Whole genome sequencing and phylogenetic analysis of SARS-CoV-2 strains isolated during the COVID-19 pandemic in Nigeria.

Objectives: The emergence and spread of SARS-CoV-2 have stimulated ongoing research into the virus transmission dynamics, circulating variants, and potential mutations. This study was conducted to understand the genomic dynamics of the epidemic in Nigeria. Design: Whole genome sequencing was conducted on SARS-CoV-2 samples collected during the first and second outbreaks using the Oxford Nanopore MinION sequencing platform. Phylogenetic analysis was conducted, and genomes were grouped into different pangolin lineages. Results: The study revealed four circulating SARS-CoV-2 variants. The Alpha (B.1.1.7) variant was the most prevalent (32.7%), followed by Beta (B.1 B.1.1, L.3, and B.1.1.318) (30.8%), Eta (B.1.525) (28.9%), and Delta (B.1.617, AY.1, AY.109, and AY.36) (7.7%). Phylogenetic analysis revealed three clusters with four Nextstrain clades (20I, 20B, 21D, and 21J). The Alpha lineages (B.1.1.7) clustered with references from Italy. The Beta lineages (Clade 20B) (B.11, B.11318, and L3) and sub-lineage B.11 were distinct. Sub-lineage B.11318 is clustered with references from the USA, whereas sub-lineage L3 is clustered with references from Russia, the Philippines, Australia, and Japan. The 21D and 21J, belonging to two Pango lineages, Eta (B.1525) and Delta (B.1.617 and AY.109), showed high genetic similarity. Conclusion: The phylogenetic relatedness of the lineages suggests multiple virus introduction, which could be a source of more virulent, locally adapted variants.

Effect of nasal carriage of Bacillus species on COVID-19 severity: a cross-sectional study.

Intranasal sprays containing Bacillus species are being researched for treating viral respiratory tract infections. The aim of this study was to assess the relationship between the nasal carriage of Bacillus and COVID-19 severity. This was a cross-sectional study that collected nasopharyngeal samples from adults 18 years and above visiting two COVID-19 testing centers in Lagos, Nigeria, between September 2020 and September 2021. Bacillus species were cultured from the samples and confirmed using 16 s rRNA gene sequencing. The dependent variable was COVID-19 status classified as negative, asymptomatic, mild, or severe. The independent variable was the nasal carriage of Bacillus species. Multinomial regression analysis was done to determine the association between nasal carriage of Bacillus and COVID-19 severity after adjusting for age, sex, and co-morbidity status. A total of 388 participants were included in the study with mean (standard deviation) age of 40.05 (13.563) years. Sixty-one percent of the participants were male, 100 (25.8%) had severe COVID-19, 130 (33.5%) had pre-existing comorbidity, and 76 (19.6%) had Bacillus cultured from their nasopharyngeal specimen. Bacillus species presence was significantly associated with higher odds of severe COVID-19 compared to having a negative COVID-19 status (AOR = 3.347, 95% CI: 1.359, 8.243). However, the presence of Bacillus species was significantly associated with lower odds of severe COVID-19 compared to having a mild COVID-19 status. The study suggests that nasal carriage of Bacillus species is associated with the clinical course of COVID-19 and supports the exploration of Bacillus species in the management of viral respiratory tract infections.IMPORTANCEWith the introduction of intranasal spray containing Bacillus species for the treatment of viral respiratory tract infections, such as COVID-19 and respiratory syncytial virus, identifying the association between the nasal carriage of Bacillus species and COVID-19 susceptibility and severity will help further substantiate the investigation of these bacteria for COVID-19 prevention and treatment. This study evaluated the association between the carriage of Bacillus species in the nasopharyngeal tract and COVID-19 severity and found that the presence of Bacillus species in the nasopharynx may significantly impact the clinical course of COVID-19.

Corrigendum: Fetoplacental transmission and placental response to SARS-CoV-2: evidence from the literature.

[This corrects the article DOI: 10.3389/fmed.2022.962937.].

