Unrecognized introduction of SARS-CoV-2 variants of concern to Central Africa: Import and local transmission of B.1.1.7 in Gabon in the very early stage of the variant spread to the African continent.

The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern with higher infectivity has already resulted in the enormous increase in infection cases worldwide. We report an unrecognized introduction of the variant B.1.1.7 in Gabon in December 2020, which was the initial phase of the variant introduction to Africa. The B.1.1.7 variant was also detected in a hospitalized patient in January 2021, indicating a rapid spread of the variant in Gabon since its first detection. Phylogenetic analysis revealed that the detected B.1.1.7 variants originated from the distinct regions, strongly suggesting that the B.1.1.7 variant had been repeatedly introduced to Gabon since December 2020. These results provide insights on the unrecognized risks of infections with variants of concern, and show the necessity to conduct continuous genomic monitoring for immediate alert and control of novel SARS-CoV-2 variant infections.

Global variation in bacterial strains that cause tuberculosis disease: a systematic review and meta-analysis.

BACKGROUND: The host, microbial, and environmental factors that contribute to variation in tuberculosis (TB) disease are incompletely understood. Accumulating evidence suggests that one driver of geographic variation in TB disease is the local ecology of mycobacterial genotypes or strains, and there is a need for a comprehensive and systematic synthesis of these data. The objectives of this study were to (1) map the global distribution of genotypes that cause TB disease and (2) examine whether any epidemiologically relevant clinical characteristics were associated with those genotypes. METHODS: We performed a systematic review of PubMed and Scopus to create a comprehensive dataset of human TB molecular epidemiology studies that used representative sampling techniques. The methods were developed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). We extracted and synthesized data from studies that reported prevalence of bacterial genotypes and from studies that reported clinical characteristics associated with those genotypes. RESULTS: The results of this study are twofold. First, we identified 206 studies for inclusion in the study, representing over 200,000 bacterial isolates collected over 27 years in 85 countries. We mapped the genotypes and found that, consistent with previously published maps, Euro-American lineage 4 and East Asian lineage 2 strains are widespread, and West African lineages 5 and 6 strains are geographically restricted. Second, 30 studies also reported transmission chains and 4 reported treatment failure associated with genotypes. We performed a meta-analysis and found substantial heterogeneity across studies. However, based on the data available, we found that lineage 2 strains may be associated with increased risk of transmission chains, while lineages 5 and 6 strains may be associated with reduced risk, compared with lineage 4 strains. CONCLUSIONS: This study provides the most comprehensive systematic analysis of the evidence for diversity in bacterial strains that cause TB disease. The results show both geographic and epidemiological differences between strains, which could inform our understanding of the global burden of TB. Our findings also highlight the challenges of collecting the clinical data required to inform TB diagnosis and treatment. We urge future national TB programs and research efforts to prioritize and reinforce clinical data collection in study designs and results dissemination.

Use of GeneXpert Remnants for Drug Resistance Profiling and Molecular Epidemiology of Tuberculosis in Libreville, Gabon.

Multidrug-resistant (MDR) and extensively drug resistant (XDR) strains of Mycobacterium tuberculosis pose major problems for global health. The GeneXpert MTB/RIF (Xpert) assay rapidly detects resistance to rifampin (RIFr), but for detection of the additional resistance that defines MDR-TB (MDR tuberculosis) and XDR-TB, and for molecular epidemiology, specimen cultures and a biosafe infrastructure are generally required. We sought to determine whether the remnants of sputa prepared for the Xpert assay could be used directly to find mutations associated with drug resistance and to study molecular epidemiology, thus providing precise characterization of MDR-TB cases in countries lacking biosafety level 3 (BSL3) facilities for M. tuberculosis cultures. After sputa were processed and run on the Xpert instrument, the leftovers of the samples prepared for the Xpert assay were used for PCR amplification and sequencing or for a line probe assay to detect mutations associated with resistance to additional drugs, as well as for molecular epidemiology with spoligotyping and selective mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing. Of 130 sputum samples from Gabon tested with the Xpert assay, 124 yielded interpretable results; 21 (17%) of these were determined to be RIFr Amplification and sequencing or a line probe assay of the Xpert remnants confirmed 18/21 samples as MDR, corresponding to 12/116 (9.5%) new and 6/8 (75%) previously treated TB patients. Spoligotyping and MIRU typing with hypervariable loci identified an MDR Beijing strain present in five samples. We conclude that the remnants of samples processed for the Xpert assay can be used in PCRs to find mutations associated with the resistance to the additional drugs that defines MDR and XDR-TB and to study molecular epidemiology without the need for culturing or a biosafe infrastructure.

