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The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection.

National public health institutes (NPHIs)-science-based governmental agencies typically part of, or closely aligned with, ministries of health-have played a critical part in many countries' responses to the COVID-19 pandemic. Through listening sessions with NPHI leadership, we captured the experiences of NPHIs in Africa. Our research was further supplemented by a review of the literature. To address issues related to COVID-19, NPHIs in Africa developed a variety of innovative approaches, such as working with the private sector to procure and manage vital supplies and address key information needs. Creative uses of technology, including virtual training and messaging from drones, contributed to sharing information and battling misinformation. Positive impacts of the pandemic response include increased laboratory capacity in many countries, modernized surveillance systems, and strengthened public-private partnerships; much of this enhanced capacity is expected to persist beyond the pandemic. However, several challenges remain, including the lack of staff trained in areas like bioinformatics (essential for genomic analysis) and the need for sustained relationships and data sharing between NPHIs and agencies not traditionally considered public health (eg, those related to border crossings), as well as the impact of the pandemic on prevention and control of non-COVID-19 conditions-both infectious and noncommunicable. Participants in the listening sessions also highlighted concerns about inequities in access to, and quality of, the public health services and clinical care with resultant disproportionate impact of the pandemic on certain populations. COVID-19 responses and challenges highlight the need for continued investment to strengthen NPHIs and public health infrastructure to address longstanding deficiencies and ensure preparedness for the next public health crisis.

Yellow fever virus is an arbovirus transmitted to humans by Aedes and Haemogogus mosquito species. To date, there is no specific treatment for yellow fever. However, an effective vaccine is available for the prevention. After a decline in yellow fever cases in Africa between 2004 and 2015, large-scale transmission of the virus was observed in Africa during 2019, with outbreaks recorded in West Africa. The objective of this study was to estimate the incidence of yellow fever cases recorded in the national reference laboratory of Togo from 2010 to 2020.Data were extracted from the National Institute of Hygiene database from 2010 to 2020 with an Excel sheet and descriptive analyses were performed.A total of 4350 samples were collected between 2010 and 2020 in Togo from yellow fever suspected cases. These cases had a median age of 12 years (IQR: 5-24), and 21% of them were from the Maritime region. Among them, 30 cases were reported by national laboratory, with a global incidence of 0.7% (confidence interval 95%: [0.4-1.0]). At the yellow fever regional laboratory, 14 cases were confirmed with an incidence of 0.33% (confidence interval 95%: [0.18-0.55]). In this population, 37.7% had been immunized against yellow fever.This study shows that Togo presents cases of yellow fever. Identification of the vectors and implementation of efficient vector control measures could help prevent this disease, as well as other diseases transmitted by the same vectors. Yellow fever vaccination should be a priority in vaccination programs.

Togo has reported seasonal meningitis outbreaks caused by non-Neisseria meningitidis serogroup A (NmA) pathogens since the introduction of meningococcal serogroup A conjugate vaccine (MACV, MenAfriVac) in 2014. From 2016 to 2017, NmW caused several outbreaks. In early 2019, a NmC outbreak was detected in the Savanes region of Togo and its investigation is described here. Under case-based surveillance, epidemiological and clinical data, and cerebrospinal fluid specimens were collected for every suspected case of meningitis. Specimens were tested for meningitis pathogens using confirmatory microbiological and molecular methods. During epidemic weeks 9 to 15, 199 cases were reported, with 179 specimens being available for testing and 174 specimens (97.2%) were tested by at least one confirmatory method. The NmC was the predominant pathogen confirmed (93.9%), belonging to sequence type (ST)-9367 of clonal complex (CC) 10217. All NmC cases were localized to the West Kpendjal district of the Savanes region with attack rates ranging from 4.1 to 18.8 per 100,000 population and case fatality rates ranging up to 2.2% during weeks 9 to 15. Of the 93 NmC confirmed cases, 63.4% were males and 88.2% were in the 5 to 29 age group. This is the first report of a NmC meningitis outbreak in Togo. The changing epidemiology of bacterial meningitis in the meningitis belt post-MACV highlights the importance of monitoring of emerging strain and country preparedness for outbreaks in the region.