Fetoplacental transmission and placental response to SARS-CoV-2: Evidence from the literature.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a dreadful novel coronavirus with global health concerns among pregnant women. To date, the vertical transmission of SARS-CoV-2 during pregnancy remains controversial. We briefly report recent findings of placental response to SARS-CoV-2 infection and updates on vertical transmission. We systematically searched PubMed and Google Scholar databases according to PRISMA guidelines for studies reporting the effects of SARS-CoV-2 infection on the placenta and possibility of vertical transmission. We identified 45 studies reporting 1,280 human placentas that were analyzed by molecular pathology methods and 11,112 placenta-derived cells from a publicly available database that was analyzed using bioinformatics tools. The main finding of this study is that the SARS-CoV-2 canonical entry receptors (ACE2 and TMPRSS2) are abundantly expressed on the placenta during the first trimester, and this expression diminishes across gestational age. Out of 45 eligible studies identified, 24 (53.34%) showed no evidence of vertical transmission, 15 (33.33%) supported the hypothesis of very rare, low possibility of vertical transmission and 6 (13.33%) were indecisive and had no comment on vertical transmission. Furthermore, 433 placentas from 12 studies were also identified for placental pathology investigation. There was evidence of at least one form of maternal vascular malperfusion (MVM), 57/433 (13.1%), fetal vascular malperfusion (FVM), 81/433 (18.7%) and placental inflammation with excessive infiltration of CD3+ CD8+ lymphocytes, CD68+ macrophages and CD20+ lymphocytes in most of the eligible studies. Decidual vasculopathy (3.2%), infarction (3.2%), chronic histiocytic intervillositis (6.0%), thrombi vasculopathy (5.1%) were also observed in most of the MVM and FVM reported cases. The results indicated that SARS-CoV-2 induces placenta inflammation, and placenta susceptibility to SARS-CoV-2 decreases across the pregnancy window. Thus, SARS-CoV-2 infection in early pregnancy may adversely affect the developing fetus.

Mucoadhesive Microspheres of Maraviroc and Tenofovir Designed for Pre-Exposure Prophylaxis of HIV-1: An in vitro Assessment of the Effect on Vaginal Lactic Acid Bacteria Microflora.

PURPOSE: To formulate and evaluate microspheres of the antiretroviral drugs maraviroc and tenofovir intended for a candidate vaginal microbicide and assess its effect on the vaginal lactic acid bacteria microflora. METHODS: Ionic gelation technique was used to formulate maraviroc and tenofovir microspheres with subsequent characterization. The effect of varying concentrations of the polymer, crosslinking agent and the curing time on the outcome variables viz: particle size, mucoadhesion and encapsulation efficiency were investigated. Lactic acid bacteria were isolated from the vagina of healthy women using standard microbiologic methods. The analysis of their 16S rRNA sequence data identified Lactobacillus fermentum and Enterococcus faecalis strains which were assigned GenBank accession numbers. The efficacy of the microspheres on HIV-1BaL strain was evaluated using TZM-bl indicator cells. RESULTS: The optimal maraviroc and tenofovir microspheres had particle sizes of (434.82 µm and 456.18 µm), mucoadhesion of (93.3% and 90%) and encapsulation efficiency (92.80% and 78.9%) respectively. Maraviroc release kinetics followed a zero-order model and tenofovir was released via Higuchi model. The assay of a 1 mg/mL suspension of the microspheres on the strains of Lactobacillus fermentum and Enterococcus faecalis showed a viability of 93.9% and 89.7%, respectively. There was a statistically significant difference between the mean absorbance readings of the test agent and that of the positive control (P = 0.001). The microspheres elicited a progressive decline in HIV infectivity until at a concentration of 1 µg/mL. CONCLUSION: The antiretroviral drugs loaded in the microspheres, had good mucoadhesion which is a potential for prolonged residence time in the vagina. The antiretroviral drugs were adequately released from the microspheres and showed efficacy against the HIV-1 BaL virus strain. There was no significant disruption in the growth of the lactic acid bacteria which constitute valuable bacteria microflora of the vagina.

Molecular analysis of low-level tetracycline resistance in clinical isolates of Helicobacter pylori among dyspeptic patients in South West Nigeria.