Pediatric tuberculosis in a high burden setting: Socio-spatial distribution, blood elements features, and outcomes.

Background: The childhood tuberculosis (TB) epidemic has been long neglected. Data on pediatric tuberculosis is needed to develop effective strategies against TB. Methods: We retrospectively reviewed 200 medical records from children aged 0-15 years who suffered from tuberculosis between 2011 and 2021 in Libreville, Gabon. We collected and analyzed socio-demographic data and clinical data. Results: 141 children files were selected (43 % girls and 57 % boys). The mean age of the patients was 9.2 years (CI: 8.5-10). Sixty per cent (60 %) of cases were from precarious housing areas, 35.34 % from mixed housing areas, and 4.51 % from residential. The cure rate was 75.24 %, 9.52 % relapsed, and 15.24 % died. Deaths were significantly higher in older children (Dunn's post-test p < 0.01). Children who recovered had higher haemoglobin and platelet counts than those who died (Dunn's test: haemoglobin p < 0.0001; thrombocytes p < 0.05). The haemoglobin threshold value of 5.5 g/dL identified children death with up to 80 % sensitivity and 86 % specificity. Thrombocytes count identified children's death with a sensitivity of 80 % and a specificity of 51 %. Conclusion: Precariousness is associated with childhood tuberculosis. The directly observed therapy (DOTS) in older children should be reinforced to limit tuberculosis-associated deaths. Haemoglobin concentration and platelet are vital prognosis markers in pediatric tuberculosis.

Biochemical Alterations Associated With the Severity of COVID-19 in Sub-Saharan Black African Individuals.

BACKGROUND: Biochemical markers are essential in the monitoring and the clinical care of patients as they inform clinicians. Here, we characterized biochemical alterations in sub-Saharan Black African individuals with COVID-19. METHODS: The study includes COVID-19 patients cared for at the Akanda Army Hospital in Libreville (Gabon). A total of 2237 patient records were extracted and reviewed. Patients were classified based on hospital admission (intensive care unit [ICU], internal medicine ward, and outpatient). RESULTS: One thousand six hundred seventy-one were included in the study. ICU patients were significantly older than non-ICU hospitalized patients (P < 0.001) and outpatients (P < 0.0001). Hyperglycemic patients had 6.4 odds of being in ICU (P < 0.0001). Patients with abnormally high urea had 54.7 odds of being in ICU (P < 0.0001). Patients with abnormally high aspartate aminotransferase (AST) (>33 IU/L) had 3.5 odds of being in ICU (P < 0.0001). Hyperlactatemia (>246 IU/L) odds in ICU patients were 14 (P < 0.0001). The odds of abnormally high alkaline phosphatase (ALP) (>147 IU/L) in ICU patients were 4.6 (P < 0.0001). Odds for hypochloremia (<98 mmol/L) were 1.6 in ICU (P < 0.05). Dysnatremia patients (<135 or >145 mmol/L) had 9.5 odds of being found in ICU patients (P < 0.0001). The odds of potassium imbalance (<3.6 or >5 mmol/L) in ICU patients were 12.2 (P < 0.0001). CONCLUSIONS: COVID-19-associated biochemical alterations observed in the Black African population are similar to those observed in other populations, and the association between COVID-19 severity, hyperglycemia, and multi-organ affection is confirmed.

