Coronavirus Tidbits #173 1/2/22

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Announcements:

First, there is now a Resources Page here for the most commonly asked questions I’m getting.

Happy to continue to answer your questions/concerns as best I can, so don’t be shy about that.

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Recent posts:

COVID Misinformation From the Top Offers False Cheer and True Risk

https://www.medscape.com/viewarticle/965724

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Climate Change And Infections

https://www.forbes.com/sites/judystone/2021/12/30/climate-change-and-infections/?sh=2b21953a3fd4

News 

See What to do if newly infected, under Tips, below:

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Omicron:

Beyond case counts: What Omicron is teaching us

STAT  By Andrew Joseph  and Helen Branswell  12/30/21

The Omicron wave in the United States is upon us.

If you were fortunate enough to tune out from Covid-19 news over the holidays, you’re coming back to startling reports about record high case counts and, in some places, increases in hospitalizations. The wave will crest, of course; the question is when.

For now, experts say, the country still has a ways to go to get through the Omicron surge. Below, STAT outlines what Omicron is already teaching us as this phase of the pandemic plays out.

A reminder: Scientists have known about this variant for just a little over a month. While a tremendous amount has been learned in a stunningly short amount of time, our understanding will continue to be refined as data pour in and key questions are answered.

https://www.statnews.com/2021/12/30/beyond-case-counts-what-omicron-is-teaching-us/

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Omicron variant largely resistant to current antibodies

The team was able to show that antibodies from recovered persons hardly inhibit the omicron variant. Antibodies after two BioNTech-Pfizer vaccinations also showed significantly reduced efficacy against the omicron variant. Better inhibition was observed after triple BioNTech-Pfizer vaccination as well as after heterologous vaccination with Oxford-AstraZeneca and BioNTech-Pfizer. Finally, most of the therapeutic antibodies evaluated in the study were not effective against the omicron variant. These results indicate that several antibodies used to treat COVID-19 will be ineffective against the omicron variant. However, they also suggest that a third immunization with the BioNTech-Pfizer vaccine (booster) and heterologous immunization may protect well against the omicron variant.

https://medicalxpress.com/news/2021-12-omicron-variant-largely-resistant-current.html

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Probe of first US Omicron cluster hints at shorter incubation period

The median incubation period in the cluster patients was 3 days, compared to about 4 days for Delta, and 5 or more days for earlier SARS-CoV-2 viruses.
Dec 28 MMWR report

https://www.cidrap.umn.edu/news-perspective/2021/12/news-scan-dec-29-2021

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Shortened CDC COVID isolation guide draws sharply mixed reviews

Facing an onslaught of Omicron variant activity amid holiday gatherings and travel, the Centers for Disease Control and Prevention (CDC) yesterday updated its COVID-19 guidance yesterday, halving the isolation and quarantine period for people with or exposed to the coronavirus.

The move, which relies on masking and accounts for sparse rapid test availability, drew praise from some experts as a needed change in the face of an evolving situation. But it also drew sharp criticism from other experts and some labor officials, who point to scientific gaps and ongoing risks.

CDC anticipates major Omicron-driven disruptions

In a press release announcing the new recommendations yesterday, the CDC recommended that anyone who tests positive, regardless of vaccination status, stay home for 5 days. If there are no symptoms or symptoms resolve after 5 days, the individual can leave the house if they mask around others for 5 days.

For those who are exposed, the CDC recommends people who aren’t boosted or are unvaccinated should stay home for 5 days, then wear a mask around others for 5 more days. Those who are boosted or recently completed their primary vaccination series should mask around others for 10 days. Both groups should test on day 5, if possible.

CDC Director Rochelle Walensky, MD, MPH, said the quickly spreading Omicron variant has the potential to impact all parts of society. She added that the new guidance takes into account what’s known about virus spread and protection from vaccines and boosters.

“These updates ensure people can safely continue their daily lives. Prevention is our best option: get vaccinated, get boosted, wear a mask in public indoor settings in areas of substantial and high community transmission, and take a test before you gather,” she said.

Leana Wen, MD, former Baltimore health commissioner and contributing columnist for the Washington Post, said on Twitter that the CDC’s decision to reduce isolation and quarantine was needed to prevent the collapse of critical infrastructure, with the nation poised to pass its previous COVID-19 peak, possibly reaching 1 million cases a day.

Ashish Jha, MD, MPH, dean of the Brown University School of Health, on Twitter today said the new guidance is a step in the right direction, taking into account the period when people are most contagious, while minimizing unnecessary constraints and encouraging more people to test and isolate.

