A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations, predominantly from Europe, which diminished following the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1 and C.1.1. Although distorted by low sampling numbers and blind-spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a breeding ground for new variants.

Antioxidant and glucosidase activities and phytochemical constituents of Chrysanthoglossum trifurcatum (Desf.)

Objective: To investigate the antioxidant and glucosidase properties and phytochemical constituents of roots, stems, leaves and flowers extracts and aerial parts oil of Chrysanthoglossum trifurcatum (Desf.) (C. trifurcatum). Methods: For extraction from roots, stems, leaves and flowers of C. trifurcatum, methanol, ethyl acetate and petroleum ether solvents were used. Phenols, flavonoids, flavonols and tannins contents were evaluated. More, C. trifurcatum aerial parts oil composition was determined using chromatography/mass spectrometry. The antioxidant effect was estimated by DPPH, ABTS and reducing power test systems. The glucosidase inhibition was determined by colorimetric assay using the enzyme from Aspergillus Niger and the p-nitrophenyl glucopyranoside (pNPG) as substrate. Results: The highest amounts of polyphenols, flavonoids, flavonols and tannins were shown by the methanolic extract of leaves. The main components of the aerial parts oil were limonene (29.21%), γ -terpinene (12.96%), 4-terpenyl acetate (12.18%) and pinene (5.76%). The activity evaluated by DPPH, ABTS and reducing power tests was important for stems (IC

Antioxidant and α-glucosidase activities and phytochemical constituents of Chrysanthoglossum trifurcatum (Desf.)

Objective:To investigate the antioxidant and α-glucosidase properties and phytochemical constituents of roots, stems, leaves and flowers extracts and aerial parts oil of Chrysanthoglossum trifurcatum (Desf.) (C. trifurcatum).Methods:For extraction from roots, stems, leaves and flowers of C. trifurcatum, methanol, ethyl acetate and petroleum ether solvents were used. Phenols, flavonoids, flavonols and tannins contents were evaluated. More, C. trifurcatum aerial parts oil composition was determined using chromatography/mass spectrometry. The antioxidant effect was estimated by DPPH, ABTS and reducing power test systems. The α-glucosidase inhibition was determined by colorimetric assay using the enzyme from Aspergillus niger and the p-nitrophenyl glucopyranoside (pNPG) as substrate.Results:The highest amounts of polyphenols, flavonoids, flavonols and tannins were shown by the methanolic extract of leaves. The main components of the aerial parts oil were limonene (29.21%), γ -terpinene (12.96%), 4-terpenyl acetate (12.18%) and α -pinene (5.76%). The activity evaluated by DPPH, ABTS and reducing power tests was important for stems (ICConclusions:Observed antioxidant and α-glucosidase activities of oil and extracts are attributed to the presence of the active phytochemicals in C. trifurcatum organs. Thus, the C. trifurcatum can be used as a source of antioxidant compounds and dietary supplement to treat patients with type 2 diabetes.

Antimicrobial activity of Tunisian Euphorbia paralias L

Objective To examine the potential antimicrobial activity of Euphorbia paralias L. (Euphorbiaeae) leaves and stems extracts. Methods The antimicrobial activity was tested against six microbial strains: Escherichia coli ATCC 8739, Bacillus subtilis ATCC 6633, Salmonella enterica CIP 8039, Staphylococcus aureus ATCC 6538, Pseudomonas aeruginosa ATCC 9027 and Candida albicans ATCC 90028 by two different methods, the disk method and the dilution method. Results Our results showed the important antimicrobial activity of the chloroform extract of the stems towards the majority of the strains by using both methods. Bacillus subtilis was the most sensitive strain (MIC = MBC = 15 μg/mL). Conclusion Thus, some extracts of Euphorbia paralias can be used in the treatment of infectious diseases caused by microbes.

Adhesive properties and extracellular enzymatic activity of Staphylococcus aureus strains isolated from oral cavity.

Staphylococcus aureus is one of prominent bacterial pathogen that occurs in oral region. In this study, 21 strains of S. aureus isolated from the oral cavity of Tunisian patients were investigated for slime production using Congo red agar method (CRA) and adherence assay. Biofilm formation of oral isolates on orthodontic biomaterials (Bis-GMA and PMMA) was also evaluated by MTT reduction assay. In addition, the production of hydrolytic enzymes by S. aureus strains was analyzed and the presence of protease, lipase and ß-hemolysin genes (sspA, sspB, geh, hlb) was achieved by polymerase chain reaction (PCR). Qualitative biofilm production tested on CRA revealed that 91% of strains were slime producers. The result of OD570 showed that five strains isolated from the oral cavity were highly biofilm positive. The metabolic activity of S. aureus biofilm formed on Bis-GMA and PMMA did not differ between tested strains. The atomic force micrographs demonstrated that biofilm formed by S. aureus strains was organized in typical cocci cells attached to each other through production of exopolymeric substances. The production of hydrolytic enzymes showed that all S. aureus strains were protease positive. Lipase (77%) and beta hemolytic (59%) activities were also detected. Among the tested strains, 17 were positive for sspA, sspB and hlb genes. While only ten S. aureus strains harbor the geh gene (48%). These data highlight the importance of evaluation of biofilm formation and exoenzyme production in oral S. aureus isolates to investigate the role of this pathogen and its impact in oral pathology.