Time to SARS-CoV-2 clearance in African, Caucasian, and Asian ethnic groups.

BACKGROUND: COVID-19 may become a seasonal disease. SARS-CoV-2 active circulation coupled with vaccination efforts has undoubtedly modified the virus dynamic. It is therefore important investigate SARS-CoV-2 dynamic in different groups of population following the course of spatiotemporal variance and immunization. METHODS: To investigate SARS-CoV-2 clearance in different ethnic groups and the impact of immunization, we recruited 777 SARS-CoV-2-positive patients (570 Africans, 156 Caucasians, and 51 Asians). Participants were followed and regularly tested for 2 months until they had two negative tests. RESULTS: The vaccination rate was 64.6%. African individuals were less symptomatic (2%), Caucasians (41%) and Asians (36.6%). On average, viral clearance occurred after 10.5 days. Viral load at diagnosis was inversely correlated with viral clearance (p < 0.0001). The time of SARS-CoV-2 clearance was higher in Africans and Caucasians than in Asians (Dunn's test p < 0.0001 and p < 0.05, respectively). On average, viral clearance occurred within 9.5 days during the second semester (higher rate of vaccination and SARS-CoV-2 exposition), whereas it took 13.6 days during the first semester (lower rate of vaccination and SARS-CoV-2 exposition) (Mann-Whitney t-test p < 0.0001). CONCLUSION: In conclusion, ethnicity and spatiotemporal changes including SARS-CoV-2 exposition and immunization affect SARS-CoV-2 clearance.

HIV-exposed uninfected infants' immune defects: From pathogen sensing, oxidative burst to antigens responses.

The progress in preventing mother-to-child transmission of HIV has led to a significant reduction in mother-to-child HIV transmission, increasing the population of HIV-exposed uninfected (HEU) infants. Studies have shown that HEU infants are more vulnerable to diseases than infants born from HIV-free mothers. Today, there is more and more evidence that helps us understand how exposure to HIV and/or its therapy affects the ability of the immune system of HEU infants to fight infections. This paper mapped out reported critical immune defects in HEU infants, from pathogen sensing and recognition, oxidative burst to antigens-specific responses. Models of neutrophils and monocyte malfunctions in these infants are proposed.

Changes of C-reactive protein and Procalcitonin after four weeks of treatment in patients with pulmonary TB.

Objective: Tuberculosis (TB) remains a public health concern worldwide, affecting millions of people every year. Detailed characterization of disease pathophysiology is key to proper diagnosis, disease progression, or treatment follow-up and evaluation. The present study investigated C-reactive protein and Procalcitonin (PCT) as candidate markers of early treatment response and disease activity. Methods: From September to December 2019, 21 HIV-negative consecutive TB patients were recruited, within the setting of the Gabonese TB specialized hospital and the National Laboratory of Public Health, in a prospective study. CRP and PCT levels were measured by chemiluminescence at diagnosis and 4 weeks following the initiation of anti-TB treatment. Results: The mean concentration of CRP in TB patients was 114.7 mg/L (95 % CI: [83.8-145.6]) at diagnosis and 20.2 mg/L (95 % CI: [14.1-26.4]) 4 weeks following anti-TB treatment. The drop in CRP concentrations between diagnosis, and week 4 following anti-TB treatment showed was significant (p < 0.0001). The average concentration of PCT at the time of diagnosis was 0.3 ng/mL (95 % CI: [0.19-0.41]). PCT Concentration dropped below 0.05 ng/mL 4 weeks following the start of anti-TB treatment (p < 0.01). Conclusion: CRP and PCT are potential TB biomarkers, each, carrying important keys. If the drop in both proteins may indicate a significant reduction of the Mtb burden, the maintenance of CRP above the inflammation threshold could indicate the presence of residual bacilli. However, the clinical translation of the present finding will require more investigation.

