RegaDB: community-driven data management and analysis for infectious diseases.

SUMMARY RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyse patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface. Availability and implementation: Source code, binaries and documentation are available on http://rega.kuleuven.be/cev/regadb. RegaDB is written in the Java programming language, using a web-service-oriented architecture.publishersversionpublishe

Ascorbic Acid Has Superior Ex Vivo Antiproliferative, Cell Death-Inducing and Immunomodulatory Effects over IFN-alpha in HTLV-1-Associated Myelopathy

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Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients

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Viral phylogeny in court: the unusual case of the Valencian anesthetist.

A large and complex outbreak of hepatitis C virus in Valencia, Spain that began 25 years ago led to the prosecution and conviction of an anesthetist who was accused of infecting hundreds of his patients. Evolutionary analyses of viral gene sequences were presented as evidence in the trial, and these are now described in detail by González-Candelas and colleagues in a paper published in BMC Biology. Their study illustrates the challenges and opportunities that arise from the use of phylogenetic inference in criminal trials concerning virus transmission.publishersversionpublishe

The Impact of Genital Ulcers on HIV Transmission Has Been Underestimated—A Critical Review

Funding Information: Funding: V.M.’s work in this study has been completed as part of the ELTE Thematic Excellence Programme 2020 supported by the National Research, Development and Innovation Office (TKP2020-IKA-05). Publisher Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland.In the early 1990s, several observational studies determined that genital ulcer disease (GUD), in either the index or the exposed person, facilitates HIV transmission. Several meta-analyses have since presented associated risk ratios (RR) over the baseline per-act transmission probability (PATP) usually in the range of 2–5. Here we review all relevant observational studies and meta-analyses, and show that the estimation of RRs was, in most cases, biased by assuming the presence of GUD at any time during long follow-up periods, while active genital ulcers were present in a small proportion of the time. Only two studies measured the GUD co-factor effect in PATPs focusing on acts in which ulcers were present, and both found much higher RRs (in the range 11–112). We demonstrate that these high RRs can be reconciled with the studies on which currently accepted low RRs were based, if the calculations are restricted to the actual GUD episodes. Our results indicate that the effect of genital ulcers on the PATP of HIV might be much greater than currently accepted. We conclude that the medical community should work on the assumption that HIV risk is very high during active genital ulcers.publishersversionpublishe

Sexually transmitted infections, their treatment and urban change in colonial Leopoldville, 1910–1960

During the colonial period sexually transmitted infections (STIs) came to be recognised as a major public health problem in African cities. Thus, STI control and urban modernisation became deeply entangled as authorities redrew spatial and social boundaries to manage populations and their cross-cultural interaction. Public health measures, urban planning and policing were part of a coordinated effort to neutralise the potential impact of rapidly growing African urban migration on the Belgian Congo’s ‘model’ capital Leopoldville. While STI control was facilitated by new drugs (arsenicals, sulfonamides and antibiotics) to treat syphilis, chancroid, gonorrhoea and chlamydia (bacterial STIs), the effects of the 1929 economic crisis and urban social change illustrated the limits of colonial authority. Redesigning urban spaces and repressive measures to curb polygyny and prostitution operated in a parallel fashion with the expansion of health coverage, new treatments and awareness campaigns. To gain a better understanding of the evolution of STI incidence among African urban populations during the colonial period between 1910 and 1960, extensive archival records and secondary literature were consulted to assess the interplay between improved screening, diagnostic and therapeutic methods with demographic and social change. They show that STI rates, probably peaked during the pre-1929 period and apart from a short period in the early 1930s associated with mass screening, declined until becoming residual in the 1950s. Reflecting upon sanitary interventions and their broader dimensions, the article analyses the evolution of treatment regimes and their impact in the changing urban organisation and environment of the colony’s capital.publishersversionpublishe

A practical guide

Publisher Copyright: © 2022 Kiekens et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Systems mapping methods are increasingly used to study complex public health issues. Visualizing the causal relationships within a complex adaptive system allows for more than developing a holistic and multi-perspective overview of the situation. It is also a way of understanding the emergent, self-organizing dynamics of a system and how they can be influenced. This article describes a concrete approach for developing and analysing a systems map of a complex public health issue drawing on well-accepted methods from the field of social science while incorporating the principles of systems thinking and transdisciplinarity. Using our case study on HIV drug resistance in sub-Saharan Africa as an example, this article provides a practical guideline on how to map a public health problem as a complex adaptive system in order to uncover the drivers, feedback-loops and other dynamics behind the problem. Qualitative systems mapping can help researchers and policy makers to gain deeper insights in the root causes of the problem and identify complexity-informed intervention points.publishersversionpublishe