Background The World Health Organization has targeted lymphatic filariasis (LF) for elimination as a public health problem and recommends, among other measures, post-elimination surveillance of LF. The identification of sensitive and specific surveillance tools is therefore a research priority. The Wuchereria bancrofti-specific antigen Wb123-based enzyme-linked immunosorbent assay (Wb123 ELISA) detects antibodies to the recombinant Wb123 antigen of W. bancrofti and may be useful as a surveillance tool for LF. Six years after stopping mass drug administration to eliminate LF and recording successful results on two post-treatment transmission assessment surveys, a study was conducted in Togo aimed at helping to identify the role of the Wb123 ELISA in post-validation surveillance of LF. Methods This was a cross-sectional study in eight previously LF-endemic districts and one non-endemic district in Togo. In each sub-district of these nine districts, two schools were selected and 15 children aged 6 to 9 years old at each school provided finger-stick blood for testing for antibodies to Wb123 using the Filaria Detect™ IgG4 ELISA kit® (InBios, International, Inc., Seattle, WA, USA). Results A total of 2654 children aged 6 to 9 years old were tested in 134 schools in the nine districts. Overall, 4.7% (126/2654) children tested positive for antibodies to the Wb123 antigen of W. bancrofti. The prevalence of Wb123 antibodies varied across the eight previously endemic LF districts, from 1.56 to 6.62%. The highest prevalence, 6.99%, was found in the non-endemic district, but this was not significantly different from the average of all the LF districts (4.49%, P = 0.062). Conclusions The Wb123 ELISA was positive in 4.7% of Togolese school-age children who were almost certainly unexposed to LF. This apparent lack of specificity in the Togo context makes it difficult to establish a seroprevalence threshold that could serve to signal LF resurgence in the country, precluding the use of this test for post-validation surveillance in Togo. There remains a need to develop a useful and reliable test for post-elimination surveillance for LF in humans. Graphical Abstract

Background In December 2019, the COVID-19 outbreak began in China and quickly spread throughout the world and was reclassified as a pandemic in March 2020. The first case of COVID-19 was declared in Togo on March 5. Two months later, few data were available to describe the circulation of the new coronavirus in the country. Objective This survey aimed to estimate the prevalence of SARS-CoV-2 in high-risk populations in Lomé. Materials and methods From April 23, 2020, to May 8, 2020, we recruited a sample of participants from five sectors: health care, air transport, police, road transport and informal. We collected oropharyngeal swabs for direct detection through real-time reverse transcription polymerase chain reaction (rRT-PCR) and blood for antibody detection by serological tests. The overall prevalence (current and past) of infection was defined by positivity for both tests. Results A total of 955 participants with a median age of 36 (IQR 32–43) were included, and 71.6% (n = 684) were men. Approximately 22.1% (n = 212) were from the air transport sector, 20.5% (n = 196) were from the police sector, and 38.7% (n = 370) were from the health sector. Seven participants (0.7%, 95% CI: 0.3–1.6%) had a positive rRT-PCR test result at the time of recruitment, and nine (0.9%, 95% CI: 0.4–1.8%) were seropositive for IgM or IgG against SARS-CoV-2. We found an overall prevalence of 1.6% (n = 15), 95% CI: 0.9–2.6%. Conclusion The prevalence of SARS-CoV-2 infection among high-risk populations in Lomé was relatively low and could be explained by the various measures taken by the Togolese government. Therefore, we recommend targeted screening.