However, other experts said the 5-day isolation period unpaired with a negative test is risky and not supported by data.

Michael Mina, MD, PhD, epidemiologist and major proponent of at-home COVID-19 antigen tests, on Twitter said the new guidance is reckless and noted that some people are infectious for 3 days, while others can still pass the virus at 12 days. He said testing negative to leave isolation early is a smart strategy, as would be wearing an N95 mask if leaving isolation.

Mina said the lack of a negative test requirement before leaving isolation probably reflects a perception that there aren’t enough rapid tests in the United States, which he said is a massive problem that can be easily changed.

Meanwhile, the Association of Flight Attendants today questioned the CDC’s new policy, saying it aligns with the number of days pushed by corporations. The group’s president, Sara Nelson, called it “less than reassuring.”

“If any business pressures a worker to return to work before they feel better we will make clear it is an unsafe work environment, which will cause a much greater disruption than any ‘staffing shortages’,” she said in a statement.

https://www.cidrap.umn.edu/news-perspective/2021/12/shortened-cdc-covid-isolation-guide-draws-sharply-mixed-reviews

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Forecasting the Omicron winter: Experts envision various scenarios, from bad to worse

https://www.statnews.com/2021/12/27/forecasting-the-omicron-winter-experts-envision-various-scenarios-from-bad-to-worse/?

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Other Covid news:

Ohio: COVID-19 infection detected in deer in six locations

Scientists have detected infection by at least three variants of the virus that causes COVID-19 in free-ranging white-tailed deer in six northeast Ohio locations, the research team has reported.

Previous research led by the U.S. Department of Agriculture had shown evidence of antibodies in wild deer. This study, published today (Dec. 23, 2021) in Nature, details the first report of active COVID-19 infection in white-tailed deer supported by the growth of viral isolates in the lab, indicating researchers had recovered viable samples of the SARS-CoV-2 virus and not only its genetic traces.

researchers estimated the prevalence of infection varied from 13.5% to 70% across the nine sites, with the highest prevalence observed in four sites that were surrounded by more densely populated neighborhoods.

The research team speculated that white-tailed deer were infected through an environmental pathway – possibly by drinking contaminated water. Research has shown that the virus is shed in human stool and detectable in wastewater.

http://outbreaknewstoday.com/ohio-covid-19-infection-detected-in-deer-in-six-locations-67729/

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COVID-19 can trigger self-attacking antibodies, even in mild or asymptomatic cases

Infection with the virus that causes COVID-19 can trigger an immune response that lasts well beyond the initial infection and recovery-even among people who had mild symptoms or no symptoms at all, according to Cedars-Sinai investigators. The findings are published in the Journal of Translational Medicine.

https://medicalxpress.com/news/2021-12-covid-trigger-self-attacking-antibodies-mild.html?

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How can I protect a child too young for a COVID-19 vaccine?

https://medicalxpress.com/news/2021-12-child-young-covid-vaccine.html?

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Burnout, Violence: How Much More Can Healthcare Workers Take?

– As COVID rages on, attention turns to healthcare worker mental health. Will help arrive in time?

https://www.medpagetoday.com/special-reports/exclusives/96428?

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Intestine ‘organoid’ grown in lab to study why bats live with viruses but don’t get sick

https://medicalxpress.com/news/2021-12-intestine-organoid-grown-lab-viruses.html?

Diagnostics:

Are We Testing for Omicron Wrong?

– South African study suggests nasal swabs aren’t the best way — combine w throat swab

https://www.medpagetoday.com/infectiousdisease/covid19/96385?

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Drugs and Vaccines:

3. We technology transferred our vaccine and helped in its co-development with BioE with NO PATENT and no strings attached. 4. As a result it should be the least expensive COVID vaccine available yet

5. It uses an older recombinant protein yeast fermentation technology similar to that used for the recombinant hepatitis B vaccine which has been around for 40 years. 6. It was authorized based on superiority studies to another well established COVID vaccine.