Prostate malignant tumor and benign prostatic hyperplasia microenvironments in black African men: Limited infiltration of CD8+ T lymphocytes, NK-cells, and high frequency of CD73+ stromal cells.

BACKGROUND: Anti-cancerous immunology has yet to be investigated in the African black population, despite being the dawn of precision medicine. AIM: Here we investigated the tumor microenvironment of prostate cancer and benign prostatic hyperplasia (BPH) in black Africans. METHODS: Through immunohistochemistry analysis of prostate cancer and BPH patients' biopsies, we investigated the expression and distribution of CD73, CCD8 T-lymphocytes, and natural killer cells. In addition, we looked at tumor-infiltrating features CD8 T-lymphocytes and natural killer cells. RESULTS: We show for the first time in black Africans a high expression of CD73 in epithelial-stromal cells and virtually no infiltration of CD8 T lymphocytes and natural killer cells in the tumoral area. In addition, CD73 was seven (7) times more likely to be expressed in prostate cancer stromal tissues than in benign prostatic hyperplasia tissues (odds ratio = 7.2; χ2 = 21; p < .0001). In addition, PSA concentration was significantly higher in prostate cancer patients than in BPH patients (p < .001). Also, the PSA-based ROC. analysis showed an area under the curve of 0.87 (p < .0001). CONCLUSION: CD73 expression is more likely expressed in prostate cancer stromal tissues than in benign prostatic hyperplasia tissues. The features of prostate cancer in Black Africans suggest CD73 expression as a possible target for immunotherapy in this population.

Allergen sensitization and polysensitization pattern of adults and children in an urban Sub-Saharan African setting (Libreville, Gabon).

Background: It is believed that allergic diseases are increasing in Africa. However, the health sector in Africa has yet to catch up with this paradigm shift. We looked at the number of patients referred to us for allergy testing and investigated allergen sensitization. Methods: A retrospective analysis was done on 97 serum allergen-specific IgE results collected from patients suspected of having allergies in Libreville from 2018 to 2021. Specific IgE responses to 180 allergens were investigated. The general sensitization patterns were analyzed. Also analyzed were sensitization patterns for adults and children. The difference in the IgE-binding allergen positivity rate between groups was calculated by using the chi-square (χ2) test. Results: The allergens most commonly causing sensitization were from mites (65%), barley (48%), peach (48%), dog and/or cat dander (44%), house dust (44%), peanut (39%), tomato (39%), cockroach (37%), crab (36%), garlic and/or onion (34%), rye (34%), egg white (32%), shrimp (32%), kiwi (32%), soya bean (32%), citrus mix (29%), cheese (27%), milk (27%), walnut (27%), ox-eye daisy (24%) and orchard grass (24%). Moreover, 60% of patients (36 of 60) were polysensitized to inhalant allergens, 53% (31 of 58) were polysensitized to food allergens, and 29% (14 of 48) were polysensitized to inhalant and food allergens; 65% of patients (53 of 81) were sensitized to allergens originating from mites, fungi (including Candida albicans, Alternaria alternata, Aspergillus fumigatus, Cladosporium herbarum, and Pennicillium notatum), or bacteria (staphylococcal enterotoxin B). Conclusions: The sensitization pattern of allergens in our setting is rich and varied, with a high prevalence of polysensitization.

Allelic frequencies of 22 short tandem repeats loci and tri-allelic patterns of Penta D and TPOX identified in Gabonese population.