OBJECTIVES: The aim of this study was to determine the occurrence of 16S rRNA mutations associated with low-level tetracycline resistance in Helicobacter pylori isolates from adult dyspeptic patients in South West Nigeria. METHODS: Susceptibility testing to tetracycline of 50 H. pylori isolates was performed by Etest. The 535-bp conserved region of the H. pylori tetracycline-binding site of 16S rRNA was amplified by PCR, followed by sequencing and multiple sequence alignment for all 50 clinical isolates. RESULTS: Of the 50 clinical isolates examined, DNA sequence analysis revealed nucleotide substitutions in 7 isolates at positions 926-928. Of the seven isolates, two demonstrated reduced susceptibility to tetracycline with Etest minimum inhibitory concentrations (MICs) of 0.75-1.0mg/L, whilst the other five isolates were resistant with MICs of 1.5-24mg/L (resistance breakpoint >1mg/L). The two isolates with reduced susceptibility had single nucleotide substitution of A926G, whilst the five resistant isolates demonstrated double base pair substitutions of G927T/A928C and A926G/A928C and a single nucleotide substitution of A926G. CONCLUSIONS: This study shows that low-level tetracycline resistance amongst H. pylori-positive dyspeptic patients is associated with reduced susceptibility and resistance to tetracycline. This is the result of 1-bp and 2-bp differences in positions 926 and 926-928, respectively, in the 16S rRNA of H. pylori.

Helicobacter pylori strains from a Nigerian cohort show divergent antibiotic resistance rates and a uniform pathogenicity profile.

Antibiotic resistance in Helicobacter pylori is a factor preventing its successful eradication. Particularly in developing countries, resistance against commonly used antibiotics is widespread. Here, we present an epidemiological study from Nigeria with 111 isolates. We analyzed the associated disease outcome, and performed a detailed characterization of these isolated strains with respect to their antibiotic susceptibility and their virulence characteristics. Furthermore, statistical analysis was performed on microbiological data as well as patient information and the results of the gastroenterological examination. We found that the variability concerning the production of virulence factors between strains was minimal, with 96.4% of isolates being CagA-positive and 92.8% producing detectable VacA levels. In addition, high frequency of bacterial resistance was observed for metronidazole (99.1%), followed by amoxicillin (33.3%), clarithromycin (14.4%) and tetracycline (4.5%). In conclusion, this study indicated that the infection rate of H. pylori infection within the cohort in the present study was surprisingly low (36.6%). Furthermore, an average gastric pathology was observed by histological grading and bacterial isolates showed a uniform pathogenicity profile while indicating divergent antibiotic resistance rates.

Fluconazole susceptibility and ERG11 gene expression in vaginal candida species isolated from Lagos Nigeria.

Fluconazole resistance is an important type of resistance in Candida because in most countries, fluconazole is the drug of choice for vulvovaginal candidiasis. Candida species resist fluconazole by various mechanisms but there is paucity of data on these in our environment. Such mechanisms include among others, over-expression of the ERG11 gene, which codes for synthesis of the target enzymes in the fungus. The aim of this study was to screen Candida spp. resistant to fluconazole for the expression of ERG11 gene. Fluconazole susceptibility test was performed on 28 clinical strains of Candida species previously obtained from students of a School of Nursing in Lagos, Nigeria. They were identified by API Candida, CHROMagar candida and germ tube test. Using 25 mcg discs, fluconazole susceptibility was determined by the disc diffusion method and results were interpreted in accordance with the Clinical Laboratory Standard Institute (CLSI) criteria; sensitive (S), resistant (R) and susceptible dose dependent (SDD). The R and SDD isolates were subsequently evaluated for the presence of ERG11 gene. Of the 28 clinical isolates, 14 were identified as C. albicans and six as C. tropicalis. The remaining isolates were identified as C. glabrata (2), C. famata (2) C. kefyr (2) one each of C. parapsilosis and C. guilliermondii respectively. In this study, 18 were susceptible (S) to fluconazole, eight were SDD and two were resistant to the antifungal agent. Out of the 14 C. albicans isolates, 12 were susceptible, one showed high level resistance and similar number showed susceptible dose dependence. ERG11 was detected in three susceptible dose dependent Candida species. This analysis demonstrates that susceptible dose dependence should not be overlooked as it may be associated with the presence of ERG11 gene and resistance to fluconazole. There is a need to consider routine antifungal susceptibility testing for Candida species causing vulvovaginitis.

