Genomic surveillance of severe acute respiratory syndrome coronavirus 2 in Burundi, from May 2021 to January 2022.

BACKGROUND: The emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants have challenged the control of the COVID-19 pandemic globally. Burundi was not spared by that pandemic, but the genetic diversity, evolution, and epidemiology of those variants in the country remained poorly understood. The present study sought to investigate the role of different SARS-COV-2 variants in the successive COVID-19 waves experienced in Burundi and the impact of their evolution on the course of that pandemic. We conducted a cross-sectional descriptive study using positive SARS-COV-2 samples for genomic sequencing. Subsequently, we performed statistical and bioinformatics analyses of the genome sequences in light of available metadata. RESULTS: In total, we documented 27 PANGO lineages of which BA.1, B.1.617.2, AY.46, AY.122, and BA.1.1, all VOCs, accounted for 83.15% of all the genomes isolated in Burundi from May 2021 to January 2022. Delta (B.1.617.2) and its descendants predominated the peak observed in July-October 2021. It replaced the previously predominant B.1.351 lineage. It was itself subsequently replaced by Omicron (B.1.1.529, BA.1, and BA.1.1). Furthermore, we identified amino acid mutations including E484K, D614G, and L452R known to increase infectivity and immune escape in the spike proteins of Delta and Omicron variants isolated in Burundi. The SARS-COV-2 genomes from imported and community-detected cases were genetically closely related. CONCLUSION: The global emergence of SARS-COV-2 VOCs and their subsequent introductions in Burundi was accompanied by new peaks (waves) of COVID-19. The relaxation of travel restrictions and the mutations occurring in the virus genome played an important role in the introduction and the spread of new SARS-COV-2 variants in the country. It is of utmost importance to strengthen the genomic surveillance of SARS-COV-2, enhance the protection by increasing the SARS-COV-2 vaccine coverage, and adjust the public health and social measures ahead of the emergence or introduction of new SARS-COV-2 VOCs in the country.

Clinical and Epidemiology Characteristics of COVID-19 Cases Detected During Mass Screening Campaign from July to October 2020 in Bujumbura, Burundi.

Background: Coronavirus disease of 2019 (COVID-19) is an infectious disease caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2 Virus). It was reported for the first time in Wuhan city, Hubei province of China. The first cases of COVID-19 in Burundi were identified on 31st March 2020. Several signs and symptoms, including mainly; fever, dry cough, fatigue, myalgia, and dyspnea are the most prominent characteristics of the disease. The aim of this study was to provide description of the clinical and epidemiological characteristics of COVID-19 cases identified during the mass screening campaign conducted between July and October, 2020 in Burundi. Methods: We conducted a retrospective secondary analysis of data of clients to the mass screening campaign in Bujumbura city that was run between July and October 2020. Clients with complete data and tested for COVID-19 with Reverse Transcription Polymerase Chain Reaction (RT-PCR) were included in the study. Epi-Info 7.2.2.6 was used to perform descriptive and analytical statistics and Quantum Geographic Information System (QGIS) was used for cases mapping. Association between positive cases and independent variables such as sex, history of contact with confirmed COVID-19 case was measured using chi-square statistical test at a p-value of .05. Results: The study included 20,114 participants. 243 (1.2%) were tested positive for COVID-19. The mean age for confirmed cases was 33 (±15) years. The majority of cases (72.8%) were between 20 and 59 years of age and they were predominantly males (67.9%). 164 (67.5%) were symptomatic and cough was the most frequent symptom observed 109 (66.5%), followed by rhinorrhea 69 (42.1%). Fever was present in only 18 (11.0%) of symptomatic patients. Participants with a history of contact with a COVID-19 confirmed case (aOR=2.2; 95%CI [1.6-3.0]; p-value <.001), were more likely to be positive for COVID-19. Also, those who were coughing (aOR=1.47; 95%CI [1.06-2.05]; p-value=.023) and having sore throat (aOR=2.4; 95%CI [1.1-4.9]; p-value=.02) were more likely to test positive for COVID-19. Conclusion: This study revealed that a significant proportion (32.5%) of COVID-19 patients were silent carriers of the virus. Data highlighted that high proportion of cases were among the active age group and contacts with confirmed cases, and noted high proportion of asymptomatic cases at diagnosis. Measures including routine testing of asymptomatic contacts could contribute to tackling corona virus in Burundi.