Short tandem repeats (STRs) are repeating DNA sequences used in forensic human identity testing and the diagnosis of aneuploidies. Many STRs like Penta D and TPOX are used routinely for paternity tests, but these tests are not widely used in sub-Saharan Africa. In this study we recruited individuals from Gabonese families seeking a paternity test. After DNA extraction from buccal swabs, we genotyped samples using a panel of 22 STRs. A total of 115 unrelated subjects from 39 families were included. Allele frequencies of the 22 STR loci were determined in unrelated Gabonese subjects. The most polymorphic loci were D21S11 (16 alleles) and FGA (17 alleles), while D3S1358 and TH01 loci were less polymorphic, with five alleles each. Deviation from Hardy-Weinberg equilibrium was observed for TPOX, D3S1358, CSFPO and D7S820 loci. We reported tri-allelic patterns that indicate aneuploidies at a combined frequency of 4% (4/115) with 3% for Penta D (1/35) and 3% for TPOX (3/102). Furthermore, we identified a new tri-allelic genotype 5-8-16 for the Penta D locus located on chromosome 21 in a healthy subject. In addition, we observed three tri-allelic variants of TPOX, located on chromosome 2, in healthy subjects, namely 8-10-11, 8-9-10, and 8-8-10. Our study revealed unsuspected polymorphic variations in Penta D and TPOX for the first time in Gabon, raising several questions about chromosomal disorders. Further population genetics studies are needed in Gabon to better characterize these variations, both qualitatively and quantitative.

Mapping Allergic Diseases in Sub-Saharan Africa.

The consensus is that allergic diseases are increasing in Africa. However, this paradigm shift has not yet been translated into practice. Focused on infectious diseases (malaria, tuberculosis, HIV), health policies in Sub-Saharan Africa have often neglected the diagnosis and management of allergies. Allergic disease mapping is crucial to grasp the full extent of Africa's allergic diseases' impact. This mapping will require diverting resources to diagnose and study allergies, even more at the dawn of precision medicine.

Emergence of B.1.1.318 SARS-CoV-2 viral lineage and high incidence of alpha B.1.1.7 variant of concern in the Republic of Gabon.

OBJECTIVE: Variants of concern (VOCs) associated with relatively high transmissibility appear to be rapidly spreading in Gabon. Therefore, it is imperative to understand the distribution of several VOCs in the population, which could have implications for transmissibility and vaccine efficacy. METHODS: Between February and May 2021, SARS-CoV-2 genomes were sequenced using the Oxford nanopore MinION method and the respective genome diversity was elucidated. Phylogenetic analysis was performed and genomes were classified using pangolin lineages. RESULTS: The results highlighted an increase (46%) in the alpha VOC (B.1.1.7) in the Gabonese population over the study period. In addition, an increase (31%) in the B.1.1.318 lineage, which is associated with high transmission and impaired vaccine efficacy (D614G+E484K+Y144del), was detected. CONCLUSION: With the second wave ongoing, these findings highlight the need for surveillance of the SARS-CoV-2 genome in the Republic of Gabon and should provide useful guidance to policymakers in selecting an appropriate vaccine for this population.

Profiles of microorganisms isolated from neonates' blood cultures, incubators, cradles, ventilators, washbasins, and health-workers of Libreville University Hospital Neonatal Service: focus on infection prevention and control measures.

BACKGROUND: Nosocomial infection outbreaks in neonatal services are a serious healthcare concern in both developed and developing countries, but few studies have been conducted in sub-Saharan Africa. OBJECTIVE: This study explored the etiology of septicemia in neonates and associated patterns of antimicrobial susceptibility in Gabon. METHODS: We analyzed cultures from neonates' blood and swabs from medical personnel and equipment located in the neonatology service. RESULTS: Sixty-eight microorganisms were isolated from the medical personnel and equipment; 46 microorganisms were isolated from neonates' blood culture. Klebsiella pneumoniae spp pneumoniae was the most common bacteria found in both (30.6% and 26.9%, respectively). All Klebsiella pneumoniae spp pneumonia isolates were resistant to amoxicillin with clavulanic acid, gentamycin resistance ranged from 93% to 100%, and cephalosporin resistance ranged from 33.3% to 47%. CONCLUSIONS: Awareness of the etiology, prevalence, and outcome of nosocomial infection is the first and most important step to appropriate interventions.

