Scientists identify antibodies that can neutralize omicron

An international team of scientists have identified antibodies that neutralize omicron and other SARS-CoV-2 variants. These antibodies target areas of the virus spike protein that remain essentially unchanged as the viruses mutate. By identifying the targets of these “broadly neutralizing” antibodies on the spike protein, it might be possible to design vaccines and antibody treatments…

Scientists identify antibodies that can neutralize omicron

OMG, Omicron

Research is what I’m doing when I don’t know what I’m doing.

Wernher von Braun

For the past year and a half, if anyone wanted, they could look to see how science is being done just by looking up research on the SARS-CoV-2 virus. If pandemics were a reality show… Now season 3 is upon us, cursing us with another variant. Like the beginning of finding out about the SARS-CoV-2 virus and finding out about the Delta variant, science is trying to figure this one out. I know that it’s frustrating that no one knows the answer right away, but one thing people miss about science is that it isn’t about knowing everything, but it’s about finding things out. And in order to find things out, we need time. However, in a pandemic, time is an enemy. What some people get wrong is that this is confused with “science is the enemy” or “those other people are the enemy” or “this country is the enemy”. Let’s skip the philosophical part and say that basically, we’re afraid of the unknown, especially if the unknown can maim/kill us.

Although science is more about questions than answers, it can and does generate light that we can shine on the unknown. For example, every Mars rover. Because of my science background (where I spent an extremely long time trying to figure out which science field I wanted to be in, while taking every science class there was), I can go through research articles and figure out what’s what. Here’s a controversial idea: every person should take a class on how to look up scholarly articles on any topic in high school. (While we’re here, let’s open up a school and call it “School of Hard Knocks”, in which every class is directly applicable to real life, such as How to Do Your Taxes, or 50 Cheap, Simple, and Healthy Meals). Anyway, for an average person without a science background (which I also once was, in the early 2000s), what sources are there for just plain facts and neutral ground?

So far, here is the general answer:

I’m happy to see that BBC is in the center, because a long time ago, someone told me that if I wanted to find something neutral, a good point of view to consider would be from people outside of the country. I mean, how good are we at being objective about the aquariums we’re swimming in? And I’m also happy to see Reuters next to BBC. What was interesting was that I had thought The Economist was more right leaning than it was. Finally, it’s nice to know others I haven’t thought of, like Associated Press, to add to my bookmarks.

So what about Omicron? Do we need a booster shot for that? How bad is it, compared to what’s happened already? The answer is, We don’t know… yet.

Now, once again, the world is watching as researchers work nights and weekends to learn what a new variant has in store for humanity. Is Omicron more infectious? More deadly? Is it better at reinfecting recovered people? How well does it evade vaccine-induced immunity? And where did it come from? Finding out will take time, warns Jeremy Farrar, head of the Wellcome Trust: “I’m afraid patience is crucial.”

‘Patience is crucial’: Why we won’t know for weeks how dangerous Omicron is

Talking about sources wasn’t random. I liked this article for its readability, its short length, its international tidbits, and that it shares knowledge (PCR, GISAID database, structural biology mapping) without sensationalizing or politicizing anything. In this day and age, it’s like gold.

Project N95

How do you know that the N95 you bought off the internet an actual N95 mask? How would you know if it’s fake? Well, here is a website that can tell you. According to its website, Project N95:

…is committed to approving suppliers that can supply quality products. We follow a multi-step process that focuses on verifying suppliers and vetting the products offered….

Project N95

A False Choice Between Individual Freedom and Public Health

I’ve been thinking about the issue of “Individual Freedom” and “Public Health” lately, in light of dozens of news articles, Facebook rants, face-palm anti-vaxxer deaths, vaccine mandates, and me being a nurse who believes in individual freedom but have a huge science background. Are there any law-based article discussing the intersection of individual freedom and public health?

