Viral Blooms Follow Pattern

Living with Coronavirus
(SARS-CoV-2)
Sunday November 21st, 2021
6:27 AM

As I have said before, Covid-19 is not going anywhere.  Covid, complete with vaccines, masks, social distancing, and perhaps even lockdowns will be our reality henceforth.  The virus blooms wherever conditions for it are ripe.  It has become an endemic deadly disease that remains at pandemic levels of infection.

Fully vaccinated people and people just over Covid are around 85%-90%+ resistant to the disease.  This resistance reduces the ability of the virus to infect cells, which in turn reduces the number of cells infected, which in turn reduces the amount of virus produced by those infected cells, which reduces viral load overall.  This makes them less likely to become seriously ill, and less likely to spread the virus, but even if they do spread it, it would be with a low viral load.

People with high antibodies against Covid are resistant, not immune.  As those antibodies wane over time, Covid finds a foothold to infect, reproduce, and spread.  That makes unvaccinated people a major spread vector.  In the near future this group will also include those who failed to keep their Covid vaccinations up to date.

Those people who had a vaccine or a case of Covid-19 more than 6 months ago, with waning antibodies will also be a spread vector, but at about half the rate of the unvaccinated.  Those people who are only half vaccinated, having had only one of two shots, will also be a half strength spread vector.  Fully vaccinated and those just recovered from Covid will be the lowest vector of spread.

Note that in all cases humans can still spread the disease, and still spread it asymptomatically; that is people spread it without realizing they even have it.  This is why I expect masks to remain a fixture for people who understand this, especially in closed indoor congregate settings like weddings, parties, and festivals.

 Fully vaccinated people and those who just recovered from Covid have the most and the strongest antibodies to the virus.  These folks, when exposed to the virus, will have a mild to moderate case of the disease, co-morbidities aside.  Infected, they will have a much lower viral load. A viral load being how much virus they have, how much virus they shed, and how fast they shed the virus. 

Viral load seems to be a key factor in this particular virus.  Those most ill in an ICU are shedding vast amounts of virus with every breath; they have a heavy viral load; it is insane how heavy that load can be.  People infected by these very ill folks start with that heavy viral load.  More load means more cells infected, more viral reproduction, and more virus shed.  That means your chance of a severe infection rises steeply if infected with a heavy load at outset.

There seems to be a direct connection between a person’s initial viral load via infection, and both how sick they get and how much virus they shed.  Vaccinated people have radically reduced viral loads, which results in less cells infected, less virus reproduced and less virus shed by them to others. So, it becomes possible that a person could meet someone with asymptomatic Covid with a low viral load and if they catch the virus, they also inherit that low viral load at the outset.  A healthy person in such an instance can expect a mild or asymptomatic case.  A person with comorbidities in the same instance mighty get very ill. 

The inverse also seems true.  For example-A person encounters an asymptomatic person with a new infection of Covid unknown to them, but with a heavy viral load.  If caught by a healthy person they may well get very ill because the virus reproduces so fast it overwhelms our system.  This is why I expect masks to become a norm for some, like in Japan.

Blooms, here, there, and everywhere seem to follow a pattern very similar to last year. In the summer Covid blooms in the hotter areas of the planet, where people congregate to escape the heat.  In the winter Covid blooms in the colder regions where people congregate to stay warm. Covid blooms in both summer and winter, unlike flu which blooms every winter. It prefers indoor congregate settings.

Covid is doing that right now in parts of the US and Europe.  It is blooming right now in Maine. 

Patterns like these can only be seen in hindsight.  We need to utilize our understanding of them to reduce the spread.  Avoid large congregations of people as much as we can, and mask when we have to as circumstances dictate, and always pay attention to washing our hands.

Global Infected      253,089,559                   257,282,155                       
Increase             4,192,596
7-day average        598,942 infections diagnosed daily –Up

Global Dead          5,098,179                                          5,148,350
Increase             50,171
7-day average        7,329 deaths daily –Down slightly

USA Infected         47,052,201                                       47,701,533
Increase             649,332
7-day average        92,761 infections diagnosed daily –Up

USA C-19 deaths      762,973                                         771,013
Increase             8,040
7-day average        1,148 deaths daily –Down slightly

Maine Infected       111,145                                           115,857                                                                
Increase             4,712
7-day average         673 infections diagnosed daily –Up

Maine deaths         1,230                                                1,271
Increase             41
7-day average        5.8571 deaths daily –Up

(Bloomberg) — It was meant to be a summer vacation to celebrate. Thousands of revelers flocked to Provincetown, Massachusetts, for the July Fourth holiday, fully immunized against Covid-19 and ready to enjoy new freedoms, including socializing without face masks.

Instead, the weather turned cool and rainy, and the festivities shifted indoors to pubs, clubs and private homes, creating a crucible for the effectiveness of vaccines used to contain the uber-transmissible delta variant. More than 1,000 Covid cases ensued over the following two weeks, rocking confidence in the inoculations and prompting the U.S. Centers for Disease Control and Prevention to reinstate an indoor masking mandate.