Chemical composition and antibacterial activity of essential oils from the Tunisian Allium nigrum L.

The chemical composition of the essential oils of different Allium nigrum L. organs and the antibacterial activity were evaluated. The study is particularly interesting because hitherto there are no reports on the antibacterial screening of this species with specific chemical composition. Therefore, essential oils from different organs (flowers, stems, leaves and bulbs) obtained separately by hydrodistillation were analyzed using gas chromatography-mass spectrometry (GC-MS). The antibacterial activity was evaluated using the disc and microdilution assays. In total, 39 compounds, representing 90.8-96.9 % of the total oil composition, were identified. The major component was hexadecanoic acid (synonym: palmitic acid) in all the A. nigrum organs oils (39.1-77.2 %). We also noted the presence of some sesquiterpenes, mainly germacrene D (12.8 %) in leaves oil) and some aliphatic compounds such as n-octadecane (30.5 %) in bulbs oil. Isopentyl isovalerate, 14-oxy-α-muurolene and germacrene D were identified for the first time in the genus Allium L. All the essential oils exhibited antimicrobial activity, especially against Enterococcus faecalis and Staphylococcus aureus. The oil obtained from the leaves exhibited an interesting antibacterial activity, with a Minimum Inhibitory Concentration (MIC) of 62.50 µg/mL against these two latter strains. The findings showed that the studied oils have antibacterial activity, and thus great potential for their application in food preservation and natural health products.

Lymphoma B-cell responsiveness to CpG-DNA depends on the tumor microenvironment.

BACKGROUND: Toll-like receptor (TLR) agonists have important properties that can be exploited for immunotherapy against tumors. Locally injected immunostimulatory oligodeoxynucleotides containing CpG motifs (CpG-ODNs), which are TLR9 agonists, have shown promise in cancer models. Several studies have demonstrated that these motifs have immunologic effects similar to those of bacterial DNA and can stimulate monocytes, macrophages, dendritic, and B cells, which then produce several proinflammatory cytokines. However, these CpG-ODNs appear to produce opposite effects on tumor B cells. METHODS: In this study, we investigated the direct effects of a murine class B CpG (1826) ODNs on lymphoma B cells in vitro and in vivo, using mouse models of non-Hodgkin B lymphomas developing in immunoprivileged sites, specifically the brain and the eye, and in subcutaneous sites. RESULTS: In vitro, CpG-ODNs produced antiproliferative and proapoptotic effects on lymphoma B cells. In vivo, it had an antitumor effect when injected into tumors in murine models of subcutaneous lymphoma (SCL) and primary cerebral lymphoma (PCL). However, its intravitreal administration into a primary intraocular lymphoma (PIOL) mouse model did not produce an antitumor effect. In vitro experiments using supernatant from mouse PIOL samples demonstrated that the PIOL molecular microenvironment inhibits the antiproliferative effect of CpG-ODNs on lymphoma B-cells. CONCLUSIONS: Responsiveness to CpG stimulation differs in subcutaneous, cerebral, and ocular tumors, according to the tumoral and molecular microenvironment, and this should be considered for further therapeutic approaches.

Quantitative analysis of human herpesvirus-6 genome in blood and bone marrow samples from Tunisian patients with acute leukemia: a follow-up study.

BACKGROUND: Infectious etiology in lymphoproliferative diseases has always been suspected. The pathogenic roles of human herpesvirus-6 (HHV-6) in acute leukemia have been of great interest. Discordant results to establish a link between HHV-6 activation and the genesis of acute leukemia have been observed. The objective of this study was to evaluate a possible association between HHV-6 infection and acute leukemia in children and adults, with a longitudinal follow-up at diagnosis, aplasia, remission and relapse. METHODS: HHV-6 load was quantified by a quantitative real-time PCR in the blood and bone marrow samples from 37 children and 36 adults with acute leukemia: 33 B acute lymphoblastic leukemia (B-ALL), 6 T acute lymphoblastic leukemia (T-ALL), 34 acute myeloid leukemia (AML). RESULTS: HHV-6 was detected in 15%, 8%, 30% and 28% of the blood samples at diagnosis, aplasia, remission and relapse, respectively. The median viral loads were 138, 244, 112 and 78 copies/million cells at diagnosis, aplasia, remission and relapse, respectively. In the bone marrow samples, HHV-6 was detected in 5%, 20% and 23% of the samples at diagnosis, remission and relapse, respectively. The median viral loads were 34, 109 and 32 copies/million cells at diagnosis, remission and relapse, respectively. According to the type of leukemia at diagnosis, HHV-6 was detected in 19% of the blood samples and in 7% of the bone marrow samples (with median viral loads at 206 and 79 copies/million cells, respectively) from patients with B-ALL. For patients with AML, HHV-6 was present in 8% of the blood samples and in 4% of the bone marrow samples (with median viral loads at 68 and 12 copies/million cells, respectively). HHV-6 was more prevalent in the blood samples from children than from adults (25% and 9%, respectively) and for the bone marrow (11% and 0%, respectively). All typable HHV-6 were HHV-6B species. No link was shown between neither the clinical symptoms nor the abnormal karyotype and HHV-6 activation. A case of HHV-6 chromosomal integration was shown in one patient with AML. CONCLUSION: This study confirms the absence of role of HHV-6 in the genesis of acute leukemia but the virus was reactivated after chemotherapy treatment.

