Pinboard (jm) https://pinboard.in/u:jm/public/ recent bookmarks from jm A new discovery about carbon dioxide is challenging decades-old ventilation doctrine 2024-06-09T14:12:36+00:00 https://www.statnews.com/2024/06/04/co2-ventilation-research-virus-airborne-life-haddrell-celebs/ jm viruses co2 carbon-dioxide sars-cov-2 covid-19 air-quality air health https://pinboard.in/u:jm/b:8314d8702e39/ High number of SARS-CoV-2 persistent infections uncovered in the UK 2024-01-05T16:52:49+00:00 https://www.medrxiv.org/content/10.1101/2023.01.29.23285160v1 jmPersistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may act as viral reservoirs that could seed future outbreaks, give rise to highly divergent lineages, and contribute to cases with post-acute [covid] sequelae (Long Covid). However, the population prevalence of persistent infections, their viral load kinetics, and evolutionary dynamics over the course of infections remain largely unknown. We identified 381 infections lasting at least 30 days, of which 54 lasted at least 60 days. These persistently infected individuals had more than 50% higher odds of self-reporting Long Covid compared to the infected controls, and we estimate that 0.09-0.5% of SARS-CoV-2 infections can become persistent and last for at least 60 days. In nearly 70% of the persistent infections we identified, there were long periods during which there were no consensus changes in virus sequences, consistent with prolonged presence of non-replicating virus. Our findings also suggest reinfections with the same major lineage are rare and that many persistent infections are characterised by relapsing viral load dynamics. Furthermore, we found a strong signal for positive selection during persistent infections, with multiple amino acid substitutions in the Spike and ORF1ab genes emerging independently in different individuals, including mutations that are lineage-defining for SARS-CoV-2 variants, at target sites for several monoclonal antibodies, and commonly found in immunocompromised patients. This work has significant implications for understanding and characterising SARS-CoV-2 infection, epidemiology, and evolution. ]]> long-covid infection viruses covid-19 sars-cov-2 evolution medicine health uk epidemiology https://pinboard.in/ https://pinboard.in/u:jm/b:674914a0c0af/ SARS-CoV-2 is a "textbook virus" 2023-03-28T08:58:35+00:00 https://twitter.com/michaelmina_lab/status/1640594589705723906 jmIve written SARS-CoV-2 is a “textbook virus” • Textbook does NOT mean mild; • Textbook viruses kill people; • Textbook viruses harm long-term immunity; • Textbook viruses cause dizzying amounts of poorly understood debilitating problems I explain w examples here! ]]> virology covid-19 sars-cov-2 viruses medicine https://pinboard.in/ https://pinboard.in/u:jm/b:04bb6d4dd486/ Study of 500,000 Medical Records Links Viruses to Alzheimer's Again And Again 2023-01-31T15:00:01+00:00 https://www.sciencealert.com/study-of-500000-medical-records-links-viruses-to-alzheimers-again-and-again jm Around 80 percent of the viruses implicated in brain diseases were considered 'neurotrophic', which means they could cross the blood-brain barrier. "Strikingly, vaccines are currently available for some of these viruses, including influenza, shingles (varicella-zoster), and pneumonia," the researchers write. "Although vaccines do not prevent all cases of illness, they are known to dramatically reduce hospitalization rates. This evidence suggests that vaccination may mitigate some risk of developing neurodegenerative disease." The impact of viral infections on the brain persisted for up to 15 years in some cases. And there were no instances where exposure to viruses was protective. ]]> viruses health medicine vaccines vaccination alzheimers parkinsons diseases https://pinboard.in/ https://pinboard.in/u:jm/b:9ed436edbf2c/ ‘Immunity debt’ 2022-11-14T18:04:08+00:00 https://globalnews.ca/news/9272293/immunity-debt-covid-19-misinformation/ jmThe term “immunity debt” is circulating widely online as an explanation for a significant surge in respiratory illness in Canada [... This] hypothesis suggests people’s immune systems are weaker now, due to a lack of exposure to viruses while observing COVID-19 public health measures over the last two-and-a-half years. But this notion [...] is simply not true, says Colin Furness, an infection control epidemiologist and assistant professor in the faculty of information at the University of Toronto. “That is, in my estimation, and any immunologist will tell you this, nonsense,” he said. Dr. Samira Jeimy, an allergist and clinical immunologist at St Joseph’s Health Care London, agrees, saying the idea that one’s immune system can be weakened due to lack of exposure to illness “shows a basic lack of understanding of how the immune system works.” “There’s almost like an old wives tale, that you need to get sick to develop a healthy immune system. That’s actually not true.”]]