7. This vaccine can be made locally all over the world, and we’ve now technology transferred our Texas Children’s vaccine to producers in India, Indonesia, Bangladesh, Botswana. 8. Our Texas Children’s Center does not plan to make money on this, it’s = a gift to the world

This was an effort of a team of 20+ scientists

@TexasChildrens @BCM_TropMed

co-led by me and my brilliant science partner for the last 20 years @mebottazzi

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A new coronavirus vaccine heading to India was developed by a small team in Texas. It expects nothing in return.

https://www.washingtonpost.com/world/2021/12/30/corbevax-texas-childrens-covid-vaccine/

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Once a ‘crazy idea,’ patent-pooling nonprofit will help bring COVID-19 pills to world’s poor

Medicine patent strategy proved its worth with HIV drugs and now a founder of group sets her sights on Pfizer’s vaccine next

Science 29 DEC 2021 BYJON COHEN

In the United States, widespread hope greeted the decision by the Food and Drug Administration last week to authorize the emergency use of two different oral treatments for SARS-CoV-2 infection, which could mark a new era in which pills taken at home can prevent severe COVID-19. Global health advocates are also celebrating the preauthorization decision by the two Big Pharmas producing the treatments to allow generic manufacturers to make low-cost versions accessible to poorer countries.

Each of the treatments, Pfizer’s combination of a new antiviral, nirmatrelvir, with an old one, and Merck’s molnupiravir, require 5 days of pills, which the U.S. government has purchased for $530 and $712 per treatment course, respectively. That’s far too expensive for much of the world, but both companies joined the Medicines Patent Pool (MPP) for their patented treatments. A nonprofit set up in 2010, MPP encourages Big Pharmas to voluntarily cut deals that allow generic manufacturers to produce and sell a company’s drugs or vaccines at steep discounts in agreed on regions of the world. “Everyone at the time said this will never happen, this is a crazy idea,” says attorney Ellen ‘t Hoen, who helped establish MPP and remains on its expert advisory group.

Generic makers are expected to cut the cost of either treatment to as low as $20 per treatment course, while Pfizer and Merck will continue to sell the pills to wealthy countries for whatever the market will bear. (Nirmatrelvir is boosted by a second drug, ritonavir, that came to market as an HIV treatment and is widely available as an inexpensive generic.)

MPP modeled itself after a cross-licensing agreement created by the U.S. government to free patents controlled by the Wright brothers and another aviation pioneer, who tied up the entire airline industry. MPP initially set out to make lifesaving antiretrovirals for HIV more accessible to low-income countries and then later branched out to include drugs for hepatitis C and tuberculosis. “This is frankly a dream coming true that the pool is moving into all these various areas of huge need and succeeding,” says ‘t Hoen, who ran the Campaign for Access to Essential Medicines for Doctors Without Borders (MSF) before starting MPP. Deals through the group have led to the supply of more than 18 billion doses of drugs.

https://www.science.org/content/article/once-crazy-idea-patent-pooling-nonprofit-will-help-bring-covid-19-pills-world-s-poor

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STAT/Harris Poll: Vaccinated Americans far more likely to take Pfizer Covid-19 pill (Paxlovid) than unvaccinated people

Only 72% of the adult population in the U.S. is fully vaccinated and just 24% have received a booster dose, according to the U.S. Centers for Disease Control and Prevention.

In studies, the pill reduced the risk of hospitalization or death by 88% compared to a placebo among patients treated within five days of experiencing Covid-19 symptoms. Yet interest in the Pfizer pill varies significantly, according to the STAT-Harris poll, which queried 2,103 Americans over 18 years old between Dec. 17 and Dec. 19, three days before the FDA endorsed the medication.

https://www.statnews.com/pharmalot/2021/12/28/covid19-vaccine-pill-pfizer-fda/?

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EXPLAINER: New easy-to-use COVID-19 pills come with a catch

Newly infected COVID-19 patients have two new treatment options that can be taken at home.

But that convenience comes with a catch: The pills have to be taken as soon as possible once symptoms appear.

The challenge is getting tested, getting a prescription and starting the pills in a short window.

U.S. regulators authorized Pfizer’s pill, Paxlovid, and Merck’s molnupiravir last week. In high-risk patients, both were shown to reduce the chances of hospitalization or death from COVID-19, although Pfizer’s was much more effective.

A closer look:

WHO SHOULD TAKE THESE PILLS?

The antiviral pills aren’t for everyone who gets a positive test. The pills are intended for those with mild or moderate COVID-19 who are more likely to become seriously ill. That includes older people and those with other health conditions like heart disease, cancer or diabetes that make them more vulnerable. Both pills were OK’d for adults while Paxlovid is authorized for children ages 12 and older.

WHO SHOULDN’T TAKE THESE PILLS?

