Epidemiology of first cases of SARS-CoV-2 infection, from March to April 2020, in Gabon.

Background After the first cases of coronaviruses disease 2019 (COVID-19) in China in January 2020, we conducted an epidemiological surveillance of COVID-19 in Gabon. Methods We led molecular investigations on nasopharyngeal and oropharyngeal samples from the 1161 first suspected cases of COVID-19. We diagnosed the first case of COVID-19 on March, 12 2020. Results Among those suspected cases, 83 were confirmed cases. There was no significant difference in prevalence of SARS-CoV-2 between age groups (p=0.14). 73% were asymptomatic. The viral loads were significantly higher in the nasopharyngeal samples than in the oropharyngeal samples (p=0.03). There was no significant difference in viral loads between age groups (p=0.9895) and no correlation between clinical symptoms and viral loads (p=0.06042). A phylogenetic analysis performed with five sequences of the spike S gene showed that two sequences had the D614G mutation. Conclusion In conclusion, this study provides the first molecular data from Gabon concerning the COVID-19 pandemic. The data showed that most of the infected people were asymptomatic. The viral load was higher in the nasopharyngeal samples. The S gene analyzed suggested both introduction of the D614 and G614 variant in Gabon.

Screening and Whole Genome Sequencing of SARS-CoV-2 Circulating During the First Three Waves of the COVID-19 Pandemic in Libreville and the Haut-Ogooué Province in Gabon.

Since the onset of the COVID-19 pandemic, the SARS-CoV-2 viral dynamics in Africa have been less documented than on other continents. In Gabon, a Central African country, a total number of 37,511 cases of COVID-19 and 281 deaths have been reported as of December 8, 2021. After the first COVID-19 case was reported on March 12, 2020, in the capital Libreville, the country experienced two successive waves. The first one, occurred in March 2020 to August 2020, and the second one in January 2021 to May 2021. The third wave began in September 2021 and ended in November 2021. In order to reduce the data gap regarding the dynamics of SARS-CoV-2 in Central Africa, we performed a retrospective genotyping study using 1,006 samples collected from COVID-19 patients in Gabon from 2020 to 2021. Using SARS-CoV-2 variant screening by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and whole genome sequencing (WGS), we genotyped 809 SARS-CoV-2 samples through qRT-PCR and identified to generated 291 new genomes. It allowed us to describe specific mutations and changes in the SARS-CoV-2 variants in Gabon. The qRT-PCR screening of 809 positive samples from March 2020 to September 2021 showed that 119 SARS-CoV-2 samples (14.7%) were classified as VOC Alpha (Pangolin lineage B.1.1.7), one (0.1%) was a VOC Beta (B.1.351), and 198 (24.5 %) were VOC Delta (B.1.617.2), while 491 samples (60.7%) remained negative for the variants sought. The B1.1 variant was predominant during the first wave while the VOC Alpha dominated the second wave. The B1.617.2 Delta variant is currently the dominant variant of the third wave. Similarly, the analysis of the 291 genome sequences indicated that the dominant variant during the first wave was lineage B.1.1, while the dominant variants of the second wave were lineages B.1.1.7 (50.6%) and B.1.1.318 (36.4%). The third wave started with the circulation of the Delta variant (B.1.617). Finally, we compared these results to the SARS-CoV-2 sequences reported in other African, European, American and Asian countries. Sequences of Gabonese SARS-CoV-2 strains presented the highest similarities with those of France, Belgium and neighboring countries of Central Africa, as well as West Africa.

Could pooled samples method affect SARS-CoV-2 diagnosis accuracy using BGI and Sansure-Biotech RT-PCR kits used in Gabon, Central Africa?

This study aims at establishing specimens pooling approach for the detection of SARS-CoV-2 using the RT-PCR BGI and Sansure-Biotech kits used in Gabon. To validate this approach, 14 positive samples, stored at -20°C for three to five weeks were analyzed individually (as gold standard) and in pools of five, eight and ten in the same plate. We created 14 pools of 5, 8 and 10 samples using 40 µL from each of the selected positive samples mixed with 4, 7 and 9 confirmed negative counterparts in a total volume of 200 µL, 320 µL and 400 µL for the pools of 5, 8 and 10 respectively. Both individual and pooled samples testing was conducted according to the BGI and Sansure-Biotech RT-PCR protocols used at the Professor Daniel Gahouma Laboratory (PDGL). Furthermore, the pooling method was also tested by comparing results of 470 unselected samples tested in 94 pools and individually. Results of our experiment showed that using a BGI single positive sample with cycle threshold (Ct) value of 28.42, confirmed by individual testing, detection occurred in all the pools. On the contrary samples with Ct >31 were not detected in pools of 10 and for these samples (Ct value as high as 37.17) their detection was possible in pool of 8. Regarding the Sansure-Biotech kit, positive samples were detected in all the pool sizes tested, irrespective of their Ct values. The specificity of the pooling method was 100% for the BGI and Sansure-Biotech RT-PCR assays. The present study found an increase in the Ct values with pool size for the BGI and Sansure-Biotech assays. This trend was statistically significant (Pearson's r = 0.978; p = 0,022) using the BGI method where the mean Ct values were 24.04±1.1, 26.74±1.3, 27.91±1.1 and 28.32±1.1 for the individual, pool of 5, 8 and 10 respectively. The testing of the 470 samples showed that one of the 94 pools had a positive test similar to the individual test using the BGI and Sansure-Biotech kits. The saving of time and economizing test reagents by using the pooling method were demonstrated in this study. Ultimately, the pooling method could be used for the diagnosis of SARS-CoV-2 without modifying the accuracy of results in Gabon. We recommend a maximum pool size of 8 for the BGI kit. For the Sansure-Biotech kit, a maximum pool size of 10 can be used without affecting its accuracy compared to the individual testing.