> immunity immunology covid-19 rsv viruses health medicine immunity-debt misinformation https://pinboard.in/ https://pinboard.in/u:jm/b:841a2cc1d747/ The hygiene hypothesis doesn't apply to viruses 2022-10-14T15:00:16+00:00 https://caitlinrivers.substack.com/p/where-are-we-with-the-hygiene-hypothesis jmAlmost no virus is protective against allergic disease or other immune diseases. In fact, infections with viruses mostly either contribute to the development of those diseases or worsen them. The opposite is true of bacteria. Pets are good, though:
We've also noticed that people who live on farms have fewer of these diseases because they're exposed to -- for lack of a better term -- the fecal material of animals. And what we have found is that it's due to these commensal bacteria. That is one of the components that helps us keep a healthy immune system. Most of us will probably not adopt farm life. But we can have a pet, we can have a dog.
]]> pets viruses bacteria hygiene hygiene-hypothesis health immune-system allergies farms https://pinboard.in/ https://pinboard.in/u:jm/b:2dc80a6fe773/ Intrahost evolution and forward transmission of a novel SARS-CoV-2 Omicron BA.1 subvariant 2022-06-01T13:12:57+00:00 https://www.medrxiv.org/content/10.1101/2022.05.25.22275533v1 jmPersistent SARS-CoV-2 infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. It has been speculated that the emergence of antigenically diverse SARS-CoV-2 variants such as the Omicron variant may be the result of intra-host viral evolution driven by suboptimal immune responses, which must be followed by forward transmission. However, while intrahost evolution has been documented, to our knowledge no direct evidence of subsequent forward transmission is available to date. Here we describe the emergence of an Omicron BA.1 sub-lineage with 8 additional amino acid substitutions within the spike (E96D, L167T, R346T, L455W, K458M, A484V, H681R, A688V) in an immune-compromised host along with evidence of 5 forward transmission cases. Our findings show that the Omicron BA.1 lineage can further diverge from its exceptionally mutated genome during prolonged SARS-CoV-2 infection; highlighting an urgent need to employ therapeutic strategies to limit duration of infection and spread in vulnerable patients. ]]> variants sars-cov-2 covid-19 evolution papers preprints immunocompromise viruses omicron https://pinboard.in/ https://pinboard.in/u:jm/b:70b0af80fe6d/ rMA 15 - 15 passages resulted in a very pathogenic variant of SARS-CoV 2022-01-26T22:37:26+00:00 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1769406/ jm viruses rma-15 sars-cov https://pinboard.in/ https://pinboard.in/u:jm/b:e2cc87f1ea1f/ Viral load is the main predictor of COVID-19 transmissibility 2021-02-03T09:47:49+00:00 https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30985-3/fulltext jm viral-load viruses covid-19 transmission spain https://pinboard.in/ https://pinboard.in/u:jm/b:75011a482a87/ Seasonality of Respiratory Viral Infections | Annual Review of Virology 2021-01-14T11:21:53+00:00 https://www.annualreviews.org/doi/full/10.1146/annurev-virology-012420-022445#abstractSection jmThe seasonal cycle of respiratory viral diseases has been widely recognized for thousands of years, as annual epidemics of the common cold and influenza disease hit the human population like clockwork in the winter season in temperate regions. Moreover, epidemics caused by viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) and the newly emerging SARS-CoV-2 occur during the winter months. The mechanisms underlying the seasonal nature of respiratory viral infections have been examined and debated for many years. The two major contributing factors are the changes in environmental parameters and human behavior. Studies