Circulating anti-SARS-CoV-2 nucleocapsid (N)-protein antibodies and anti-SARS-CoV-2 spike (S)-protein antibodies in an African setting: herd immunity, not there yet!

OBJECTIVE: Herd immunity is achieved when in a population, immune individuals are in a sufficiently large proportion. Neutralizing antibodies specific to SARS-CoV-2 that are produced following infection or vaccination are critical for controlling the spread of COVID-19. The objective of the present work was to investigate the rate of SARS-CoV-2 natural immunization in Gabonese. RESULTS: One thousand, four hundred and ninety two people were enrolled. The overall prevalence of anti-SARS-CoV-2 antibodies was 36.2%. Moreover, 76.4% of people who developed a humoral response to SARS-CoV-2 produced both anti-SARS-CoV-2 N-protein antibodies and anti-SARS-CoV-2 S-protein antibodies, which correspond to 27.7% of the total population. In infants (0-9 month), children (1-17 years) and adults, the prevalence of anti-SARS-CoV-2 antibodies was relatively the same, between 33 and 37% (any antibody types) and between 25 and 28.6% (neutralizing antibodies). In this African context, one-third (1/3) of the screened population was exposed to SARS-CoV-2 and three-quarter (3/4) of those exposed individuals developed neutralizing antibodies against SARS-CoV-2. This data suggest that herd immunity is not yet to be achieved in Gabon.

Mycobacterium tuberculosis-stimulated whole blood culture to detect host biosignatures for tuberculosis treatment response.

Host markers to monitor the response to tuberculosis (TB) therapy hold some promise. We evaluated the changes in concentration of Mycobacterium tuberculosis (M.tb)-induced soluble biomarkers during early treatment for predicting short- and long-term treatment outcomes. Whole blood samples from 30 cured and 12 relapsed TB patients from diagnosis, week 1, 2, and 4 of treatment were cultured in the presence of live M.tb for seven days and patients followed up for 24 weeks after the end of treatment. 57 markers were measured in unstimulated and antigen-stimulated culture supernatants using Luminex assays. Top performing multi-variable models at diagnosis using unstimulated values predicted outcome at 24 months after treatment completion with a sensitivity of 75.0% (95% CI, 42.8-94.5%) and specificity of 72.4% (95% CI, 52.8-87.3%) in leave-one-out cross validation. Month two treatment responder classification was correctly predicted with a sensitivity of 79.2% (95% CI, 57.8-92.9%) and specificity of 92.3% (95% CI, 64.0-99.8%). This study provides evidence of the early M.tb-specific treatment response in TB patients but shows that the observed unstimulated marker models are not outperformed by stimulated marker models. Performance of unstimulated predictive host marker signatures is promising and requires validation in larger studies.

Evidence and implications of pre-existing humoral cross-reactive immunity to SARS-CoV-2.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged throughout the world. Building knowledge around Covid-19 is crucial to devise facts based approaches to respond efficiently against this pandemic. AIM: We aimed to investigate pre-existing humoral cross-reactive immunity to SARS-CoV-2. METHOD: We have tested the reactivity against SARS-CoV-2 nucleocapsid (N) antigen of sera collected from healthy healthcare volunteers in 2014. We assessed immunoglobulins reactive against SARS-CoV-2 N-antigen using a well-validated serological platform; Elecsys assay. RESULTS: Sera from 32 subjects (out of 135 [23.7%]) were reactive to SARS-CoV-2 N-antigen, suggesting the presence of anti-SARS-CoV-2 N-antigen antibodies. CONCLUSION: Although the clinical relevance of the observed reactivity can only be speculated and needs to be investigated, the implication of this finding for coronavirus disease 2019 seroepidemiological survey and vaccines' clinical trials is critical.

Dynamic and features of SARS-CoV-2 infection in Gabon.

