Genetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya

Background: The variation of human papillomavirus (HPV) genotypes shapes the risks of cervical cancer and these variations are not well defined in Africa. Nucleotide changes within the L1 gene, nucleotide variability, and phylogeny were explored in relation to HIV in samples from Botswana and Kenya. Methods: A total of 98 HPV-positive cervical samples were sequenced to identify diferent HPV variants. Phylogenetic inferences were used to determine HPV genotypes and investigate the clustering of sequences between women living with HIV (WLWHIV) and -women not living with HIV (WNLWHIV). Results: Out of 98 generated sequences, 83.7% (82/98) participants had high-risk (HR) HPV genotypes while 16.3% (16/98) had low-risk (LR) HPV genotypes. Among participants with HR-HPV genotypes, 47.6% (39/82) were coinfected with HIV. The prevalence of HR-HPV genotypes was statistically higher in the Botswana population compared to Kenya (p-valu

Genetic complexity of Plasmodium falciparum in two ethnic groups of Burkina Faso with marked differences in susceptibility to malaria.

We have characterized Plasmodium falciparum genotypes among the Mossi and Fulani sympatric ethnic groups in villages in Burkina Faso during the rainy season. Differences in clinical malaria presentation and in immune responses to malaria occur between the two groups. Asexual parasite rate, density, and gametocyte rate were higher among the Mossi than the Fulani. There was no difference in frequencies of alleles of the P. falciparum merozoite surface protein 1 (msp-1), msp-2, and glutamate-rich protein (glurp) genes among the parasites in each group. However, there were significant differences in the mean number of P. falciparum clones in the two populations, with there being more in the Mossi than in the Fulani. This effect was especially marked in older children. These differences can most probably be attributed to genetic differences in immune responsiveness to malaria between the two ethnic groups

Association of CYP2B6 Genetic Variation with Efavirenz and Nevirapine Drug Resistance in HIV-1 Patients from Botswana

CYP2B6 liver enzyme metabolizes the two non-nucleoside reverse transcriptase inhibitors Efavirenz (EFV) and Nevirapine (NVP) used in the antiretroviral therapy (ART) regimens for HIV-infected individuals. Polymorphisms of the CYP2B6 gene influence drug levels in plasma and possibly virological outcomes. The aim of this study was to explore the potential impact of CYP2B6 genotype and haplotype variation on the risk of developing EFV/NVP drug resistance mutations (DRMs) in HIV-1 patients receiving EFV-/NVP-containing regimens in Botswana

Genetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya

Background The variation of human papillomavirus (HPV) genotypes shapes the risks of cervical cancer and these variations are not well defined in Africa. Nucleotide changes within the L1 gene, nucleotide variability, and phylogeny were explored in relation to HIV in samples from Botswana and Kenya. Methods A total of 98 HPV-positive cervical samples were sequenced to identify different HPV variants. Phylogenetic inferences were used to determine HPV genotypes and investigate the clustering of sequences between women living with HIV (WLWHIV) and -women not living with HIV (WNLWHIV). Results Out of 98 generated sequences, 83.7% (82/98) participants had high-risk (HR) HPV genotypes while 16.3% (16/98) had low-risk (LR) HPV genotypes. Among participants with HR-HPV genotypes, 47.6% (39/82) were coinfected with HIV. The prevalence of HR-HPV genotypes was statistically higher in the Botswana population compared to Kenya (p-value < 0.001). Multiple amino acid mutations were identified in both countries. Genetic diversity differed considerably among WLWHIV and WNLWHIV. The mean pairwise distances between HPV-16 between HIV and HIV/HPV as well as for HPV-18 were statistically significant. Six (6) new deleterious mutations were identified in the HPV genotypes based on the sequencing of the L1 region, HPV-16 (L441P, S343P), HPV-18 (S424P), HPV-45 (Q366H, Y365F), and HPV-84 (F458L). The majority of the patients with these mutations were co-infected with HIV. Conclusions Genomic diversity and different genomic variants of HPV sequences were demonstrated. Candidate novel mutations within the L1 gene were identified in both countries which can be further investigated using functional assays

Failure to detect Plasmodium vivax in West and Central Africa by PCR species typing

