SARS-CoV2 mutations and impact on mortality: observational study in a sub-saharan Africa hospital.

BACKGROUND: One year after the coronavirus disease 2019 (COVID-19) pandemic, the focus of attention has shifted to the emergence and spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs). The aim of the study was to assess the frequency of VOCs in patients followed for COVID-19 at Kinshasa university hospital (KUH) during the 3rd and 4th waves of the pandemic in Kinshasa. Hospital mortality was compared to that of the first two waves. METHOD: The present study included all patients in whom the diagnosis of SARS-CoV-2 infection was confirmed by the polymerase chain reaction (PCR). The laboratory team sequenced a subset of all SARS-CoV-2 positive samples with high viral loads define as Ct < 25 to ensure the chances to generate complete genome sequence. RNA extraction was performed using the Viral RNA Mini Kit (Qiagen). Depending on the platform, we used the iVar bioinformatics or artic environments to generate consensus genomes from the raw sequencing output in FASTQ format. RESULTS: During the study period, the original strain of the virus was no longer circulating. The Delta VOC was predominant from June (92%) until November 2021 (3rd wave). The Omicron VOC, which appeared in December 2021, became largely predominant one month later (96%) corresponding the 4th wave. In-hospital mortality associated with COVID-19 fell during the 2nd wave (7% vs. 21% 1st wave), had risen during the 3rd (16%) wave before falling again during the 4th wave (7%) (p < 0.001). CONCLUSION: The Delta (during the 3rd wave) and Omicron VOCs (during the 4th wave) were very predominant among patients followed for Covid-19 in our hospital. Contrary to data in the general population, hospital mortality associated with severe and critical forms of COVID-19 had increased during the 3rd wave of the pandemic in Kinshasa.

Genomic Microevolution of Vibrio cholerae O1, Lake Tanganyika Basin, Africa.

Africa's Lake Tanganyika basin is a cholera hotspot. During 2001-2020, Vibrio cholerae O1 isolates obtained from the Democratic Republic of the Congo side of the lake belonged to 2 of the 5 clades of the AFR10 sublineage. One clade became predominant after acquiring a parC mutation that decreased susceptibility to ciprofloxacin.

The Case for Fungal Keratitis to Be Accepted as a Neglected Tropical Disease.

Amongst the treatable cause of blindness among young people, fungal keratitis ranks high. There are an estimated 1,051,787 to 1,480,916 eyes affected annually, with 8-11% of patients having to have the eye removed. Diagnosis requires a corneal scraping, direct microscopy and fungal culture with a large number of airborne fungi implicated. Treatment involves the intensive application of antifungal eye drops, preferably natamycin, often combined with surgery. In low-resource settings, inappropriate corticosteroid eye drops, ineffective antibacterial therapy, diagnostic delay or no diagnosis all contribute to poor ocular outcomes with blindness (unilateral or bilateral) common. Modern detailed guidelines on fungal keratitis diagnosis and management are lacking. Here, we argue that fungal keratitis should be included as a neglected tropical disease, which would facilitate greater awareness of the condition, improved diagnostic capability, and access to affordable antifungal eye medicine.

SARS-CoV2 infection in symptomatic patients: interest of serological tests and predictors of mortality: experience of DR Congo.

BACKGROUND: In symptomatic patients, the diagnostic approach of COVID-19 should be holistic. We aimed to evaluate the concordance between RT-PCR and serological tests (IgM/IgG), and identify the factors that best predict mortality (clinical stages or viral load). METHODS: The study included 242 patients referred to the University hospital of Kinshasa for suspected COVID-19, dyspnea or ARDS between June 1st, 2020 and August 02, 2020. Both antibody-SARS-CoV2 IgM/IgG and RT-PCR method were performed on the day of admission to hospital. The clinical stages were established according to the COVID-19 WHO classification. The viral load was expressed by the CtN2 (cycle threshold value of the nucleoproteins) and the CtE (envelope) genes of SARS- CoV-2 detected using GeneXpert. Kappa test and Cox regression were used as appropriate. RESULTS: The GeneXpert was positive in 74 patients (30.6%). Seventy two patients (29.8%) had positive IgM and 34 patients (14.0%) had positive IgG. The combination of RT-PCR and serological tests made it possible to treat 104 patients as having COVID-19, which represented an increase in cases of around 41% compared to the result based on GeneXpert alone. The comparison between the two tests has shown that 57 patients (23.5%) had discordant results. The Kappa coefficient was 0.451 (p < 0.001). We recorded 23 deaths (22.1%) among the COVID-19 patients vs 8 deaths (5.8%) among other patients. The severe-critical clinical stage increased the risk of mortality vs. mild-moderate stage (aHR: 26.8, p < 0.001). The values of CtE and CtN2 did not influence mortality significantly. CONCLUSION: In symptomatic patients, serological tests are a support which makes it possible to refer patients to the dedicated COVID-19 units and treat a greater number of COVID-19 patients. WHO Clinical classification seems to predict mortality better than SARS-Cov2 viral load.