have revealed the effect of temperature and humidity on respiratory virus stability and transmission rates. More recent research highlights the importance of the environmental factors, especially temperature and humidity, in modulating host intrinsic, innate, and adaptive immune responses to viral infections in the respiratory tract. Here we review evidence of how outdoor and indoor climates are linked to the seasonality of viral respiratory infections. We further discuss determinants of host response in the seasonality of respiratory viruses by highlighting recent studies in the field. ]]> infection viruses colds flu covid-19 seasonality diseases https://pinboard.in/ https://pinboard.in/u:jm/b:06f8b10472ac/ Florian Krammer on the current SARS-CoV-2 vaccine candidates 2020-09-28T13:51:34+00:00 https://twitter.com/florian_krammer/status/1310372301314101250 jm florian-krammer vaccines sars-cov-2 covid-19 viruses https://pinboard.in/ https://pinboard.in/u:jm/b:de8740457a81/ Cillian De Gascun on Twitter: "A short thread on PCR #SARSCoV2" 2020-09-14T12:04:34+00:00 https://twitter.com/CillianDeGascun/status/1305250887246458880 jm ireland covid-19 testing ct-levels viral-load viruses cillian-de-gascun twitter https://pinboard.in/ https://pinboard.in/u:jm/b:6c88f66d42e2/ "Three new important studies came out in the past week about kids & COVID-19" 2020-08-04T10:18:09+00:00 https://twitter.com/meganranney/status/1289192833790877698 jm parenting kids schools covid-19 transmission pandemics viruses sars-cov-2 https://pinboard.in/ https://pinboard.in/u:jm/b:878fee02a9e0/ Why Aren't We Talking More About Ventilation? - The Atlantic 2020-07-31T09:28:03+00:00 https://www.theatlantic.com/health/archive/2020/07/why-arent-we-talking-more-about-airborne-transmission/614737/ jmIt seems baffling that despite mounting evidence of its importance, we are stuck practicing hygiene theater — constantly deep cleaning everything — while not noticing the air we breathe. How is it that six months into a respiratory pandemic, we still have so little guidance about this all-important variable, the very air we breathe? ]]> hygiene-theatre deep-cleaning covid-19 aerosols infection air viruses transmission zeynep-tufekci https://pinboard.in/ https://pinboard.in/u:jm/b:55ca0138e0f4/ Wearing masks may reduce severity of COVID-19, if it is caught 2020-07-13T11:30:58+00:00 https://twitter.com/Bob_Wachter/status/1281786641456205825 jm covid-19 bob-wachter virology masks facemasks theories viruses infection https://pinboard.in/ https://pinboard.in/u:jm/b:979fb854b505/ Rapid, inexpensive home testing for COVID-19 may get us out of this mess before a vaccine 2020-07-05T23:07:41+00:00 https://blogs.jwatch.org/hiv-id-observations/index.php/rapid-inexpensive-home-testing-for-covid-19-may-get-us-out-of-this-mess-before-a-vaccine/2020/07/05/ jmWe should welcome [rapid covid] tests, even if less accurate, and broadly adopt them for widespread community use. Here’s why: They will be cheap. Estimates are that they would cost between 1 and 5 dollars. That’s around the price of a cup of coffee. They can be done on saliva. No brain biopsy required. They can be done frequently. Every day for college students, or healthcare workers, or bus drivers? Every third day for everyone? They will answer the key question — am I contagious to others right now? Finally, and most importantly, they will answer this last question quickly. Results back in less than an hour. Anyone with a positive test can self-isolate, be reported to public health officials, participate in a contact tracing program, and be monitored for symptoms. Maybe pre-emptive antiviral therapy will prevent severe illness. We can choose to do a rapid home test any day we go to work, or to the gym, or to meet friends in a restaurant, or to attend a concert, or to pray in a house of worship, or to visit an elder loved one, or indeed partake in any activity we do in groups that now sadly may sustain the pandemic. And for those worried about lack of sensitivity, two items of reassurance. First, false negatives are less likely when people have the highest amounts of virus in saliva and respiratory secretions — and this is when they’re most contagious to others. If the test is falsely negative due to low titers of virus, it may not matter very much. Second, this modeling study finds that the frequency