Application of stool-PCR for the diagnosis of Helicobacter pylori from stool in Nigeria- a pilot study.

There are various methods for detection of Helicobacter pylori and the gold standard for non-invasive detection is the urea breath test (UBT). The aim of the study is therefore to detect H. pylori from the stool of patients with dyspepsia by PCR and compare results obtained with UBT. A total of 97 stool samples from patients presenting with dyspeptic symptoms in Lagos University Teaching Hospital (LUTH) were screened for urea breath test (UBT) and the presence of H. pylori DNA using stool-PCR. Out of 97 stool samples analysed, 38 (39.2%) were positive for Helicobacter spp. and 20 (20.6%) positive for H. pylori by PCR, through amplification of 16S rRNA and glmMgenes respectively. Of the 20 positive by glmM gene, the cagAgene was detected in 8 (40%) samples, while 47 (48.5%) out of 97 stool samples were positive for H. pylori by UBT. The sensitivity and specificity of the glmM gene compared with UBT as the gold standard is 42.6% and 100% respectively. The positive predictive value (PPV) was 100% while the negative predictive value (NPV) was 60%.The method may be useful for detecting H. pylori from stool amongst children especially where most hospitals lack endoscope for children although the method is expensive.

Comparison of PCR with other diagnostic techniques for the detection of H. pylori infection in patients presenting with gastroduodenal symptons in Nigeria.

The study was aimed at comparing PCR methods of direct detection from biopsy using the boiling method and one other method with two known gold standards (histology and CLO test) for the diagnosis of H. pylori in Nigeria. A total of 168 biopsies (three from antrum and one from corpus each) were taken from 42 patients presenting with various gastroduodenal symptons after informed consent was obtained from them.The biopsies were analysed using the CLO test kit and histology, while the boiling method as described by Holmes and Quigley (1981) was used to obtain DNA and then PCR using the 16S rRNA gene, glmM gene and cagA gene. With CLO test 15/42 (35.71%) were positive, histology 13/42 (30.95%) were positive, 16S rRNA 22/42 (52.38%) were positive, glmM 19/42 (45.24%) were positive, cagA 19/42 (45.24%) were positive. The sensitivity and specificity of the PCR tests with CLO as the gold standard showed that the tests were 100% sensitive and varied between 74.1% to 84.1% in specificity. The PPV and NPV showed that the NPV was almost 100%, while the PPV was between 68.2% and 75%. Using the histology as the gold standard, the sensitivity was almost 100% while the specificity, the PPV were reduced in comparison to the CLO test. The PCR test using the glmM gene appears to be the most reliable test for diagnosis of H. pylori in Nigeria most especially where culture is difficult due to the power outages.

Molecular typing of Salmonella spp isolated from food handlers and animals in Nigeria.

A total of 61 isolates of Salmonella spp (made up of 26 clinical isolates and 20 food handler and 15 animal isolates) were typed by RAPD-PCR for the purpose of screening for epidemiologically related isolates. The RAPD -PCR typing method used comprised six primers namely 787, 797, 784, 1254, RAPD 1 and RAPD 2 but 784 and 1254 did not produce discriminatory patterns and so were dropped. From the 61 strains, RAPD fingerprinting with primers RAPD 1, 2 produced 22 and 24 fingerprint patterns respectively. RAPD fingerprinting with primers 787, 797 produced 17, 11 fingerprinting patterns respectively. Combinations of the two RAPD 1 and 2 primers increased the discrimination of Salmonella strains to 32 patterns rather than the other primers used. Primer 797 was the least discriminatory. This study showed that the RAPD 1 and 2 primers would be useful for epidemiological typing of the Salmonella spp in Nigeria.