Background In Togo, the prevalence of Hepatitis B Virus Surface Antigen (HBsAg) among young people aged 15–24 years was estimated at 16.4% in 2010; however, risk factors for HBsAg carriage are poorly documented. We sought to identify risk factors for HBsAg carriage and the serological profile of HBsAg carriers in Lomé (capital city of Togo). Method We conducted a case control study from October 2016 to March 2017 in Lomé. Cases and controls were randomly selected from a database of Institut National d’Hygiène (INH) of Lomé during a free screening campaign for hepatitis B. We calculated means, frequencies, proportions, odds ratios (OR), and 95% confidence interval (CI) and performed logistic regression. Results We included 83 confirmed cases and 249 controls. The median age was 31 years among cases and 30 years among the controls. The sex ratios (M/F) were 11/6 among cases and 4/3 for the controls. The independent risk factors for HBsAg carriage were the awareness of hepatitis B serological status (OR = 3.56, 95% CI [1.80–7.04]) and Kabyè-tem ethnic group (OR = 3.56, 95% CI [1.98–6.39]). Among HBsAg carriers, 13.3% were at the viral replication stage (all of whom were between 30 and 45 years of age) and 1.2% were at the acute stage of the disease. The prevalence of co-infection with hepatitis B and C was 4.80%. All co-infections were in women aged 24–28 years. Conclusion The Kabyè-tem ethnic group is at risk of HBsAg carriage in Lomé. Of note, most HBsAg carriers in this ethnic group are aware of their HBsAg serological status. Furthermore, the prevalence of Hepatitis among adults of reproductive age is high and is cause for concern. We therefore recommend screening and vaccination campaigns at subsidized prices among people aged 30 years and older.

Background During the last ten years, a resurgence of syphilis has occurred in many countries worldwide, including Togo. Previous studies have shown a wide range of syphilis infection among the female sex workers (FSWs), from 1.5 to 42.1%. In Togo, Key populations, including FSWs, are rarely involved in the sentinel surveillance programs to determine the prevalence of HIV and syphilis. The aim of this study was to determine the prevalence of syphilis among female sex workers (FSWs) and their clients in Togo. Methods We conducted a cross-sectional study in December 2011 targeting FSWs and their clients in Togo. Among participant who consented, we collected blood samples for syphilis and HIV testing. Results In total, 1,836 participants (1,106 FSWs and 730 clients) were included in the survey. Their mean age was 28.6 ± 9 years. The prevalence of syphilis was 2.2% (2.2% among FSWs compare to 2.3% among their clients, p = 0.82). This prevalence was higher among FSWs over 30 years old compare to those less than 30 years old (Odd Ratio (OR) =5.03; 95% CI [1.95-13.49]). Single FSWs were three times less likely to have syphilis than those living in couple or married (OR = 3.11; CI 95% [1.16-8.83]). Brothel based or declared FSWs were 4 times more likely to be infected by syphilis than secret ones (OR = 3.89; CI 95% [1.60-9.54]). Out of the 1,836 participants of the survey, 165 (8.9%) were HIV positive. Having syphilis was associated with HIV infection (OR = 3.41; IC 95% [1.53-7.41]). Conclusion This study showed that: i) the prevalence of syphilis among FSWs and their clients was high; ii) syphilis was significantly associated with HIV infection. It is necessary to increase awareness campaigns and emphasize on condom use among this key population group.

Background Togo has conducted annual, integrated, community-based mass drug administration (MDA) for soil-transmitted helminths (STH) and schistosomiasis since 2010. Treatment frequency and target populations are determined by disease prevalence, as measured by baseline surveys in 2007 and 2009, and WHO guidelines. Reported programmatic treatment coverage has averaged over 94%. Togo conducted a cross-sectional survey in 2015 to assess the impact of four to five years of MDA on these diseases. Methodology/Principal findings In every sub-district in the country outside the capital, the same schools were visited as at baseline and a sample of fifteen children age 6 to 9 years old was drawn. Each child submitted urine and a stool sample. Urine samples were tested by dipstick for the presence of blood as a proxy measure of Schistosoma haematobium infection. Stool samples were analyzed by the Kato-Katz method for STH and Schistosoma mansoni. At baseline, 17,100 children were enrolled at 1,129 schools in 562 sub-districts; in 2015, 16,890 children were enrolled at the same schools. The overall prevalence of both STH and schistosomiasis declined significantly, from 31.5% to 11.6% for STH and from 23.5% to 5.0% for schistosomiasis (p, Author summary Mass drug administration (MDA) is a key component of programs aimed at controlling soil-transmitted helminths (STH) and schistosomiasis, diseases that disproportionately impact individuals in developing countries and adversely affect physical and cognitive development. The World Health Organization recommends evaluating the impact of mass drug administration on the prevalence of these infections after five years of MDA. We present here a study of the impact of four to five years of MDA on the prevalence and intensity of STH and schistosomiasis infections in school children in Togo. The prevalence and intensity of these infections in 2015 were significantly reduced compared to a baseline survey conducted in 2009. Local baseline prevalence in 2009 was the strongest predictor of infection in 2015. These infections are more prevalent in boys than in girls, and in older versus younger children. We found that in areas with high baseline prevalence of hookworm the risk of rebound of infection is high among children who do not receive bi-annual treatment. This information is important for programs weighing the decision to stop MDA in areas where prevalence has been reduced through treatment. This and other findings from this study may help refine treatment recommendations for these diseases.