Well, Google scrounged up this article called “Individual Freedom or Public Health? A False Choice in the Covid Era.” It makes a good point: every argument, decision, rant, etc. has been falsedly based on one (individual freedom) or the other (public health). Our communities, politicians, and talking heads have set up this dichotomy and most of us have fallen head first into it and taken sides. They have set up this dichotomy in that we lose whether we choose one or the other. Instead, they could have set it up so that it’s a win-win situation.

For the real sacrifice involved in social distancing and stay-at-home orders is not individual freedom. It is the reality that these measures can cause more hardship for some people than others. For some, that hardship may be lost income; for others it may be the inability to visit their parents in a long-term care facility; for still others, it may be domestic violence…

…we should be providing people with the economic and social supports they need to maintain physical distancing. The problem is that these supports are the very things that many politicians are loathe to provide…

It is not authoritarian to demand that people maintain physical distance to save lives. It is authoritarian to demand it without giving diverse people the means to do it.

-Jonathan Cohen, “Individual Freedom or Public Health? A False Choice in the Covid Era

Can you be re-infected with the novel coronavirus? A case study.

“An 82-year-old male with a history of advanced Parkinson’s disease, insulin-dependent diabetes, chronic kidney disease, and hypertension presented to the emergency department (ED) in early-April 2020 with one week of fever and shortness of breath. He was hemodynamically stable, but tachypneic, hypoxic to 89% on six liters of oxygen via nasal cannula, and febrile to 100.4 °F. Chest x-ray revealed peripheral and basilar patchy opacities concerning for COVID-19 (Fig. 1A). His respiratory status declined in the ED, and he was intubated for hypoxemic respiratory failure and admitted to the intensive care unit (ICU). An RT-PCR for SARS-CoV-2 sent from the ED resulted as positive. He remained intubated in the ICU for 28 days at which point he was successfully extubated and transferred to the medicine floor. He demonstrated clinical and radiographical improvement (Fig. 1B), and in early May 2020 two subsequent RT-PCRs for SARS-CoV-2 sent 24 h apart resulted as negative. On hospital day 39, he was discharged to a rehabilitation facility breathing comfortably on room air.

Ten days post-discharge (48 days after first presentation), he re-presented to the ED with fever and hypoxia. On arrival he was tachypneic, hypotensive to 70/40 mmHg, and tachycardic to 110 beats/min, with a temperature of 99.9 °F and oxygen saturations of 83% on room air which improved to 96% on eight liters via Oxymizer®. Chest x-ray (Fig. 2A) and computed tomography (CT) scan (Fig. 2B) demonstrated bilateral ground glass opacities again concerning for COVID-19, as well as unilateral focal consolidations concerning for bacterial pneumonia. RT-PCR for SARS-CoV-2 sent from the ED again resulted as positive.”

Was this reinfection? Alternate considerations include the patient shedding virus for a longer period or inaccurate testing.

Genetic material from viruses can stay in a host longer even after live virus has been cleared and after symptoms have resolved. Also, how much virus is shed can depend on how sick the patient was.

According to the article, testing can be inaccurate and imprecise, with test sensitivities of 66% to 80%, depending on what instrument is used. Some tests are sensitive to “multiple different gene targets, some of which are very specific to SARS-CoV-2 infection, and some of which are quite sensitive to detection but may be common among many or all SARS-like coronaviruses.”

However, for this case study, “For our patient, while his RT-PCR on re-presentation was in fact positive, the cycle threshold required for detection was relatively high suggesting a low viral load. This could be explained by either prolonged low-level viral shedding, or inadequacy of the submitted sample. Additionally, at the time of representation and repeat positive testing, further assessment of his results revealed that while the gene assessed which was very sensitive for infection but common among all SARS-coronaviruses was detected, the gene assessed which was specific to SARS-CoV-2 was not identified.”

In conclusion, “There is large variability between instruments used for SARS-CoV-2 RT-PCR testing, and many of these results are largely open to interpretation. As in our case, interpreting cycle thresholds and understanding more about the targets of a particular instrument used for SARS-CoV-2 RT-PCR can be crucial for clinicians assessing for the possibility of true reinfection in their patients.”