Altered Toll-Like Receptor-4 Response to Lipopolysaccharides in Infants Exposed to HIV-1 and Its Preventive Therapy.

Pathogen sensing and recognition through pattern recognition receptors, and subsequent production of pro-inflammatory cytokines, is the cornerstone of the innate immune system. Despite the fact that HIV-exposed uninfected (HEU) infants are prone to serious bacterial infections, no study has focused on the functionality of their bacteria recognition system. This is the first study to investigate baseline levels of three critically important immune response molecules in this population: complement component (C)-3, toll-like receptor (TLR)-4, and C-reactive protein (CRP). We enrolled 16 HEU and 6 HIV-unexposed (HU) infants. TLR4 function was investigated by stimulating whole blood with increasing concentrations of TLR4-agonist ultrapure lipopolysaccharides. TLR4/TLR4-agonist dose response were assessed by measuring IL-6 secretion. Complement C3 and CRP were measured by photo spectrometry. Data showed no significant differences in baseline concentration of CRP between HEU and HU infants. Complement C3 was significantly higher in HEU infants than HU infants. TLR4 anergy was observed in 7 of 12 HEU infants, whereas the rest of HEU infants (n = 4) and the control HU infants tested (n = 3) showed responsive TLR4. None of the HEU infants investigated in this study had severe infections in the year after their birth. In conclusion, TLR4 anergy can occur in HEU infants without necessarily translating to increased vulnerability to infectious diseases.

Mother-to-child HIV-transmission prevention programs in a sub-Saharan African setting: The Gabonese experience.

In many developing countries, mothers' awareness remains a challenge despite the scaling up of antenatal care and programs preventing mother-to-child (MTC) HIV transmission. The present study was done in Libreville, Gabon where all antenatal care (delivery included) is free of charge. Here we assessed the timing of antenatal antiretroviral (ARV) prophylaxis initiation, HIV-exposed infants' age at their first postnatal HIV check visit and investigated the association between mothers' awareness or knowledge on their ARV therapy and infants' HIV infection. We interviewed HIV-positive mothers on their first and subsequent laboratory visits to investigate infants' HIV status and tested infants for HIV RNA and antibody between 2012 and 2014. We established that (1) of 718 HIV-positive mothers, only 6% were fully aware and knew what ARV treatment they were on during pregnancy; (2) half of the women (54%) start their antenatal ARV prophylaxis initiation during the second trimester of pregnancy; (3) 64% of HIV-exposed infants had their first HIV infection screening between birth and three months of age; (4) the overall prevalence of HIV infection in infants born from infected mothers was 8.9%; and (5) infants born from mothers uncertain about taking prophylactic ARV therapy were 13.3 times more likely to be infected by HIV than infants born from mothers certain about taking prophylactic ARV therapy. In conclusion, the study showed that despite free antenatal care, early access and adherence to components of MTC, HIV transmission preventive care remains unsatisfactory.

Cases of Impaired Oxidative Burst in HIV-Exposed Uninfected Infants' Neutrophils-A Pilot Study.

An increased risk of serious bacterial infections in HIV-exposed uninfected (HEU) infants has been demonstrated. Although neutrophils are essential for the protection of infants against bacterial infections, no study has investigated their profile in HEU infants to date. In this study, we assessed the function of neutrophils in HEU infants using the nitroblue tetrazolium reduction test. Among 25 HEU infants, 9 (36%) showed a reduced ability of their neutrophils to produce reactive oxygen species upon stimulation with bacteria. No alteration of total neutrophil counts was noted in the blood of HEU infants indicating that the alteration observed in the 36% of HEU infants may only be functional. Conclusively, impaired neutrophil function could be a factor of vulnerability in HEU infants.