Uptake of Modern Contraceptive Methods among Burundian Women and Associated Factors: Analysis of Demographic and Health Survey Data, Burundi 2016-2017.

BACKGROUND: Globally in 2017, Burundi was the 9th country with the highest population growth rate of 3.2% and a fertility rate of 5.5 children per woman. This probably suggested low uptake of Modern Contraceptive methods (MCM) in the country. Our analysis investigated factors associated with low uptake of MCM among women of reproductive age in Burundi. METHODS: Cross sectional data of non-pregnant women aged 15-49 years was extracted from the Burundi Demographic and Health Survey (2016-2017). We analysed the data at univariate, bivariate and multivariate levels to assess factors influencing MCM uptake among these women using Epi-Info 7.2.2.6. RESULTS: Of the 9,945 women, 2,372 (23.8%) were using MCM. Ngozi province had the highest prevalence of MCM users [284/691(37.7%)]. The most used MCM among respondents was injectable contraceptive (48.3%). As respondent's age increases, the odds of using MCM decreases; 20-24 years (aOR=0.9, 95% CI [0.6-1.2]), 30-34 years (aOR=0.8, 95% CI [0.5-1.0]), 35-39 years (aOR=0.7, 95% CI [0.5-0.9]), 40-44 years (aOR=0.5, 95% CI [0.5-0.9]) and 45-49 years (aOR=0.4, 95% CI [0.2-0.5]) compared with those in the age group 15-19 years. Muslims (aOR=1.5, 95% CI [1.2-1.9]) and Jehovah witnesses (aOR=3.1, 95% CI [1.7-6.5]) were more likely to use MCM than Catholics. CONCLUSION: The prevalence of MCM remains low among women of reproductive age in Burundi, with injectables being the most used method. Factors such as respondent's age and religion were significantly associated with MCM use. Enhanced access to family planning information and services targeting women who are 30 years or more and engaging religious leaders for their active participation is recommended.

Use of long-lasting insecticidal nets among women attending antenatal clinic at a tertiary hospital in Bayelsa State, Nigeria 2019.

BACKGROUND: Malaria in pregnancy remains a major contributor to maternal and infant morbidity and mortality despite scale up in interventions. Its prevention is one of the major interventions in reducing maternal and infant morbidity and mortality. The ownership, utilization and predictors of use of long-lasting insecticide-treated nets (LLINs) for malaria prevention among women attending antenatal clinic (ANC) at a tertiary hospital in Bayelsa State Nigeria was assessed. METHODS: A cross-sectional study of 297 women recruited through systematic sampling was carried out. Information on sociodemographic characteristics, ownership, source and utilization of LLINs, were collected with a pre-tested structured interviewer-administered questionnaire. The relationship between use of LLIN and sociodemographic characteristics was examined using chi square and logistic regression at 5% level of significance. RESULTS: The mean age of respondents was 28.8 ± 2.6 years. Most (59.2%) had tertiary education and were mainly (88.2%) urban dwellers. Two hundred and fifty (84.2%) owned LLINs, and 196 (78%) used LLIN the night prior to the interview. Almost half of the respondents purchased their LLINs. Those who purchased LLINs were 3 times more likely to have used it (OR: 3.13, 95% CI 1.62-6.04) compared to those that got it free. Those who were gainfully employed (OR: 3.16, 95% CI 1.59-6.29) and those who earned above the minimum wage (OR: 2.88, 95% CI 1.45-5.72) were 3 times more likely to have used LLIN in their index pregnancy. CONCLUSION: The use of LLIN as a preventive measure against malaria was relatively high among the participants in this study, though still below national target. The major factors determining the use of LLIN among these women were purchase of LLINs and being gainfully employed. It was recommended that efforts should be made to enforce the policy of free LLINs at ANC registration at the tertiary hospitals, as this would further drive up ownership and utilization rates.

