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Biology subjects

Camacho, R.

Publications and source records attributed to Camacho, R..

2 recordsLinked to original sources
bioRxiv2019

Drivers of HIV-1 transmission: the Portuguese case

BackgroundPortugal has one of the most severe HIV-1 epidemic in Western Europe. Two subtypes circulate in parallel since the beginning of the epidemic. Comparing their transmission patterns and its association with transmitted drug resistance (TDR) is important to pinpoint transmission hotspots and to develop evidence-based treatment guidelines.\n\nMethods3599 HIV-1 naive patients collected between 2001 and 2014 were included in the study. Sequences obtained from drug resistance testing were used for subtyping, TDR determination and transmission clusters (TC) analyses.\n\nResultsSubtype B transmission was significantly associated with young males, while subtype G was associated with older heterosexuals. Young males infected with subtype B were more likely to be included in TC. Consistently, a decreasing trend of prevalence and transmission of subtype G in Portuguese originated people was observed. Active TCs were associated with subtype B-infected males residing in Lisbon. TDR was significantly different when comparing subtypes B (10.8% [9.5-12.2]) and G (7.6% [6.4-9.0]) (p=0.001).\n\nDiscussionTC analyses shows that the subtype B epidemic is active and fueled by young male patients residing in Lisbon and that transmission of subtype G in Portugal is decreasing. Despite similar treatment rates for both subtypes in Portugal, TDR is different between subtypes.

molecular biology↗
bioRxiv2019

Identifying microbial species by single-molecule DNA optical mapping and resampling statistics

Single molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Secondly, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Thirdly, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.

genomics↗