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Spread and Control of Microbes
Published in Jim Lynch, What Is Life and How Might It Be Sustained?, 2023
From my own experience as Dean of a Biomedical School with a large Nutrition Department, these means all make sense and in my opinion a supplement like vitamin D can be important as so many people are deficient. Just how effective all this could be is still unclear but most of us, including Moseley, considered that a vaccine is the only effective measure. The only problem is that most people with any background in the area, particularly the UK Government’s Chief Scientific Advisor Sir Patrick Vallance, a clinician who had previously been Chief Scientist to one of the world’s leading pharma companies Glaxo Smith Kline, saw that even with a fair wind behind the science the regulatory barriers with trials would mean that a vaccine would take at least 18 months to develop. A further complication was that there are several variants of the virus because of its mutations. Under the new WHO scheme, it developed the variants of concern from 2020 and countries of the first detection are:
Vaccines Don't Save Lives, Vaccination Does
Published in Norman Begg, The Remarkable Story of Vaccines, 2023
The R0 is used by mathematical modellers to predict what will happen to a disease in different scenarios. Mathematical models are theoretical simulations of disease transmission. These models can be used to work out the impact of control measures such as reducing social contact, and also the percentage of people that need to be vaccinated to achieve herd immunity and stop the disease spreading. With increasing computer power, the number of scenarios that can be modelled is almost limitless. However, models are based on all kinds of assumptions; how many contacts each person has with other people and for how long, how long an infectious person stays infectious for, how long people live for, and so on. In reality, society is much more complicated. Teenagers mix more amongst themselves than older people do, Londoners behave differently to people from Scotland, Turkish people have different social habits to Chinese. Infectious diseases also behave differently over time; as COVID-19 has shown, viruses can mutate, causing variants which may be more (or less) infectious and dangerous. Someone with a weakened immune system may take longer to get rid of the virus than a healthy person. Getting the R0 down through changing population behaviour has become the mantra for governments, but this calculation has many limitations, as society does not divide into neat predictable packages. Mathematical models are a useful tool, but are not the be all and end all. Knowing how much disease there is and where and how it is spreading is what counts.
Genomic Informatics in the Healthcare System
Published in Salvatore Volpe, Health Informatics, 2022
Genomic informatics is evolving from individual gene or single nucleotide polymorphism variant testing to exome or genome testing by the use of NGS technologies. The discovery of both rare and common variants has increased exponentially in the past few years. As we discussed above, many variants can confidently be designated but often have uncertain pathogenicity. In fact, only a few novel variants are sufficiently understood, and they can be considered for reporting to patients. For example, ACMG recommends that pathogenic variants in 59 genes be returned to tested patients regardless of the indication for sequencing. The association between variants within these genes and specific medical conditions in cardiology, oncology, and many other medical specialties are well established and should contribute to individual risk assessments or to justify additional screening (Table 21.3). Different outcomes are expected, and these are dependent on whether the NGS information and variants are returned to individuals or family members.
Association of epidemiological and clinical features with PCR cycle threshold values of SARS-CoV-2 infection: a cross-sectional study
Published in Pathogens and Global Health, 2023
Marlies Heudobler, Hansjörg Baurecht, Helen Schmied, Daniel Heudobler, Carmen Jochem, Anja M Sedlmeier, Andrea Weber, Stilla Bauernfeind, Michael Leitzmann, Bernd Salzberger, Benedikt M J Lampl
Our results have the following implications: It can be postulated that symptomatic SARS-CoV-2 positive patients are in general more infectious, based on lower Ct values in this group [33]. Most cases, symptomatic and asymptomatic, had intermediate Ct values and must be regarded as infectious at the time of diagnosis. The questions regarding transmission from asymptomatic cases can only be fully answered by regular close-knit testing, which, in practice, is neither achievable nor reasonable. In asymptomatic cases or cases presenting with intermediate or high Ct value at the time of first testing (asymptomatic/intermediate or high Ct value; 23%/73% of all/asymptomatic cases in our cohort), re-testing within short intervals could be an option to shorten isolation time considerably. For prevention strategies, infection control measures (particularly for potentially infected, asymptomatic cases), vaccination, and rapid diagnosis of symptomatic patients remain crucial with the occurrence of new, potentially more contagious variants of concern. As vaccination does not sufficiently protect against infection, testing will remain pivotal in vulnerable settings such as elderly care homes and hospitals in the future. To confirm our results for other variants and in vaccinated individuals, further research is necessary. Uniform standards for reporting PCR results including Ct values would be of use for the public health authorities’ containment efforts.
Feasibility and early clinical impact of precision medicine for late-stage cancer patients in a regional public academic hospital
Published in Acta Oncologica, 2023
Morten Ladekarl, Anne Krogh Nøhr, Mads Sønderkær, Simon Christian Dahl, Lone Sunde, Charles Vestereghem, Christophe Kamungu Mapendano, Charlotte Aaquist Haslund, Anja Pagh, Andreas Carus, Tamás Lörincz, Kinga Nowicka-Matus, Laurids Ø. Poulsen, René Johannes Laursen, Karen Dybkær, Birgitte Klindt Poulsen, Jens Brøndum Frøkjær, Anja Høegh Brügmann, Anja Ernst, Alkwin Wanders, Martin Bøgsted, Inge Søkilde Pedersen
The bioinformatic procedure used in this study has previously been described [27]. Using the Genome Analysis Tool Kit (GATK) the process largely follows the GATK-recommendations [28]. The filtered variant file (VCF) is uploaded together with information on sex, age, diagnosis, and detected fusion transcripts, gene losses or gains, to Qiagen Clinical Insight Interpret (QCI) for automatic classification of variants [29]. All variants of clinical significance are manually verified by visual inspection of the DNA and RNAseq data. Variants are classified as pathogenic, likely pathogenic, variants of unknown significance (VUS), or benign/likely benign [30]. QCI is also used prospectively to link variants and approved treatments or clinical trials into tiers [31]: Tier 1 – variants of strong clinical significance and tier 2 – variants of potential clinical significance. Tier 3 – variants of unknown significance – is in the present analysis merged with variants with no QCI-annotation.
Antibodies to watch in 2022
Published in mAbs, 2022
Hélène Kaplon, Alicia Chenoweth, Silvia Crescioli, Janice M. Reichert
As has been widely reported, the initial cases of infection with SARS-CoV-2 were first observed in China in late 2019, and this highly transmissible and often deadly coronavirus triggered a global pandemic that remains in effect 2 y later. When [accessed in early November 2021, the Johns Hopkins University of Medicine Coronavirus Research Center (coronavirus.jhu.edu/map.html) indicated that nearly 250 million people located world-wide have been infected and over 5 million of these have died. Cases of infection in the US exceed 45 million, and approximately 725,000 of the infected people have died. The virus has mutated multiple times, resulting in the so-called variants of concern, some of which are more transmissible than the original virus. Such variants of concern include (1) alpha (B.1.1.7 (501Y.V1)), which contains an N501Y mutation in the spike protein; (2) beta (B.1.351 (501Y.V2)), which has nine mutations (L18F, D80A, D215G, Δ242-244, K417N, E484K, N501Y, D614G, and A701V); (3) gamma (P.1 (501Y.V3)), which shares mutations with the Beta variant; and (4) delta (B.1.617.2), which contains a substantial number of mutations and is more than twice as transmissible as the original strain.3,4