PCR detection of Burkholderia multivorans in water and soil samples

Background: Although semi-selective growth media have been developed for the isolation of Burkholderia cepacia complex bacteria from the environment, thus far Burkholderia multivorans has rarely been isolated from such samples. Because environmental B. multivorans isolates mainly originate from water samples, we hypothesized that water rather than soil is its most likely environmental niche. The aim of the present study was to assess the occurrence of B. multivorans in water samples from Flanders (Belgium) using a fast, culture-independent PCR assay. Results: A nested PCR approach was used to achieve high sensitivity, and specificity was confirmed by sequencing the resulting amplicons. B. multivorans was detected in 11 % of the water samples (n = 112) and 92 % of the soil samples (n = 25) tested. The percentage of false positives was higher for water samples compared to soil samples, showing that the presently available B. multivorans recA primers lack specificity when applied to the analysis of water samples. Conclusions: The results of the present study demonstrate that B. multivorans DNA is commonly present in soil samples and to a lesser extent in water samples in Flanders (Belgium)

Newly discovered archival data show coincidence of a peak of sexually transmitted diseases with the early epicenter of pandemic hiv-1

Funding Information: The research done by J.D.S. and A.-M.V. in this study has been supported in part by grant G.0692.14, funded by the Fonds voor Wetenschappelijk Onderzoek?Flanders (FWO, http://www.fwo.be/en/ (accessed on 28 July 2021)), Belgium. V.M.?s work in this study has been completed as part of the ELTE Thematic Excellence Programme 2020 supported by the National Research, Development and Innovation Office (TKP2020-IKA-05). Funding Information: Funding: The research done by J.D.S. and A.-M.V. in this study has been supported in part by grant G.0692.14, funded by the Fonds voor Wetenschappelijk Onderzoek—Flanders (FWO, http://www.fwo.be/en/ (accessed on 28 July 2021)), Belgium. V.M.’s work in this study has been completed as part of the ELTE Thematic Excellence Programme 2020 supported by the National Research, Development and Innovation Office (TKP2020-IKA-05). Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.To which extent STDs facilitated HIV-1 adaptation to humans, sparking the pandemic, is still unknown. We searched colonial medical records from 1906–1958 for Leopoldville, Belgian Congo, which was the initial epicenter of pandemic HIV-1, compiling counts of treated STD cases in both Africans and Europeans. Almost all Europeans were being treated, while for Africans, generalized treatment started only in 1929. Treated STD counts in Europeans thus reflect STD infection rates more accurately compared to counts in Africans. In Africans, the highest recorded STD treatment incidence was in 1929–1935, declining to low levels in the 1950s. In Europeans, the recorded treatment incidences were highest during the period 1910–1920, far exceeding those in Africans. Europeans were overwhelmingly male and had frequent sexual contact with African females. Consequently, high STD incidence among Europeans must have coincided with high prevalence and incidence in the city’s African population. The data strongly suggest the worst STD period was 1910–1920 for both Africans and Europeans, which coincides with the estimated origin of pandemic HIV-1. Given the strong effect of STD coinfections on HIV transmission, these new data support our hypothesis of a causal effect of STDs on the epidemic emergence of HIV-1.publishersversionpublishe

The epidemic emergence of HIV: what novel enabling factors were involved?

Humans acquired retroviruses from simians, mainly through bushmeat handling. All epidemically successful HIV groups started to spread in early 20th century, contrasting with the antiquity of T-cell lymphotropic viruses, implying that novel enabling factors were involved in HIV emergence. Here we review the Parenteral Serial Transmission and the Enhanced Heterosexual Transmission hypotheses for the adaptation and early spread of HIV. Epidemic start roughly coincides in time with peak genital ulcer disease in cities, suggesting a major role for sexual transmission. Only ill-adapted and rare HIV groups emerged after approximately 1950, when injections and transfusions attained their maximal levels, suggesting that if parenteral serial transmission was necessary for HIV adaptation, it had to be complemented by sexual transmission for HIV to reach epidemic potential