of testing is the key determinant of how well a broad testing strategy will limit the spread of the virus. It’s even more important than test sensitivity, and evidence that imperfect testing is better than no testing at all. ]]> testing covid-19 pcr rt-pcr false-positives false-negatives viruses https://pinboard.in/ https://pinboard.in/u:jm/b:866b1f021772/ The Risks - Know Them - Avoid Them 2020-05-11T14:09:49+00:00 https://www.erinbromage.com/post/the-risks-know-them-avoid-them jm Ignoring the terrible outbreaks in nursing homes, we find that the biggest outbreaks are in prisons, religious ceremonies, and workplaces, such a meat packing facilities and call centers. Any environment that is enclosed, with poor air circulation and high density of people, spells trouble. [....] Basically, as the work closures are loosened, and we start to venture out more, possibly even resuming in-office activities, you need to look at your environment and make judgments. How many people are here, how much airflow is there around me, and how long will I be in this environment. If you are in an open floorplan office, you really need critically assess the risk (volume, people, and airflow). If you are in a job that requires face-to-face talking or even worse, yelling, you need to assess the risk. If I am outside, and I walk past someone, remember it is “dose and time” needed for infection. You would have to be in their airstream for 5+ minutes for a chance of infection. While joggers may be releasing more virus due to deep breathing, remember the exposure time is also less due to their speed. ]]> covid-19 health viruses infection epidemiology diseases work https://pinboard.in/ https://pinboard.in/u:jm/b:90456ebc25f8/ "A recent Nature paper reveal a remarkable trick SARS-Cov-2 learned that makes it nastier than the first SARS" 2020-04-06T09:09:07+00:00 https://threadreaderapp.com/thread/1246975275021348865.html jm viruses sars covid-19 sars-cov-2 medicine science https://pinboard.in/ https://pinboard.in/u:jm/b:8dcd0a0c6047/ Professor Sara Sawyer's Decon Station Instructions 2020-03-23T12:20:58+00:00 https://www.colorado.edu/mcdb/coronavirus-information/professor-sara-sawyers-decon-station-instructions?fbclid=IwAR357fQ9wQirpAPn9oxExZ7r8we8-yplmzA61eKGcrokFae6a3wQbNeDoFc jmIf you are sheltering-in-place and feel that you need to take extra precautions for a high-risk member of your household, you can decontaminate things before they come into your house.  Read on if you want to know how. This post addresses common questions that I am getting about mail, fruits, groceries, etc. The following advice is my own, tailored for this specific situation, and is the best advice I can come up with based on the extensive biosafety training that I have received as a research scientist who works with human viruses. (via Pam)]]> biosafety viruses covid-19 decontamination sterilising sterilizing health via:pam https://pinboard.in/ https://pinboard.in/u:jm/b:f8df1d799b20/ Jen Heemstra on Remdesivir 2020-03-23T12:02:12+00:00 https://twitter.com/jenheemstra/status/1241823517181698052 jm remdesivir viruses science chemistry medicine drugs covid-19 treatment https://pinboard.in/ https://pinboard.in/u:jm/b:ab0845dd7de2/ Nextstrain / narratives / ncov / sit-rep / 2020-03-05 2020-03-09T11:55:04+00:00 https://nextstrain.org/narratives/ncov/sit-rep/2020-03-05 jm genetics phylogenetics nextstrain covid-19 diseases epidemics viruses https://pinboard.in/ https://pinboard.in/u:jm/b:53d503bf8a50/ A biotech firm made a smallpox-like virus on purpose. Nobody seems to care - Bulletin of the Atomic Scientists 2020-02-22T22:02:25+00:00 https://thebulletin.org/2020/02/a-biotech-firm-made-a-smallpox-like-virus-on-purpose-nobody-seems-to-care/ jmThe loosely regulated market for synthetic DNA, the normalization of synthetic orthopoxvirus research, and a large number of capable facilities and researchers creates an environment in which a rogue state, unscrupulous company, reckless scientist, or terrorist group could potentially reintroduce one of the worst microbial scourges in human history. Unless world bodies, national governments, and scientific organizations put in place stronger safeguards on synthetic virus research, the next press release touting a new breakthrough in synthetic biology might announce that an unknown scientist in an obscure lab has successfully