Merck’s molnupiravir is not authorized for children because it might interfere with bone growth. It also isn’t recommended for pregnant women because of the potential for birth defects. Pfizer’s pill isn’t recommended for patients with severe kidney or liver problems. It also may not be the best option for some because it may interact with other prescriptions a patient is taking. The antiviral pills aren’t authorized for people hospitalized with COVID-19.

https://medicalxpress.com/news/2021-12-easy-to-use-covid-pills.html

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Early remdesivir for COVID-19 lowers hospitalization, death risk by 87%

An early 3-day course of remdesivir lowered the risk for hospitalization or death among nonhospitalized patients at high risk for severe COVID-19 by 87%, according to a study published in The New England Journal of Medicine.

In treatment guidelines for COVID-19, the Infectious Diseases Society of America suggests remdesivir for certain hospitalized patients – a departure from WHO, which does not recommend it for any patients hospitalized with COVID-19, regardless of how sick they are.

https://www.healio.com/news/infectious-disease/20211227/early-remdesivir-for-covid19-lowers-hospitalization-death-risk-by-87

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Beneath a Covid Vaccine Debacle, 30 Years of Government Culpability

Washington has rejected plans to revamp vaccine preparedness for decades and repeatedly paid a price. The Biden administration is at a similar crossroads.

New York Times   By Chris Hamby and Sheryl Gay Stolberg  Dec. 23, 2021

WASHINGTON – As the Biden administration tries to stanch yet another wave of the coronavirus pandemic, senior White House officials have also been considering a proposal to ensure the nation is better prepared for the next infectious disease outbreak.

Key to the plan is the creation of a taxpayer-funded “vaccine hub” where experienced drug makers would partner with the government, reliably churning out millions of doses under federal oversight.

The proposal is partly a response to a searing failure by a once obscure Maryland biotech firm, Emergent BioSolutions. While Pfizer and Moderna had spectacular success producing vaccines, the government entrusted the manufacturing of two of the other leading candidates to Emergent, which was forced to toss tens of millions of doses of Johnson & Johnson’s vaccine and to quit producing the AstraZeneca vaccine because of serious quality problems that ultimately led the Biden administration to cancel its contract.

The government’s partnership with Emergent, which cost taxpayers hundreds of millions of dollars over the past decade, was supposed to be a pillar of the nation’s pandemic preparedness. Instead, it proved to be the culmination of 30 years of frustrations.

Three times over the past three decades, presidential administrations explored plans for a vaccine overhaul like the one President Biden is now considering, only to be thwarted by pharmaceutical lobbying, political jockeying and cost concerns, a New York Times investigation found.

In each case, the nation was left ill prepared for the next crisis – while creating a vacuum that Emergent eagerly filled.

“The reason why Emergent got so many contracts is mostly because they were the only ones willing to do the work,” said Dr. Kenneth Bernard, a top biodefense adviser to Presidents Bill Clinton and George W. Bush.

https://www.nytimes.com/2021/12/23/us/covid-vaccine-biden-trump.html

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Devices and Masks:

N95 masks: A must-have with Omicron, but fakes abound

https://medicalxpress.com/news/2021-12-n95-masks-must-have-omicron-fakes.html?

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Epidemiology/Infection control:

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https://twitter.com/dgurdasani1/status/1475061938010865665?s=20

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https://twitter.com/LonnieRhea/status/1475555196189040643?s=20

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Tips, general reading for public:

Tatiana Prowell (@tmprowell) and others have tips for newly infected and/or exposed, below. See also https://cleanaircrew.org/someone-in-my-home-has-covid-how-do-we-isolate-safely/

1/ The first thing to say is that if someone has #COVID19 symptoms (#Omicron most common: nasal congestion/runny nose, scratchy sore throat, fever, & aches), you have to assume they have it. You may not have a test (urgent cares are still open & do) or they may still be neg.

2/ You, as the person exposed to the one with symptoms, have to assume that you both do & don’t have #Omicron too. Wait, what?  I mean: assume you could infect others now & take care to avoid exposing them, BUT don’t assume it’s too late for you to avoid getting it.

3/ Especially in households with #vaccinated (& #boosted) family members, I have seen people manage to limit #Omicron to the first person who was infected. This #CovidVariant is incredibly contagious, but It CAN be done. Don’t give up on the idea!

4/ If you have N95/KN95/KF94 masks, get in them immediately. If you have only 1, put the sick person in it for source control. If you have >1 but not enough for all put the sick one & the highest risk (older, #immunocompromised) people in them. Then get outside, & leave door open.

5/ Fresh air is a friend & shared air is an enemy. The more you can ventilate your , now & until this is over, the better. You want the concentration of #omicron in air as low as possible. This decreases odds of infection & may make you less sick if you do get infected.