Background The only available vaccine that could be potentially beneficial against mycobacterial diseases contains live attenuated bovine tuberculosis bacillus (Mycobacterium bovis) also called Bacillus Calmette-Guérin (BCG). Even though the BCG vaccine is still widely used, results on its effectiveness in preventing mycobacterial diseases are partially contradictory, especially regarding Buruli Ulcer Disease (BUD). The aim of this case-control study is to evaluate the possible protective effect of BCG vaccination on BUD. Methodology The present study was performed in three different countries and sites where BUD is endemic: in the Democratic Republic of the Congo, Ghana, and Togo from 2010 through 2013. The large study population was comprised of 401 cases with laboratory confirmed BUD and 826 controls, mostly family members or neighbors. Principal Findings After stratification by the three countries, two sexes and four age groups, no significant correlation was found between the presence of BCG scar and BUD status of individuals. Multivariate analysis has shown that the independent variables country (p = 0.31), sex (p = 0.24), age (p = 0.96), and presence of a BCG scar (p = 0.07) did not significantly influence the development of BUD category I or category II/III. Furthermore, the status of BCG vaccination was also not significantly related to duration of BUD or time to healing of lesions. Conclusions In our study, we did not observe significant evidence of a protective effect of routine BCG vaccination on the risk of developing either BUD or severe forms of BUD. Since accurate data on BCG strains used in these three countries were not available, no final conclusion can be drawn on the effectiveness of BCG strain in protecting against BUD. As has been suggested for tuberculosis and leprosy, well-designed prospective studies on different existing BCG vaccine strains are needed also for BUD., Author Summary After tuberculosis and leprosy, Buruli Ulcer Disease (BUD) is the third most common human mycobacterial disease. The only available vaccine that could be potentially beneficial against these diseases is BCG. Even though BCG vaccine is widely used, the results on its effectiveness are partially contradictory, probably since different BCG strains are used. The aim of this study was to evaluate the possible protective effect of BCG vaccines on BUD. The present study was performed in three different countries and sites where BUD is endemic: in the Democratic Republic of the Congo, Ghana, and Togo from 2010 through 2013. The large study population was comprised of 401 cases with laboratory confirmed BUD and 826 controls, mostly family members or neighbors. Considering the three countries, sex, and age, the analysis confirmed that the BCG vaccination did not significantly decrease the risk for developing BUD or for developing severe forms of BUD. Furthermore, the status of BCG vaccination was also not significantly related to duration of BUD or to time to healing of lesions. In our study, we could not find any evidence of a protective effect of routine BCG vaccination on BUD.