resurrected the smallpox virus. ]]> smallpox weapons scary diseases biological-weapons dna viruses https://pinboard.in/ https://pinboard.in/u:jm/b:82ca1901a817/ Brain Cells Share Information With Virus-Like Capsules - The Atlantic 2018-01-12T23:07:48+00:00 https://www.theatlantic.com/science/archive/2018/01/brain-cells-can-share-information-using-a-gene-that-came-from-viruses/550403/ jm...a gene called Arc which is active in neurons, and plays a vital role in the brain. A mouse that’s born without Arc can’t learn or form new long-term memories. If it finds some cheese in a maze, it will have completely forgotten the right route the next day. “They can’t seem to respond or adapt to changes in their environment,” says Shepherd, who works at the University of Utah, and has been studying Arc for years. “Arc is really key to transducing the information from those experiences into changes in the brain.” Despite its importance, Arc has been a very difficult gene to study. Scientists often work out what unusual genes do by comparing them to familiar ones with similar features—but Arc is one-of-a-kind. Other mammals have their own versions of Arc, as do birds, reptiles, and amphibians. But in each animal, Arc seems utterly unique—there’s no other gene quite like it. And Shepherd learned why when his team isolated the proteins that are made by Arc, and looked at them under a powerful microscope. He saw that these Arc proteins assemble into hollow, spherical shells that look uncannily like viruses. “When we looked at them, we thought: What are these things?” says Shepherd. They reminded him of textbook pictures of HIV, and when he showed the images to HIV experts, they confirmed his suspicions. That, to put it bluntly, was a huge surprise. “Here was a brain gene that makes something that looks like a virus,” Shepherd says. That’s not a coincidence. The team showed that Arc descends from an ancient group of genes called gypsy retrotransposons, which exist in the genomes of various animals, but can behave like their own independent entities.* They can make new copies of themselves, and paste those duplicates elsewhere in their host genomes. At some point, some of these genes gained the ability to enclose themselves in a shell of proteins and leave their host cells entirely. That was the origin of retroviruses—the virus family that includes HIV. ]]> brain evolution retroviruses viruses genes arc gag proteins memory biology https://pinboard.in/ https://pinboard.in/u:jm/b:96a8d10c1752/ The World Is Getting Hacked. Why Don’t We Do More to Stop It? - The New York Times 2017-05-15T09:09:01+00:00 https://www.nytimes.com/2017/05/13/opinion/the-world-is-getting-hacked-why-dont-we-do-more-to-stop-it.html jmFirst, companies like Microsoft should discard the idea that they can abandon people using older software. The money they made from these customers hasn’t expired; neither has their responsibility to fix defects. Besides, Microsoft is sitting on a cash hoard estimated at more than $100 billion (the result of how little tax modern corporations pay and how profitable it is to sell a dominant operating system under monopolistic dynamics with no liability for defects). At a minimum, Microsoft clearly should have provided the critical update in March to all its users, not just those paying extra. Indeed, “pay extra money to us or we will withhold critical security updates” can be seen as its own form of ransomware. In its defense, Microsoft probably could point out that its operating systems have come a long way in security since Windows XP, and it has spent a lot of money updating old software, even above industry norms. However, industry norms are lousy to horrible, and it is reasonable to expect a company with a dominant market position, that made so much money selling software that runs critical infrastructure, to do more. Microsoft should spend more of that $100 billion to help institutions and users upgrade to newer software, especially those who run essential services on it. This has to be through a system that incentivizes institutions and people to upgrade to more secure systems and does not force choosing between privacy and security. Security updates should only update security, and everything else should be optional and unbundled. More on this twitter thread: https://twitter.com/zeynep/status/863734133188681732]]> security