6 research outputs found
APOBEC3G Variants and Protection against HIV-1 Infection in Burkina Faso.
No full textStudies on host factors, particularly the APOBEC3G gene, have previously found an association with AIDS progression in some populations and against some HIV-1 strains but not others. Our study had two main objectives: firstly, to screen a population from Burkina Faso for three variants of APOBEC3G previously described, and secondly to analyze the effect of these three variants and their haplotypes on HIV-1 infection with Circulating Recombinant Forms (CRFs) present in Burkina Faso. This case control study involved 708 seropositive and seronegative individuals. Genotyping was done by the TaqMan allelic discrimination method. Minor allele frequencies of rs6001417 (p<0.05), rs8177832 (P<0.05), and rs35228531 (P<0.001) were higher in seronegative subjects. The rs6001417 and rs8177832 SNPs were associated with HIV-1 infection in an additive model (P<0.01). Furthermore the SNP rs35228531 was also associated with HIV-1 infection in a dominant model (P<0.001). Odds ratio analysis of genotypes and alleles of the different APOBEC3G variants showed that there is a strong association between the minor genetic variants, genotype of the three SNPs, and HIV-1 status. Haplotype analysis demonstrated that rs6001417, rs8177832, and rs35228531 are in linkage disequilibrium. The haplotype GGT from the rs6001417, rs8177832 and rs35228531 respectively has a protective effect OR = 0.54 [0.43-0.68] with P<0.001. There was also associations between the haplotypes GGC OR = 1.6 [1.1;-2.3] P<0.05, and CGC OR = 5.21 [2.4-11.3] P<0.001, which increase the risk of infection by HIV-1 from almost two (2) to five (5) fold. This study demonstrates an association of rs6001417, rs8177832, and rs35228531 of APOBEC3G with HIV-1 infection in a population from Burkina Faso
Distribution of the cases and controls haplotypes.
No full text<p>Distribution of the cases and controls haplotypes.</p
Haploview APOBEC3G linkage disequilibrium plots for case and controls.
No full text<p>The figures are oriented 5’ to 3’, right to left, relative to the gene orientation on the minus strand. Fig 1a represents the LD plot of the case pairwise D’ between markers, and Fig 1b shows the LD plot of the control pairwise D’ between markers. Strong LD is indicated by red, while pink indicate uninformative values. LD blocks were created with the default algorithm in the Haploview software (version 4.1) that creates 95% confidence bounds. D’ was considered strong where 95% of the comparisons made are informative.</p
Crossbreeding and consanguinity management in pig farms in the departments of Ouémé and Plateau in Benin
No full textpeer reviewedBackground: The improvement in pig zootechnical performances is a common practice in Benin. This improvement of the performances is made by the choice of the best reproducers in farms and the crossbreeding between the different breeds. Aim: This study aims to characterize practices related to consanguinity management in pigs reared in Ouémé and Plateau. Materials and Methods: Crossbreeding and consanguinity data were collected from 60 farms in these two departments. Frequencies and averages were calculated and compared between departments, genetic types, and origin of progenitors. Results: The majority of the investigated pig farmers in both departments were married men of primary or secondary education level. Most of them cross animals without a specific crossbreeding scheme. These crossings were performed to a greater extent (p<0.05) in Ouémé (94.28%) than in Plateau (52%). In general, farmers cross improved animals of high breeding values with the crossbred ones. These crossings were mainly performed to improve zootechnical performances. Renewing animals were commonly chosen from the farm or were provided from nearby farms. The majority of pig breeders in Ouémé (100%) and Plateau (86.67%) obtained reproductive animals from nearby farms. Males and females were sometimes bought from the same farm or from farms that pig breeders have sold reproductive animals in the previous years. In the case of selection within their own farm, male and female progenitors are separated at puberty by the majority of the breeders of Plateau (42.11%) and Ouéme (50%). Inbred mating was reported by breeders. More than half of breeders mate animals having a parental link in both departments. The mating was performed between animals of the same mother in 37.93% of farms in Ouémé and in 45.46% in Plateau. The main consanguinity consequences mentioned by the breeders were the high mortality at birth and weaning, piglets’ weakness at the birth, the slow growth, and the decrease in litter size. Sows with at least one parent from external farm had a litter size at birth and weaning and a live-born piglets’ number significantly higher than sows with both parents from the same farm. Conclusion: Rigorous monitoring of crossing and the filial links are necessary for pig farms for ensuring the improvement of zootechnical performances. Dotché, et al. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated
Emergence and spread of the SARS-CoV-2 omicron (BA.1) variant across Africa: an observational study.
No full textIn mid-November, 2021, the SARS-CoV-2 omicron variant (B.1.1.529; BA.1 sublineage) was detected in southern Africa, prompting international travel restrictions. We aimed to investigate the spread of omicron BA.1 in Africa. In this observational study, samples from patients infected with SARS-CoV-2 from 27 laboratories in 24 African countries, collected between June 1, 2021 and April 14, 2022, were tested for omicron BA.1 and delta (B.1.617.2) variants using real-time RT-PCR. Samples that tested positive for BA.1 by RT-PCR and were collected before estimated BA.1 emergence according to epidemiological properties were excluded from downstream analyses. The diagnostic precision of the assays was evaluated by high-throughput sequencing of samples from four countries. The observed spread of BA.1 was compared with mobility-based mathematical simulations and entries for SARS-CoV-2 in the Global Initiative on Sharing All Influenza Data (GISAID) genomic database. We estimated the effective reproduction number (R ) at the country level considering the BA.1 fraction and the reported numbers of infections. Phylogeographical analyses were done in a Bayesian framework. Through testing of 13 294 samples from patients infected with SARS-CoV-2, we established that, by November-December, 2021, omicron BA.1 had replaced the delta variant of SARS-CoV-2 in all African subregions, following a south-north gradient, with a median R of 2·60 (95% CI 2·46-2·71). This south-north spread, established on the basis of PCR data, was substantiated by phylogeographical reconstructions, ancestral state reconstructions, and GISAID data. PCR-based reconstructions of country-level BA.1 predominance and the availability of BA.1 genomic sequences in GISAID correlated significantly in time (p=0·0002, r=0·78). The first detections of BA.1 in high-income settings beyond Africa were predicted accurately in time by mobility-based mathematical simulations (p<0·0001). Comparing PCR-based reconstructions with mobility-based mathematical simulations suggested that SARS-CoV-2 infections in Africa were under-reported by approximately ten times. Inbound travellers infected with BA.1, departing from five continents, were identified in six African countries by early December, 2021. Omicron BA.1 was widespread in Africa when travel bans were implemented, limiting their effectiveness. Combined with genomic surveillance and mobility-based mathematical modelling, PCR-based strategies can inform R and the geographical spread of emerging pathogens in a cost-effective and timely manner, and can guide evidence-based, non-pharmaceutical interventions such as travel restrictions or physical distancing. Bill & Melinda Gates Foundation. For the French, Portugese and Spanish translations of the abstract see Supplementary Materials section. [Abstract copyright: Copyright © 2025 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.
