), with high parasitemia (59.8%), treated with Arthemeter (90.9%) and the mortality were 5.9%. Significant associations were observed between occupation, level of parasitemia and outcome with resistance to antimalarial treatment (p<0.05). Patients with normal Hb [OR: 0.75 (95% CI: 0.39–1.44), p = 0.393], RBC [OR: 0.83 (95% CI: 0.40–1.72), p = 0.632], RDW [OR: 0.54 (95% CI: 0.27–1.09), p = 0.088], MCV [OR: 0.61 (95% CI: 0.28–1.31), p = 0.204] were less likely to have malaria treatment failures after artemisinin-based therapy failure. In contrast, those with normal values of segmented neutrophils [OR: 0.32 (95% CI: 0.11–0.96), p = 0.042] and lymphocyte counts [OR: 0.24 (95% CI: 0.05–1.04), p = 0.055]. We also found that patients with significant low levels of Hct [OR: 0.31 (95% CI: 0.15–0.64) p = 0.002], and high leukocytes [OR: 8.88 (95% CI: 2.02–37.2), p = 0.004] and normal platelet values [OR: 1.42 (95% CI: 0.73–2.95), p = 0.280] demonstrated high probability of treatment failure. Conclusion: The importance of blood cell count parameters in monitoring malaria therapy necessitates the urgent need to re-evaluate Artemether-based therapy. Future studies involving more participants in different settings are needed to provide further evidence.

Background: SARS-CoV-2 emerged in China and spread throughout the world due to its rapid transmission. The exposure rate in the healthy population is unknown, mainly in resource-limited countries. Herein, we estimated the seroprevalence of anti-SARS-CoV-2 antibodies and risk factors among blood donors in Luanda, the capital city of Angola. Methods: This was a retrospective study conducted with 343 blood donors. Chi-square and logistic regression were calculated to predict the independent variable for SARS-CoV-2 infection and deemed significant when p < 0.05. Results: Seroprevalence of anti-SARS-CoV-2 was 4.7%. Positivity rates varied to age groups (3.5–14.3%), gender (0–5%), area of residence (3.1–.6%), educational level (5.1–10.2%), occupation (4.4–7.7%), and the blood donor category (2.0–5.1%). Past and recent infections were detected in 3.2% and 1.5%, respectively. Blood donors under the age of 20 years (OR: 4.58, p = 0.241) and from non-urbanized areas (OR: 1.86, p = 0.293) presented a high risk related to infection. The infection was higher in blood group A and lower in blood group O. The risk of SARS-CoV-2 infection has increased from January 2020 (OR: 0.03, p = 0.001) to August 2020 (OR: 0.57, p = 0.426). Conclusions: We provide an estimate of the exposure of healthy blood donors in Luanda. Also, we detected anti-SARS-CoV-2 in January 2020, indicating that the SARS-CoV-2 could have been imported during the first month of 2020. Further studies should be performed to assess the exposure rate in different groups from Angola.