Antibacterial, antifungal and cytotoxic activities of two flavonoids from Retama raetam flowers.

We have investigated the antibacterial, antifungal and cytotoxic activities of two flavonoids isolated from Retama raetam flowers using the disc diffusion and micro-dilution broth methods. The cytotoxic activity was tested against Hep-2 cells using the MTT assay. The compounds licoflavone C (1) and derrone (2) were active against Pseudomonas aeruginosa and Escherichia coli (7.81-15.62 µg/mL) and showed important antifungal activity. Strong antifungal activity against Candida species (7.81 µg/mL) was for example found with compound 2. The tested compounds also showed strong cytotoxicity against Hep-2 cells. These two compounds may be interesting antimicrobial agents to be used against infectious diseases caused by many pathogens.

Seroprevalence of hepatitis E virus infection in rural and urban populations, Tunisia.

Hepatitis E virus (HEV) is one of the leading agents of acute hepatitis. This study investigated the prevalence and risk factors of HEV infection in the Tunisian adult general population, either in blood donors (n=687) or in patients hospitalized for acute hepatitis (n=202). The mode of transmission differed between these two populations: contact with animals and living in a rural habitat were the main risk factors for being in contact with HEV in asymptomatic blood donors, while HEV was contracted through contaminated water in symptomatic cases. HEV seroprevalence in adult blood donors in Tunisia was relatively low (5.4%) and increased with age.

Evolutionary pattern of 5'-UTR of enteroviruses and primer update for the detection of enteroviral RNA in environmental samples

OBJECTIVE@#To study the recombination events among enterovirus strains and the development of specific primers for the detection of enteroviruses in environmental samples.@*METHODS@#Nucleotide sequence analysis of enteroviruses deposited in the international database GenBank (www.ncbi.nlm.nih.gov/Genbank) was conducted to develop specific primers for the detection of these viruses. The specificity and sensitivity of the method were tested using coxackievirus B3 strain Nancy, environmental isolate of human hepatitis A virus and human rotavirus strain WA. Seventy sewage samples were analyzed.@*RESULTS@#Enterovirus genome was detected in all positive samples. The genome of enterovirus was not detected in negative samples. The level of detection of these viruses was 10(2) TCID(50)/mL.@*CONCLUSIONS@#The development of new primers is an important issue for the detection of enteroviruses in the environment and the assessment of risk factors to human health.

Multiplex nested RT-PCR for the detection of porcine enteric viruses.

Porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine group A rotavirus (PRV-A) are major viruses causing enteric diseases of piglets. A multiplex nested reverse transcription polymerase chain reaction (multiplex nested RT-PCR) was developed for the detection of these viruses in field samples from piglets with diarrhea. A mixture of (1) three external pairs of primers, yielding in the amplification step two different amplicons with sizes of 950 bp and 317 bp and (2) three pairs of internal primers in a second round of PCR (nested PCR), yielding two different amplicons with sizes of 792 bp and 208 bp for TGEV and porcine PRV-A, respectively. The genome of PEDV was not detected after the amplification step but it was detected in the second round of PCR, yielding amplicon with size of 291 bp. Multiplex nested RT-PCR can detect TGEV, PRV-A, and PEDV up to concentration 10(2) TCID(50)/mL, 10(1) TCID(50)/mL, and 27.2 microg/microl of RNA, respectively. A total of 175 field samples were collected from swine with diarrhea from January 2005 until July 2007. The samples were tested for the presence of three viruses by a multiplex nested RT-PCR. Dual infections with PEDV and PRV-A were identified in seven specimens (4%) (n = 6). Twenty-one (25%) infections were caused by PEDV and thirty-four infections (41%) were caused by PRV-A. The genome of TGEV was not detected in any of these field samples, however TGEV was detected in piglets infected experimentally. The multiplex nested RT-PCR is rapid, sensitive, and a cost-effective detection method for the detection of porcine enteric viruses.

Antibacterial and cytotoxic activity of the acetone extract of the flowers of Salvia sclarea and some natural products.

The aim of this study was to investigate the antibacterial and the cytotoxic activity of the acetone extract of the flowers of Salvia sclarea and of some natural products (sclareol, sclareolide and ambrox). The antibacterial and the cytotoxic activity were determined by the dilution method. Sclareolide, ambrox and sclareol demonstrated a good antibacterial activity against Staphylococcus aureus ATCC 25923, Pseudomonas aeruginosa ATCC 27950, Escherichia coli ATCC 25922 and Enterococcus faecalis ATCC 29212. The acetonic extract of the flowers of Salvia sclarea has a significant cytotoxic activity against Hep-2 cells.