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.
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.
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.
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.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We used portable genome sequencing to investigate reported dengue virus transmission in Angola. Our results show that autochthonous transmission of dengue serotype 2 (cosmopolitan genotype) occurred ...in January 2018.
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DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of ...viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high cost, narrow scope of detection, lengthy protocols and/or cross-contamination. Here, we developed metagenomic sequencing with spiked primer enrichment (MSSPE), a method for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. We evaluated MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels was comparable in sensitivity to specific PCR, demonstrating 95% accuracy for the detection of Zika, Ebola, dengue, chikungunya and yellow fever viruses in plasma samples from infected patients. Notably, sequences from re-emerging and/or co-infecting viruses that have not been specifically targeted a priori, including Powassan and Usutu, were successfully enriched using MSSPE. MSSPE is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making this method directly applicable for diagnostic laboratory and field use.
Introdução: Luanda é a capital de Angola, um país, que se situa no sudoeste africano. Os médicos, enfrentavam o problema do atendimento de inúmeros casos de síndromes febris de uma série de ...potenciais etiologias. O pacote de testes laboratorial, não incluía a avaliação de rotina da presença do vírus da dengue. A descoberta da circulação do vírus em Angola data de 1973, porém continuou sem registo até 2013. O objectivo do presente estudo foi, avaliar a consideração da probabilidade da infecção pelo vírus da dengue pela equipa de médicos, a frequência da infecção, o perfil sócio-demográfico, referente a idade, sexo, e os principais sintomas relacionados a infecção pela dengue, no período de Abril à Julho de 2022, para a produção de evidências científicas que possam mostrar a necessidade de colocar a dengue dentro da importância, no quadro nosológico de doenças transmissíveis em Angola. Métodos: Após assinatura de um documento de consentimento livre e esclarecido, foram analisadas clinicamente 140 pacientes adultos com síndromes febril e laboratorialmente as respectivas amostras de soro, colhidas em consultas, nas secções de Medicina Interna dos Hospitais dos Cajueiros e Américo Boavida, localizados em áreas sub-urbanas de Luanda. O diagnóstico laboratorial foi feito por testes seroimunológicos imunocromatográficos de diagnóstico rápido (TDRs), da marca SD Bioline, para a pesquisa de antigénios NS1, e paralelamente outro teste da presença de anticorpos IgM/IgG específicos contra o vírus da Dengue. Resultados: No total de 140 pacientes avaliados nas consultas, a dengue não foi considerada como hipótese diagnóstica, 35% (49/140) apresentaram infecções pelo vírus da dengue, detectada em indivíduos nas idades de 18 à 58 anos, tendo se constatado maior predominância de infecção em indivíduos mais jovens, de 18 à 28 anos, representando 40.81% (20/49) anos dos indivíduos, 57% e 43% foram do sexo masculino e feminino, respectivamente. Os sintomas mais frequentes, da dengue foram: febre (100% (49/49), dor retro-orbitrária (90% (44/49), cefaleias (100% (49/49), artralgias (100% (49/49), geralmente nos membros superiores, mialgias (41% (20/49). Conclusão: O vírus da dengue, pode ser o agente etiológico de inúmeros síndromes febris, que desafiam diariamente os médicos. O estudo epidemiológico da Dengue, envolvendo um maior é um necessidade prioritária para colocar a dengue na devida importância no quadro de doenças das doenças transmissíveis em Luanda, Angola.