In a context where SARS-CoV-2 population-wide testing is implemented, clinical features and antibody response in those infected have never been documented in Africa. Yet, the information provided by analyzing data from population-wide testing is critical to understand the infection dynamics and devise control strategies. We described clinical features and assessed antibody response in people screened for SARS-CoV-2 infection. We analyzed data from a cohort of 3464 people that we molecularly screened for SARS-CoV-2 infection in our routine activity. We recorded people SARS-CoV-2 diagnosis, age, gender, blood types, white blood cells (WBC), symptoms, chronic disease status and time to SARS-CoV-2 RT-PCR conversion from positive to negative. We calculated the age-based distribution of SARS-CoV-2 infection, analyzed the proportion and the spectrum of COVID-19 severity. Furthermore, in a nested sub-study, we screened 83 COVID-19 patients and 319 contact-cases for anti-SARS-CoV-2 antibodies. Males and females accounted for respectively 51% and 49% of people screened. The studied population median and mean age were both 39 years. 592 out of 3464 people (17.2%) were diagnosed with SARS-CoV-2 infection with males and females representing, respectively, 53% and 47%. The median and mean ages of SARS-CoV-2 infected subjects were 37 and 38 years respectively. The lowest rate of infection (8%) was observed in the elderly (aged > 60). The rate of SARS-Cov-2 infection in both young (18-35 years old) and middle-aged adults (36-60 years old) was around 20%. The analysis of SARS-CoV-2 infection age distribution showed that middle-aged adults accounted for 54.7% of SARS-CoV-2 positive persons, followed respectively by young adults (33.7%), children (7.7%) and elderly (3.8%). 68% (N = 402) of SARS-CoV-2 infected persons were asymptomatic, 26.3% (N = 156) had influenza-like symptoms, 2.7% (N = 16) had influenza-like symptoms associated with anosmia and ageusia, 2% (N = 11) had dyspnea and 1% (N = 7) had respiratory failure, which resulted in death. Data also showed that 12% of SARS-CoV-2 infected subjects, had chronic diseases. Hypertension, diabetes, and asthma were the top concurrent chronic diseases representing respectively 58%, 25% and 12% of recorded chronic diseases. Half of SARS-CoV-2 RT-PCR positive patients were cured within 14 days following the initiation of the anti-COVID-19 treatment protocol. 78.3% of COVID-19 patients and 55% of SARS-CoV-2 RT-PCR confirmed negative contact-cases were positive for anti-SARS-CoV-2 antibodies. Patients with severe-to-critical illness have higher leukocytes, higher neutrophils and lower lymphocyte counts contrarily to asymptomatic patients and patients with mild-to-moderate illness. Neutrophilic leukopenia was more prevalent in asymptomatic patients and patients with mild-to-moderate disease for 4 weeks after diagnosis (27.1-42.1%). In Patients with severe-to-critical illness, neutrophilic leukocytosis or neutrophilia (35.6-50%) and lymphocytopenia (20-40%) were more frequent. More than 60% of participants were blood type O. It is also important to note that infection rate was slightly higher among A and B blood types compared with type O. In this African setting, young and middle-aged adults are most likely driving community transmission of COVID-19. The rate of critical disease is relatively low. The high rate of anti-SARS-CoV-2 antibodies observed in SARS-CoV-2 RT-PCR negative contact cases suggests that subclinical infection may have been overlooked in our setting.

Purifying Selection in Human Immunodeficiency Virus-1 pol Gene in Perinatally Human Immunodeficiency Virus-1-Infected Children Harboring Discordant Immunological Response and Virological Nonresponse to Long-Term Antiretroviral Therapy.