6/ Plan to bundle up if you’re in a  climate, because you’re going to need to leave doors & windows open enough for air exchange, esp for next 5d or so, & a cross draft. If you have a fresh HVAC filter, change it. If a hardware place is open, get a MERV13 HVAC filter. (Amazon has too.)

7/ Run the fan on your thermostat on high. Filter that #Omicron ! If you need supplies of any kind, please do curbside pickup or same-day delivery or drive-thru. No one exposed should be indoors in public, & def not the one with symptoms, to prevent further spread.

8/ If you don’t have any N95/KN95/KN94 masks, please see if a nearby friend or neighbor has unused ones you can have & order them replacements. The nonprofit @projectn95  (http://projectn95.org) is a great place to get them. Your backup plan for right now is a surgical mask.

9/ A surgical mask (ASTM level 3, 3-ply is best) has good filtration but usually not good fit. There are often gaps. Knot ear loops where they join the mask & then tuck to improve the mask fit. Here’s a short video demo: https://youtu.be/GzTAZDsNBe0. Put a cloth mask over the surg mask.

10/ Now it’s time to create the space where the infected person or people will isolate for 10d to let #Omicron run its course. This prior  of mine covers what is helpful to have in there & other things to consider.

11/ This whole scenario assumes that things are going ok with the person who has #Omicron. How do you know if they are ok? As I mentioned before, if you have a pulse oximeter (O2 sat monitor)-the thing drs put on your fingertip to measure O2-use it. See guide in .

12/ If you don’t have a pulse oximeter, many pharmacies carry them. They are over the counter. Ask the pharmacist if you don’t see them. You can order them online from many places too. Get one highly rated by many people. They need not be expensive. $15 gets a very good one.

13/ Some of your devices (smart watches, fitness trackers) can detect heart rate (60-100 normal for adults) & less reliably O2 levels. If you have them & they read low O2 levels, def do call a dr or seek care. Video calls are helpful to check on the sick as well.

14/ If the person w/ #Omicron is high-risk (especially #immunocompromised, organ or bone marrow transplant, active #cancer#pregnant#diabetes, older, etc), they should contact a dr even if they seem ok. There are outpatient treatments that sig risk of being hospitalized.

15/ These include monoclonal antibodies (some brands no longer work vs #Omicron, but 1 called sotrovimab remains effective). It is given IV as a single dose. There are also two types of pills taken for 5d at home. All are in short supply at the moment. https://google.com/amp/s/abcnews.go.com/amp/Health/omicron-treatments-monoclonal-antibodies-work-variant/story%3fid=81893922….

16/ All of these things to treat outpatients w/ #Omicron, the monoclonal antibody sotrovimab, as well as the pills (Paxlovid: https://google.com/amp/s/www.nytimes.com/2021/12/22/health/pfizer-covid-pill-fda-paxlovid.amp.html…) & (molnupiravir: https://google.com/amp/s/www.nytimes.com/2021/12/23/health/covid-pill-merck.amp.html…) are new, so they are being reserved for higher-risk folks while supply increases. [Paxlovid is better imho] 17/ If you are not the sick person, but one of the exposed, & you can walk-up/drive-up (NOT indoors & ONLY in a !) to #GetVaccinated, do it. If age 16+ & 6+ mos post dose 2 of vaccine (or 2+ post J&J), go #GetBoosted now! The booster protects w/in a wk! 19/ If you are high-risk #immunocompromised or #immunosuppressed, we know that #vaccineswork less well in many of you. While you should still #GetVaccinated & #GetBoostedan injection (Evusheld) can decrease your risk of #COVID19. It’s given every 6 mos. ~ ~ ~ Also #Remdesivir might be available as an outpatient for high-risk- (1.6%) in the remdesivir group and 21 of 252 (8.3%) hosp or death in placebo https://www.nejm.org/doi/full/10.1056/NEJMoa2116846 I suggest contacting the local health department +/- hospital to see where any of these drugs might be available. There are very limited supplies.

Politics:

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https://twitter.com/CrynJohannsen/status/1475702312295444484?s=20

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Mayo Physician Fired Over COVID Book

https://www.medpagetoday.com/special-reports/exclusives/93266?

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Feel good du jour:

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https://twitter.com/buitengebieden_/status/1475960982488993796?s=20

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Comic relief:

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https://threadreaderapp.com/thread/1475721124365287427.html

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https://twitter.com/buitengebieden_/status/1474701392212279298?s=20

Perspective/Poem

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Bits of beauty:

It’s nice seeing this bright spot leading the way on these gray, dreary days.
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