Trends in Malaria Cases and Deaths: Assessing National Prevention and Control Progress in Burundi.

BACKGROUND: Malaria is associated with high morbidity and mortality especially in World's tropical regions. In 2016, an estimated 216 million and 445,000 cases of malaria and deaths associated with malaria respectively were reported globally. Malaria is the first leading cause of outpatient visits, hospitalization and death in Burundi. We therefore examined the trend in malaria cases and deaths in Burundi. METHODS: We extracted data from Burundi National Health Information System (BNHIS) and assessed trends in malaria cases and deaths from January 2015 to December 2017. A suspected case of malaria was defined as any person treated by anti-malarial drugs without testing while a confirmed case as any person with a positive microscopy or rapid diagnostic test for malaria parasite. We described malaria cases and deaths, and calculated malaria case incidence rate. RESULTS: A total of22,225,699 malaria cases with 8,660 deaths (CFR 0.04%) was documented during the study period. Out of 22,225,699 cases, 45,291 cases (0.2%) were suspected malaria cases. The observed peak season of malaria infection in any of the studied year was in the raining season (March-June). All provinces of the country were affected. Kirundo and Cankuzo provinces the incidence of malaria cases increased from 10.1 cases per 1,000 persons in 2015 to 13.2 cases per 1,000 persons in 2017. The case fatality rate decreased from 0.06% in 2015 to 0.01% in 2017. CONCLUSION: An increasing trend in malaria prevalence was observed in Burundi but Kirundo and Cankuzo provinces were the most affected. However, the case fatality decreased within the studied period. Malaria intervention should be intensified/scaled up in the raining season and the most affected provinces.

Outbreak of human monkeypox in Nigeria in 2017-18: a clinical and epidemiological report.

BACKGROUND: In September, 2017, human monkeypox re-emerged in Nigeria, 39 years after the last reported case. We aimed to describe the clinical and epidemiological features of the 2017-18 human monkeypox outbreak in Nigeria. METHODS: We reviewed the epidemiological and clinical characteristics of cases of human monkeypox that occurred between Sept 22, 2017, and Sept 16, 2018. Data were collected with a standardised case investigation form, with a case definition of human monkeypox that was based on previously established guidelines. Diagnosis was confirmed by viral identification with real-time PCR and by detection of positive anti-orthopoxvirus IgM antibodies. Whole-genome sequencing was done for seven cases. Haplotype analysis results, genetic distance data, and epidemiological data were used to infer a likely series of events for potential human-to-human transmission of the west African clade of monkeypox virus. FINDINGS: 122 confirmed or probable cases of human monkeypox were recorded in 17 states, including seven deaths (case fatality rate 6%). People infected with monkeypox virus were aged between 2 days and 50 years (median 29 years [IQR 14]), and 84 (69%) were male. All 122 patients had vesiculopustular rash, and fever, pruritus, headache, and lymphadenopathy were also common. The rash affected all parts of the body, with the face being most affected. The distribution of cases and contacts suggested both primary zoonotic and secondary human-to-human transmission. Two cases of health-care-associated infection were recorded. Genomic analysis suggested multiple introductions of the virus and a single introduction along with human-to-human transmission in a prison facility. INTERPRETATION: This study describes the largest documented human outbreak of the west African clade of the monkeypox virus. Our results suggest endemicity of monkeypox virus in Nigeria, with some evidence of human-to-human transmission. Further studies are necessary to explore animal reservoirs and risk factors for transmission of the virus in Nigeria. FUNDING: None.

Reemergence of Human Monkeypox in Nigeria, 2017.

In Nigeria, before 2017 the most recent case of human monkeypox had been reported in 1978. By mid-November 2017, a large outbreak caused by the West African clade resulted in 146 suspected cases and 42 laboratory-confirmed cases from 14 states. Although the source is unknown, multiple sources are suspected.