Antimicrobial profiles of bacterial clinical isolates from the Gabonese National Laboratory of Public Health: data from routine activity.

BACKGROUND: The present study is one of the first to provide a picture of antimicrobial resistance for a range of bacteria and antimicrobial classes in Gabon, Central Africa. METHODS: During the year 2010, 146 urine cytology, 143 blood cultures, 107 vaginal swabs, 23 urethral swabs, and 18 other culture examinations were positives. All isolates were tested for antibiotic sensitivity. RESULTS: Four hundred thirty-seven microorganisms were isolated: 210 enterobacteria, 166 staphylococci, 38 streptococci, 14 Acinetobacter, and nine Stenotrophomonas. Of the Klebsiella isolates, 18% and 30% were found to be resistant to selected third-generation cephalosporins (3CG) and fourth-generation cephalosporins (4CG), respectively. Sixty-seven percent of Escherichia coli isolates were resistant to amoxicillin with clavulanic acid. Between 3% and 30% of E. coli isolates were resistant to selected 3CG. All Enterobacter cloacae isolates were sensitive to imipenem. Resistance to quinolones/fluoroquinolones was seen in 21-50% of E. coli isolates. Twenty-six percent of E. cloacae showed resistance to ceftazidime and 37% to cefotaxime. The resistance rate to quinolones ranged between 58% and 78%. Thirty-two percent of Staphylococcus isolates were resistant to gentamicin. Low resistance rates to teicoplanin (2-4%) were observed. Thirty-seven percent of isolated Staphylococcus aureus and 61% of isolated Staphylococcus saprophyticus were resistant to both penicillin G and oxacillin. Streptococcus isolates had low resistance rates to erythromycin, ceftriaxone, and ciprofloxacin (5%, 7%, and 14%, respectively) and were highly resistant to tetracycline, gentamicin, and sulfamethoxazole-trimethoprim (92%, 91%, and 62%, respectively). CONCLUSIONS: The antimicrobial resistance profiles seen here are of concern. To control the spread of drug-resistant bacteria, clinicians should be cognizant of their local antimicrobial resistance patterns.

Protective properties of non-nucleoside reverse transcriptase inhibitor (MC1220) incorporated into liposome against intravaginal challenge of Rhesus macaques with RT-SHIV.

In the absence of an effective vaccine against HIV, it is urgent to develop an effective alternative such as a microbicide. Single and repeated applications of MC1220 microbicide were evaluated in macaques. First, animals were given a single application of 0.5% or 1.5% MC1220-containing liposomal gel. A second group were treated with 0.5% MC1220 once a day for 4 days. The control groups were treated by liposomal gel alone. Thirty minutes after the last application, animals were challenged with RT-SHIV. In the first protocol, 2 of 4 animals treated by 0.5% of the MC1220 and 2 of 5 treated by 1.5% were protected. In the second protocol, 3 of 5 treated animals were protected and 5 of 5 controls were infected. The RNA viral load at necropsy was significantly lower (p=0.05) in treated-infected animals than in controls. In both protocols, the number of CD4+ T cells was lower at viremia peak in infected than in protected animals.

Prevalence and molecular diversity of hepatitis B virus and hepatitis delta virus in urban and rural populations in northern Gabon in central Africa.

The prevalence of hepatitis B virus (HBV) surface antigen was significantly higher in urban (12.9%) than in rural (7.6%) populations (P = 0.003), but no difference was found in the prevalence of hepatitis delta virus (HDV), which was high in both populations. Phylogenetic analysis showed the circulation of HBV-A3 and -E genotypes and the presence of HDV-1, HDV-7, and HDV-8 clades.

High HIV Type 1 prevalence and wide genetic diversity with dominance of recombinant strains but low level of antiretroviral drug-resistance mutations in untreated patients in northeast Gabon, Central Africa.

The northeast of Gabon, central Africa is characterized by high population density and a high rate of immigration from the surrounding countries. To determine the prevalence, circulating subtypes, and antiretroviral resistance mutations of HIV-1, 810 blood samples were collected from the general population of the two main cities (Oyem and Makokou) of this region. Of these, 61 (7.5%) were found to be positive for HIV-1. Analysis of the env (gp120), pol, and gag (p24) sequences as well as phylogenetic analyses showed at least eight different viral lineages. The most prevalent strains were CRF02 recombinants, followed by subtypes A, D, and C. The remaining strains were found to be F, J, G, and also, for the first time in Gabon, the recombinant form CRF11cpx. Analysis of antiretroviral drug-resistance mutations in protease and reverse transcriptase from this untreated population showed a low level of specific mutations. These mutations were associated with subtype polymorphism rather than with resistance to antiretroviral drugs. The wide diversity and the emergence of recombinant strains are in accordance with the rapid spread of new HIV strains in the population and, thus, the dynamic evolution of the epidemic.