microsoft upgrades windows windows-xp zeynep-tufekci worms viruses malware updates software https://pinboard.in/ https://pinboard.in/u:jm/b:5288449ba31e/ Global ‘Wana’ Ransomware Outbreak Earned Perpetrators [just] $26,000 So Far 2017-05-13T20:25:22+00:00 https://krebsonsecurity.com/2017/05/global-wana-ransomware-outbreak-earned-perpetrators-26000-so-far/ jmAs thousands of organizations work to contain and clean up the mess from this week’s devastating Wana ransomware attack, the fraudsters responsible for releasing the digital contagion are no doubt counting their earnings and congratulating themselves on a job well done. But according to a review of the Bitcoin addresses hard-coded into Wana, it appears the perpetrators of what’s being called the worst ransomware outbreak ever have made little more than USD $26,000 so far from the scam. ]]> money fraud ransomware wana brian-krebs bitcoin cryptocurrency viruses https://pinboard.in/ https://pinboard.in/u:jm/b:885d7eff43ad/ Microsoft Security Essentials reporting false positives on the Bitcoin blockchain 2014-05-16T13:21:03+00:00 https://answers.microsoft.com/en-us/protect/forum/mse-protect_updating/microsoft-security-essentials-reporting-false/0240ed8e-5a27-4843-a939-0279c8110e1c jmEarlier today, a virus signature from the virus "DOS/STONED" was uploaded into the Bitcoin blockchain, which allows small snippets of text to accompany user transactions with bitcoin.  Since this is only the virus signature and not the virus itself, there apparently is no danger to users in any way.  However, MSE recognizes the signature for the virus and continuously reports it as a threat, and every time it deletes the file, the bitcoin client will simply re-download the missing blockchain. What a heinous prank! Hilarity ensues (via gwire)]]> via:gwire av antivirus false-positives fp blockchain microsoft bitcoin pranks viruses https://pinboard.in/ https://pinboard.in/u:jm/b:282b4844c93b/ Russia: Hidden chips 'launch malware attacks from irons' 2013-10-28T22:17:00+00:00 http://www.bbc.co.uk/news/blogs-news-from-elsewhere-24707337 jmCyber criminals are planting chips in electric irons and kettles to launch spam [jm: actually, malware] attacks, reports in Russia suggest. State-owned channel Rossiya 24 even showed footage of a technician opening up an iron included in a batch of Chinese imports to find a "spy chip" with what he called "a little microphone". Its correspondent said the hidden devices were mostly being used to spread viruses, by connecting to any computer within a 200m (656ft) radius which were using unprotected Wi-Fi networks. Other products found to have rogue components reportedly included mobile phones and car dashboard cameras. ]]> wifi viruses spam malware security russia china toasters kettles appliances https://pinboard.in/ https://pinboard.in/u:jm/b:0035e7ed34c4/ A Closer Look: Email-Based Malware Attacks 2012-06-21T13:00:26+00:00 http://krebsonsecurity.com/2012/06/a-closer-look-recent-email-based-malware-attacks/ jm via:fanf fail malware filtering av smtp email viruses https://pinboard.in/ https://pinboard.in/u:jm/b:0e1513006509/ The Cybercrime Wave That Wasn’t - NYTimes.com 2012-04-16T09:51:36+00:00 http://www.nytimes.com/2012/04/15/opinion/sunday/the-cybercrime-wave-that-wasnt.html?src=tp jm fail science pr press cybercrime ms via:mark-russinovitch data surveys spam malware viruses phishing https://pinboard.in/ https://pinboard.in/u:jm/b:bbfa0250ffd0/ Computer Virus Hits U.S. Drone Fleet 2011-10-07T20:25:09+00:00 http://www.wired.com/dangerroom/2011/10/virus-hits-drone-fleet/ jm air-gap security drones viruses firewalls https://pinboard.in/ https://pinboard.in/u:jm/b:afc684a17975/ Computer gamers solve problem in AIDS research that puzzled scientists for years 2011-09-19T12:30:01+00:00 http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/ jm foldit gaming games science biology aids viruses protease protein-folding proteins vr https://pinboard.in/ https://pinboard.in/u:jm/b:a50dad86da5a/ Signature-based AV is failing 2010-06-29T13:09:37+00:00 http://krebsonsecurity.com/2010/06/anti-virus-is-a-poor-substitute-for-common-sense/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+KrebsOnSecurity+%28Krebs+on+Security%29 jm via:tzink malware av fail accuracy detection false-negatives scanners viruses https://pinboard.in/u:jm/b:ef5705175552/