<p>Abstract</p> <p>Background</p> <p><it>Plasmodium vivax </it>is estimated to affect 75 million people annually. It is reportedly absent, however, from west and central Africa due to the high prevalence of the Duffy negative phenotype in the indigenous populations. Despite this, non-African travellers consistently return to their own countries with <it>P. vivax </it>malaria after visiting this region. An attempt was made, therefore, to detect the presence of <it>P. vivax </it>parasites in blood samples collected from the indigenous populations of west and central Africa.</p> <p>Methods</p> <p>Parasite species typing (for all four human malaria parasites) was carried out by PCR on 2,588 blood samples collected from individuals from nine African malaria-endemic countries.</p> <p>Results</p> <p>Most infections (98.5%) were <it>Plasmodium falciparum</it>, <it>Plasmodium malariae </it>was identified in 8.5% of all infections, and <it>Plasmodium ovale </it>in 3.9%. The prevalence of both parasites varied greatly by country. Only one case of <it>P. vivax </it>was detected from Sao Tome, an island off the west coast of Africa, confirming the scarcity of this parasite in Africa.</p> <p>Conclusion</p> <p>The prevalence of <it>P. vivax </it>in local populations in sub-Saharan Africa is very low, despite the frequent identification of this parasite in non-African travellers.</p

The sudden death of Alaric I (c. 370–410AD), the vanquisher of Rome: A tale of malaria and lacking immunity

BACKGROUND Alaric I (c. 370-410AD), King of the Visigoths, sacked Rome for the second time in over eight centuries of history. Historians suggest that malaria, probably contracted either in Rome or in the Pontine Marshes, was responsible for his sudden death in Cosenza (Calabria) in the autumn of 410AD, where he was allegedly buried in the River Busento. In this article, we aim to examine this hypothesis through a full pathographic reassessment of the most likely cause of Alaric's demise. METHODS To achieve this, we resorted to a dual philological-medical approach: clinical likelihood and malaria seasonality coupled with primary historical sources (mainly Jordanes' work De origine actibusque Getarum) and the reconstruction of the itineraries followed by Alaric and his army after the sack of Rome. RESULTS Sudden death is caused by several factors. The possibility that Alaric died of a cardiovascular disease was discarded since no description of potentially pathological signs emerged from the available sources. Given his lack of semi-immunity, falciparum malaria was considered as the most likely cause of his demise. It took him over two months to reach the coasts of Calabria during the peak of malaria's transmission (summer-autumn). During the march, Alaric did not suffer from recurrent fevers or other ailments, which would have been reported by historians. CONCLUSION The scenario emerging from this multidisciplinary reanalysis allows us to hypothesise that Plasmodium falciparum malaria, contracted during his journey through Calabria, was the most likely candidate responsible for Alaric's unexpected demise

Molecular detection of human papillomavirus (HPV) in highly fragmented DNA from cervical cancer biopsies using double-nested PCR

Archived Formalin-Fixed Paraffin-Embedded (FFPE) tissue specimens can be a valuable source of human papillomavirus (HPV) nucleic acids for molecular biological analyses in retrospective studies. Although successful amplification with polymerase chain reaction (PCR) is essential for analysis of HPV DNA extracted from cervical FFPE specimens, extensive DNA damage due to cross-linking and fragmentation results in poor yield. Therefore, techniques to improve the diagnostic rate and sensitivity from FFPE tissues through PCR is highly desired and of wider interest. To overcome this, a highly sensitive double-nested PCR methodology was designed and optimized for limited-resource laboratories coupled with an organic extraction of DNA. This method allows the detection of a broad range of HPV genotypes and also allowing the sequencing of the final amplicon. Validation of the new approach developed was done with an automated DNA extraction coupled with Real Time PCR. Results showed that the proposed method achieves 96.3% of HPV detection as compared to 100% Abbott m2000rt used as ‘gold standard’. Moreover, the concordance rate between the two methods was equal for detecting HPV -16 or -18 genotypes. Nevertheless, the newly introduced assay has an advantage of: • Simultaneously identifying broad range of HPV genotypes besides HPV-16 and -18 from clinical samples. • It is an easy and cost-effective method that can be beneficial in resource-limited setting and can be employed for various molecular applications. • The method is indicated for highly degraded FFPE samples. Method name: Double-nested PCR for detecting and genotyping HPV, Keywords: HPV, FFPE, DNA, Double-nested PCR, RFLP, DNA sequencin