Duggan NM, Ludy SM, Shannon BC, Reisner AT, Wilcox SR. A case report of possible novel coronavirus 2019 reinfection [published online ahead of print, 2020 Jul 4]. Am J Emerg Med. 2020;S0735-6757(20)30583-0. doi:10.1016/j.ajem.2020.06.079

Prone positioning

“In the setting of critical COVID-19 illness, SARS-CoV-2 infection often results in severe pneumonia and hypoxemia with many patients developing acute respiratory distress syndrome (ARDS)… Several interventions for ARDS have been evaluated over the last two decades. In particular, prone positioning is one of few therapeutic interventions for patients with severe ARDS that has demonstrated improved oxygenation and a survival benefit. Awake prone positioning outside of the intensive care unit (ICU) is safe and may decrease respiratory rate and improve oxygenation with early application potentially delaying need for intubation in patients with COVID-19… In the ICU setting, prone positioning of patients receiving non-invasive ventilation or high-flow nasal canula, with or without sedation, may also be beneficial. Physiologically, prone positioning may improve matching of ventilation and perfusion, but studies have not linked physiologic changes to clinical outcomes, especially in COVID-19.”

–Shelhamer M, Wesson PD, Solari IL, et al. Prone positioning in moderate to severe acute respiratory distress syndrome due to COVID-19: A cohort study and analysis of physiology. Preprint. Res Sq. 2020; Published 2020 Aug 17. doi:10.21203/

Interesting COVID 19 Research

“The most characteristic symptom of patients with COVID-19 is respiratory distress, and most of the patients admitted to the intensive care could not breathe spontaneously. Additionally, some patients with COVID-19 also showed neurologic signs, such as headache, nausea, and vomiting. Increasing evidence shows that coronaviruses are not always confined to the respiratory tract and that they may also invade the central nervous system inducing neurological diseases. The infection of SARS-CoV has been reported in the brains from both patients and experimental animals, where the brainstem was heavily infected. Furthermore, some coronaviruses have been demonstrated able to spread via a synapse-connected route to the medullary cardiorespiratory center from the mechanoreceptors and chemoreceptors in the lung and lower respiratory airways.”

— Li YC, Bai WZ, Hashikawa T. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients. J Med Virol. 2020;92(6):552-555. doi:10.1002/jmv.25728.

“A 93-year-old woman was admitted with a 10-day history of cough and prostration. Thoracic computed tomography revealed extensive ground-glass opacities in both the lungs. The polymerase chain reaction test of sputum for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) was positive. She was treated with antiviral agents and steroid pulse therapy. However, her oxygen saturation gradually declined, and she died 10 days after hospitalization. The most important autopsy finding was fuzzily segmented diffuse alveolar damage (DAD) that expanded from the subpleural to the medial area. No remarkable changes were observed in organs other than the lungs. Therefore, pneumocytes were suggested as the primary target for SARS-CoV-2, which might explain why coronavirus infectious disease-19 is a serious condition. Thus, early treatment is essential to prevent viral replication from reaching a level that triggers DAD.”

— Okudela K, Hayashi H, Yoshimura Y, et al. A Japanese case of COVID-19: An autopsy report [published online ahead of print, 2020 Aug 13]. Pathol Int. 2020;10.1111/pin.13002. doi:10.1111/pin.13002.

“A relatively high mortality of severe coronavirus disease 2019 (COVID-19) is worrying, and the application of heparin in COVID-19 has been recommended by some expert consensus because of the risk of disseminated intravascular coagulation and venous thromboembolism. However, its efficacy remains to be validated.

“Anticoagulant therapy mainly with low molecular weight heparin appears to be associated with better prognosis in severe COVID-19 patients meeting SIC criteria or with markedly elevated D-dimer.”

— Tang N, Bai H, Chen X, Gong J, Li D, Sun Z. Anticoagulant treatment is associated with decreased mortality in severe coronavirus disease 2019 patients with coagulopathy. J Thromb Haemost. 2020;18(5):1094-1099. doi:10.1111/jth.14817.