Background Infection with Penicillium marneffei is a common opportunistic infection in Southeast Asia where it is endemic. We report a case of Penicillium marneffei infection with fatal outcome in a Togolese woman infected with Human Immunodeficiency Virus (HIV). Case presentation A 45-years-old patient, infected with Human Immunodeficiency Virus had consulted for ongoing febrile pneumonia since two weeks. Clinical examination revealed fever of 38.5°C, dyspnea, pulmonary syndrome condensation and papulo-nodular of “molluscum contagiosum” like lesions located on the face, arms, neck and trunk. Sputum smear was negative for tuberculosis. The chest radiograph showed reticulonodular opacities in the right upper and middle lobes and two caves in the right hilar region. The CD4 count was 6 cells/mm3 after a year of antiretroviral treatment (Zidovudine-Lamivudine-Efavirenz). She was treated as smear negative pulmonary tuberculosis after a lack of gentamicin and amoxicillin plus clavulanic acid response. Culture of skin samples and sputum had revealed the presence of P. marneffei. A treatment with ketoconazole 600 mg per day was initiated. After two weeks of treatment, there was a decrease in the size and number of papules and nodules, without any new lesions. We noted disappearance of cough and fever. The chest X-ray showed a decrease of pulmonary lesions. There was no reactivation of P. marneffei infection but the patient died from AIDS after two years of follow up. Conclusion We report a case of P. marneffei infection in a HIV-infected patient in a non-endemic country. Clinicians should think of P. marneffei infection in all HIV-infected patients with “molluscum contagiosum” like lesions.

Background In a previous study PCR analysis of clinical samples from suspected cases of Buruli ulcer disease (BUD) from Togo and external quality assurance (EQA) for local microscopy were conducted at an external reference laboratory in Germany. The relatively poor performance of local microscopy as well as effort and time associated with shipment of PCR samples necessitated the implementation of stringent EQA measures and availability of local laboratory capacity. This study describes the approach to implementation of a national BUD reference laboratory in Togo. Methodology Large scale outreach activities accompanied by regular training programs for health care professionals were conducted in the regions “Maritime” and “Central,” standard operating procedures defined all processes in participating laboratories (regional, national and external reference laboratories) as well as the interaction between laboratories and partners in the field. Microscopy was conducted at regional level and slides were subjected to EQA at national and external reference laboratories. For PCR analysis, sample pairs were collected and subjected to a dry-reagent-based IS2404-PCR (DRB-PCR) at national level and standard IS2404 PCR followed by IS2404 qPCR analysis of negative samples at the external reference laboratory. Principal Findings The inter-laboratory concordance rates for microscopy ranged from 89% to 94%; overall, microscopy confirmed 50% of all suspected BUD cases. The inter-laboratory concordance rate for PCR was 96% with an overall PCR case confirmation rate of 78%. Compared to a previous study, the rate of BUD patients with non-ulcerative lesions increased from 37% to 50%, the mean duration of disease before clinical diagnosis decreased significantly from 182.6 to 82.1 days among patients with ulcerative lesions, and the percentage of category III lesions decreased from 30.3% to 19.2%. Conclusions High inter-laboratory concordance rates as well as case confirmation rates of 50% (microscopy), 71% (PCR at national level), and 78% (including qPCR confirmation at external reference laboratory) suggest high standards of BUD diagnostics. The increase of non-ulcerative lesions, as well as the decrease in diagnostic delay and category III lesions, prove the effect of comprehensive EQA and training measures involving also procedures outside the laboratory., Author Summary Buruli ulcer disease (BUD), the third most common mycobacterial disease worldwide, is treated with standardized antimycobacterial therapy. According to WHO recommendations at least 50% of cases should be laboratory confirmed by polymerase chain reaction (PCR). In a previous study PCR analysis of clinical samples from suspected BUD cases from Togo and external quality assurance (EQA) for local microscopy were conducted at an external reference laboratory in Germany. The relatively poor performance of local microscopy as well as time and effort associated with shipment of clinical samples abroad necessitated the availability of a local BUD reference laboratory and the implementation of stringent EQA measures. All processes in the laboratories as well as in the field were defined by standard operating procedures, microscopy conducted at regional facilities was subjected to EQA at national and external reference level, and PCR samples were analyzed in parallel at national and external reference laboratories. Inter-laboratory concordance rates of >90% and case confirmation rates of 50% (microscopy) and >70% (PCR) respectively suggest high standards of BUD diagnostics. Furthermore, an increase of non-ulcerative lesions and a decrease in diagnostic delay and category III lesions reflect the impact of comprehensive EQA measures also involving procedures outside the laboratory on the quality of BUD control.