Monitoring genetic diversity and drug resistance mutations (DRMs) is critical for understanding HIV epidemiology. Here, we report HIV-1 genetic diversity and DRMs in blood samples from 42 ...HIV-positive pregnant women naive to antiretroviral therapy (ART), in Luanda. The samples were subjected to nested-PCR, followed by sequencing of HIV-1 pol gene, targeting the protease and reverse transcriptase fragments. HIV-1 diversity was analyzed using the REGA HIV-1 subtyping tool and DRMs were identified using the Calibrated Population Resistance tool. A total of 34 sequences were obtained. The data revealed wide HIV-1 subtypes heterogeneity, with subtype C (38%, 13/34) the most frequent, followed by the subtypes F1 (18%, 6/34), A1 (9%, 3/34), G (9%, 3/34), D (6%, 2/34) and H (3%, 1/34). In addition, recombinants strains were detected, with CRF02_AG (6%, 2/34) the most frequent, followed by CRF37_cpx, F1/C, A1/G and H/G, all with 3% (1/34). A total of 6/34 (18%) of the sequences presented DRMs. The non-nucleoside reverse transcriptase inhibitors presented 15% (5/34) of resistance. Moreover, 1/34 (3%) sequence presented resistance against both non-nucleoside reverse transcriptase inhibitors and nucleoside reverse transcriptase inhibitors, simultaneously. Despite the small sample size, our results suggest the need to update currently used ART regimens. Surveillance of HIV-1 subtypes and DRMs are necessary to understand HIV epidemiology and to guide modification of ART guidelines in Angola.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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. 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. 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). 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.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Adolescents have poorer outcomes across the HIV cascade compared with adults. We aimed to assess progress in HIV case finding, antiretroviral treatment (ART), viral load coverage (VLC), and viral ...load suppression (VLS) among adolescents enrolled in the US President's Emergency Plan for AIDS Relief (PEPFAR)-supported programs over a 3-year period that included the beginning of the COVID-19 pandemic.
We analyzed PEPFAR program data in 28 countries/regions for adolescents aged 10-19 years between year 1 (October 2017to September 2018), year 2 (October 2018 to September 2019), and year 3 (October 2019 to September 2020). We calculated the number and percent change for HIV tests, HIV-positive tests, and total number on ART. Calculated indicators included positivity, percent of positives newly initiated on ART (ART linkage), VLC (percent of ART patients on ART for ≥6 months with a documented viral load result within the past 12 months), and VLS (percent of viral load tests with <1000 copies/mL).
Between years 1 and 3, the number of HIV tests conducted decreased by 44.2%, with a 29.1% decrease in the number of positive tests. Positivity increased from 1.3%-1.6%. The number of adolescents receiving ART increased by 10.4%. In addition, ART linkage increased (77.8%-86.7%) as did VLC (69.4%-79.4%) and VLS (72.8%-81.5%).
Our findings demonstrate PEPFAR's success in increasing the adolescent treatment cohort. We identified ongoing gaps in adolescent case finding, linkage, VLC, and VLS that could be addressed with a strategic mix of testing strategies, optimal ART regimens, and adolescent-focused service delivery models.
The dissemination of the dengue virus (DENV) in endemic regions with HIV is a public health concern with greater importance when there is evidence of vertical transmission of DENV during pregnancy. ...Herein, we investigated DENV among HIV-infected pregnant women in Luanda, the capital city of Angola. This was part of a cross-sectional study carried out on 42 pregnant women newly diagnosed with HIV. A total of 36 plasma samples from the 42 HIV-positive pregnant women were screened for DENV using RT‐PCR and ELISA. None of the specimens tested positive for DENV by RT-PCR. Regarding seroprevalence, 94.4% of the samples were positive for IgG and 11.1% for IgM. Recent infection (IgG-/IgM+ or IgG+/IgM+) was detected in 11.1% of the samples and past infection (IgG+/IgM-) in 83.3%. The risk of recent infection was higher in pregnant women over 25 years of age OR: 13.0 (95% CI: 1.14–148), p = 0.039. Our study showed laboratory evidence of a recent DENV infection among HIV-infected pregnant women attending antenatal care in Luanda. Our findings provide critical data regarding DENV infection among HIV-infected pregnant women in Luanda. Future studies involving a larger sample size of HIV-infected pregnant women are necessary to support ongoing public health programs to combat arboviruses in Angola.
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