Four months later, researchers studying those who contracted the virus are gaining important insights into the immunity-bolstering effects of natural infection after vaccination. Importantly, their findings offer clues about the immune protection needed for the coronavirus to cease being a public-health menace and, ultimately, to end the pandemic.

“Our data really puts a different perspective on the Provincetown cohort,” said Dan Barouch, a Harvard Medical School professor and head of Boston’s Beth Israel Deaconess’ Center for Virology and Vaccine Research. “Initially, it was viewed as evidence of vaccine failures. I would actually argue it’s evidence of vaccine success. These vaccines are doing what they are intended to do.”

The outbreak in Provincetown, the small resort town located at the tip of Cape Cod that’s known colloquially as “P-town,” was the first well-described, large cluster of infections with the delta variant in a highly vaccinated population. Some three-quarters of the Covid cases occurred in people who had two doses of either the Pfizer Inc. or Moderna Inc. vaccines, or the single Johnson & Johnson shot, at least 14 days earlier.

Almost 80% of these so-called breakthrough infections were symptomatic. Although the majority led to only mild-to-moderate illness, the Covid surge in the face of high vaccination rates prompted an intense investigation by state and local health officials.

They found the amount of viral material on nasal swabs was similar in vaccinated and unvaccinated people. That surprising finding undercut overly optimistic expectations that the inoculations could eliminate SARS-CoV-2 transmission, particularly given the twice-as-infectious delta strain.

Disease detectives at Boston’s Broad Institute used genomic sequence data to trace the outbreak to just a handful of infected people, including one who was the likely source of more than 80% of cases. Their work proved Covid could spread between fully vaccinated people. Intriguingly, the disease sleuths also found those infected in Provincetown — who came from 21 states — contributed only modestly to the delta-fueled U.S. epidemic after they returned home.

The outcome was comforting because it backed what’s already known about immunization, said Helen Petousis-Harris, a vaccinologist at the University of Auckland.

“Vaccination against Covid-19 is the best way to prevent getting severely ill and dying from Covid, but it doesn’t completely stop everyone who gets it from being infected with the SARS-CoV-2 virus or from transmitting it,” she said. “However, if you are vaccinated and you get infected, you’re less likely to spread the virus than if you’re unvaccinated.”

(USA Today) –America’s recovery from the delta variant surge dropped the pace of new infections to under 500,000 per week in late October. Now cases are above 600,000 per week and are rising in 34 states, a USA TODAY analysis of Johns Hopkins University data shows.

The numbers are not close to January, when weekly infections peaked at 1.7 million. But the recovery from one wave has reversed into another wave, more than six months after free, safe, effective vaccines became widely available to all adults. The United States is again reporting an average of more than 1 case every second.

Unvaccinated people remain at highest risk for infection. The good news: 80% of Americans 12 and over have had at least one coronavirus vaccine shot.

Melissa Nolan, an assistant professor of epidemiology and biostatistics at the University of South Carolina Arnold School of Public Health, told USA TODAY that seasonal flu infection increases risk in winter. 

“Sadly, this virus will never leave our society,” Nolan said. “To help mitigate spread as we go into this next winter respiratory disease season, it is vitally important that Americans get both their booster shot and their flu shot.”

(NBC)–The Data Point: Less than half of Americans have strong immunity against Covid

Only 40 percent of Americans are at their strongest immunity level against Covid-19, even as health officials warn that waning immunity among vaccinated people is leading to a rise in hospitalizations. 

While about 6 in 10 Americans are fully vaccinated, more than half received their last shot more than six months ago, the threshold currently recommended for those getting a Moderna or a Pfizer booster. When combined with the 100 million unvaccinated people, about 60 percent of the population is heading into the winter months with reduced protection against the coronavirus.

“What we’re starting to see now is an uptick in hospitalizations among people who’ve been vaccinated but not boosted,” Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, said Tuesday in an NBC News interview.

Nearly 10 percent of the country, or 31 million people have received a booster shot, according to data from the Centers for Disease Control and Prevention.

On Friday, the Food and Drug Administration authorized Moderna and Pfizer boosters for all adults. Combined with those eligible for a Johnson and Johnson booster, about 96 million people — or 29 percent of the total U.S. population — would be eligible, according to an NBC News analysis of CDC data.

Children ages 5 to 11 started receiving vaccinations this month, and at a briefing Wednesday, the White House announced that 2.6 million, or 10 percent, of kids have received their first dose.

(CNN)–Scientists have found SARS-CoV-2 spreads like, well, a virus, among white-tailed deer and other wild animals in the United States.

People are the likely source, but that doesn’t mean the virus can’t evolve among these animals and then spill back into humans, and researchers are worried about what this spread means for the risk of future pandemics.