BACKGROUND: Biological monitoring of antiretroviral treatment (ART) in human immunodeficiency virus (HIV)-infected pediatric population remains challenging. The aim of the present study was to assess the long-term HIV-1 genetic diversity in pol gene in HIV-1-infected children in virological failure under antiretroviral regimen adapted according to the successive World Health Organization (WHO) guidelines for resource-constrained settings. METHODS: HIV-1 diversity in pol gene was assessed in HIV-1-infected children and adolescents born from HIV-infected mothers (median age at follow-up: 13.8 years) in virological failure (VF+) despite long-term regimen recommended by the WHO. The numbers of nonsynonymous substitutions per potential nonsynonymous site (dN) and of synonymous substitutions at potential synonymous sites (dS) in HIV-1 pol gene and the dN/dS ratios were used to estimate the selective pressure on circulating HIV-1. RESULTS: The immunological responses to ART basically corresponded to: 1) Full therapeutic failure with immunological (I-) and virological nonresponses in one-quarter (24.6%) of study children ((I-, VF+) subgroup); 2) Discordant immunovirological responses with paradoxical high CD4 T cell counts (I+) and high HIV-1 RNA load in the remaining cohort patients (75.4%) ((I+, VF+) subgroup). The mean dS was 1.8-fold higher in (I+, VF+) than (I-, VF+) subgroup (25.9 ± 18.4 vs. 14.3 ± 10.8). In the (I+, VF+) subgroup, the mean dS was 1.6-fold higher than the mean dN. Finally, the mean dN/dS ratio was 2.1-fold lower in (I+, VF+) than (I-, VF+) subgroup (0.6 ± 0.3 vs. 1.3 ± 0.7), indicating purifying selection in the immunovirological discordant (I+, VF+) subgroup and positive selection in the immunovirological failure (I-, VF+) subgroup. CONCLUSIONS: Children and adolescents in immunovirological therapeutic failure harbor positive selection of HIV-1 strains favoring diversifying in pol-encoded amino acids. In contrast, children with persistent discordant immunovirological responses show accumulation of mutations and purifying selection in pol gene sequences, indicating limited genetic evolution and likely suggesting genetic adaptation of viruses to host functional constraints.

Escalating and sustained immunovirological dissociation among antiretroviral drug-experienced perinatally human immunodeficiency virus-1-infected children and adolescents living in the Central African Republic: A STROBE-compliant study.

Sub-Saharan Africa has the vast majority (∼90%) of new pediatric acquired immunodeficiency syndrome cases worldwide. Biologically monitoring HIV-infected pediatric populations remains challenging. The differential interest of human immunodeficiency virus (HIV)-1 RNA loads and CD4 T-cell counts is debated for the treatment of pediatric acquired immunodeficiency syndrome patients.Long-term antiretroviral treatment (ART) outcomes regarding immunological and virological surrogate markers were longitudinally evaluated between 2009 and 2014 (over 57 months) in 245 perinatally HIV-1-infected children and adolescents born from HIV-infected mothers, treated at inclusion for at least 6 months by the World Health Organization-recommended ART in Bangui, Central African Republic.Patients were monitored over time biologically for CD4 T-cell counts, HIV-1 RNA loads, and drug resistance mutation genotyping.Children lost to follow-up totaled 6%. Four categories of immunovirological responses to ART were observed. At baseline, therapeutic success with sustained immunological and virological responses was observed in 80 (32.6%) children; immunological and virologic nonresponses occurred in 32 (13.0%) children; finally, the majority (133; 54.2%) of the remaining children showed discordant immunovirological responses. Among them, 33 (13.4%) children showed rapid virological responses to ART with an undetectable viral load, whereas immunological responses remained absent after 6 months of treatment and increased progressively over time in most of the cases, suggesting slow immunorestoration. Notably, nearly half of the children (40.8% at baseline and 48.2% at follow-up) harbored discordant immunovirological responses with a paradoxically high CD4 T-cell count and HIV-1 RNA load, which are always associated with high levels of drug resistance mutations. The latter category showed a significant increase over time, with a growth rate of 1.23% per year of follow-up.Our STROBE-compliant study demonstrates the high heterogeneity of biological responses under ART in children with frequent passage from 1 category to another over time. Close biological evaluation with access to routine plasma HIV-1 RNA load monitoring is crucial for adapting the complex outcomes of ART in HIV-infected children born from infected mothers.