Serious fungal diseases in Democratic Republic of Congo - Incidence and prevalence estimates.

A literature review was conducted to assess the burden of serious fungal infections in the Democratic Republic of the Congo (DRC) (population 95,326,000). English and French publications were listed and analysed using PubMed/Medline, Google Scholar and the African Journals database. Publication dates spanning 1943-2020 were included in the scope of the review. From the analysis of published articles, we estimate a total of about 5,177,000 people (5.4%) suffer from serious fungal infections in the DRC annually. The incidence of cryptococcal meningitis, Pneumocystis jirovecii pneumonia in adults and invasive aspergillosis in AIDS patients was estimated at 6168, 2800 and 380 cases per year. Oral and oesophageal candidiasis represent 50,470 and 28,800 HIV-infected patients respectively. Chronic pulmonary aspergillosis post-tuberculosis incidence and prevalence was estimated to be 54,700. Fungal asthma (allergic bronchopulmonary aspergillosis and severe asthma with fungal sensitization) probably has a prevalence of 88,800 and 117,200. The estimated prevalence of recurrent vulvovaginal candidiasis and tinea capitis is 1,202,640 and 3,551,900 respectively.Further work is required to provide additional studies on opportunistic infections for improving diagnosis and the implementation of a national surveillance programme of fungal disease in the DRC.

Seventh Pandemic Vibrio cholerae O1 Sublineages, Central African Republic.

Four cholera outbreaks were reported in the Central African Republic during 1997-2016. We show that the outbreak isolates were Vibrio cholerae O1 serotype Inaba from 3 seventh pandemic El Tor sublineages originating from West Africa (sublineages T7 and T9) or the African Great Lakes Region (T10).

Tests diagnostiques de l'infection à Coronavirus (COVID-19) : des atouts et des limites

Le monde entier fait face à une crise sanitaire sans précédent due à la pandémie de maladie à virus SARS-COV-2 alias COVID-19. Malgré les connaissances très incomplètes sur la COVID-19, on a constaté une contagiosité interhumaine élevée au début de la pandémie actuelle, et on estime que chaque nouveau cas de COVID-19 infecte en moyenne deux à trois personnes. En conséquence, la stratégie de lutte contre la pandémie à COVID-19 qui ébranle nos sociétés passe nécessairement par une intensification des tests de détection de l'infection. Ces tests diagnostiques de la COVID-19 sont un outil essentiel pour suivre la propagation de la pandémie. Ainsi, l'objectif de la présente revue de la littérature est d'aborder le diagnostic de l'infection à Coronavirus (COVID-19) en s'attardant sur les tests de diagnostic, leurs atouts et leurs limites. Il y a deux catégories de test : ceux qui recherchent la présence directe du virus ou de ses fragments, et ceux qui recherchent les anticorps résultant de l'infection par le virus du COVID-19. Le test real time ­Reverse Transcriptase ­Polymerase chain reaction (rt-RT-PCR) reste le gold standard pour le diagnostic de la COVID-19. Sa sensibilité sur les écouvillons nasopharyngés semble élevée, mais des faux négatifs peuvent se produire, avec une fréquence incertaine (environ 30% des cas). Les tests sérologiques détectent les anticorps spécifiques du SARSCoV-2. Ils permettent l'identification des individus qui ont été infectés par le virus, se sont rétablis, et ont développé, en théorie, une réponse immunitaire efficace contre le virus. Ils constituent des tests d'orientation diagnostique de la COVID19. A ce jour, aucun de ces tests n'est fiable à 100 %, mais, utilisés par un personnel médical qualifié et en combinaison, ils permettent l'identification de la majorité des individus infectés et immunisés