There’s little doubt SARS-Cov-2, the virus that caused the ongoing pandemic, came from an animal — almost certainly a bat. And the prevailing scientific opinion is that there as an intermediate host, an animal of some sort, that was infected by a bat or bats and then infected people.

It’s also clear that people can infect animals. Pets such as cats, zoo animals such as gorillas and snow leopards and farmed mink can all be infected. Multiple cases have been reported, and evidence of changes in the virus’s infecting mink have led to mass culls of those animals on fur farms.

The latest species to capture the attention of wildlife biologists are white-tailed deer. It’s little surprise that farmed deer would catch the virus from people. Any visitor to a deer farm knows the animals behave like goats, shoving their wet noses into the pockets, hands and faces of human visitors or caregivers as they clamor for food and treats — and setting themselves up for infection.

But how are wild deer catching it?

“If somebody might bite an apple and throw it or even if I sneeze in a tissue and drop it,” speculated Dr. Suresh Kuchipudi of the Animal Diagnostic Laboratory at Pennsylvania State University, who helped lead one study published earlier this month that found a third of deer they tested across Iowa between September of 2020 and January of 2021 showed evidence of infection.

Sewage has been found to carry the virus, so polluted water might be a source, he added, or people spitting or contaminating the environment in other ways. The deer may then spread the virus to one another.

“Keep in mind these are highly susceptible animals and while you do not know how much virus they need to be infected,” Kuchipudi told CNN. “It raises the urgent question — we know the deer are effectively transmitting virus among themselves, and then who are they giving it to?”

It’s also possible another species could be picking up the virus from people and infecting deer.

“We don’t know what’s going on in our very own country and we need to find out,” said Hon Ip of the United States Geological Survey in Wisconsin.

There are several reasons scientists do not want to see a virus like the one that causes Covid-19 infecting animals. For one, it creates what’s known as a reservoir — so that even in the unlikely case that everyone got vaccinated and the virus stopped circulating among people, it would still circulate among animals and could re-infect people eventually.

More likely however, is the risk that it could change and evolve. That can happen in two ways.

One is steady adaptation. As it infects different species, the virus will change to better adapt to those species and that could make it either more or less dangerous to humans.

Another route to change: viruses can take shortcuts by swapping big chunks of genetic material in a process called recombination. Influenza is especially good at this, but coronaviruses can do it, as well. If an animal is infected with more than one coronavirus at a time, the two types can mix and match genes and potentially come up with new variants.

“Recombination is one of the major mechanisms for coronavirus evolution,” Ip said. “So, if animals are already carrying their own varieties of coronavirus, and people are then infecting them with strains that cause pandemics among humans — the potential exists for these viruses to infect animals at the same time, trade genetic material, and give rise to new pandemic viral species.”

(dw.com)-Germany has reported the highest rate of coronavirus infections since the pandemic began. State premiers are set to meet to discuss measures to curb the spread. Germany on Wednesday reported record levels of COVID-19 cases as the country faces a virulent fourth wave of the pandemic.

The country’s public health agency, the Robert Koch Institute, reported 52,826 new cases of coronavirus infection in the past 24 hours, the highest rate registered since the pandemic began in early 2020. That represents an increase of 13,150 cases compared with the same day a week ago.  The seven-day incidence rate measuring cases per 100,000 people also reached a record high of 319.5, up from 312.4 the day before. The death toll from COVID-related causes rose in 24 hours by 294 to 98,274.

Despite the high infection rate, the death toll still remains below that at the peak of the pandemic in December 2020 owing largely to the fact that around two-thirds of the population is vaccinated.

However, experts have warned from the beginning of the rollout that the number is not high enough to keep the virus under control. One of Germany’s top virologists, Christian Drosten, predicted last week that the country could see 100,000 more COVID deaths over the winter if the vaccination rate did not increase and other measures were not taken to stem the spread.

Experts say that infection numbers are likely to continue rising over the winter, partly owing to an increase in indoor gatherings as Christmas approaches.

BERLIN (AP) — Germany has entered a “nationwide state of emergency” because of surging coronavirus infections, the head of the country’s disease control agency said Friday.

Lothar Wieler, the head of the Robert Koch Institute, said regular medical care cannot be guaranteed anymore in some parts of the country because hospitals and intensive care wards are overstretched. The German air force confirmed a report by daily Bild that it was preparing to help transfer patients to clinics with free beds.

“All of Germany is one big outbreak,” Wieler told reporters in Berlin. “This is a nationwide state of emergency. We need to pull the emergency brake.”  Wieler’s comments came as the upper house of parliament on Friday approved new measures to control the outbreak –

The measures include requirements for people to prove they are vaccinated, recently recovered from COVID-19 or have tested negative for the virus in order to access communal workplaces or public transport.

Separately, outgoing Chancellor Angela Merkel agreed with the governors of Germany’s 16 states to introduce a new threshold linked to the number of hospital admissions of COVID-19 patients per 100,000 people over a seven-day period. Some states are also considering mandatory vaccinations for some professional groups such as medical staff and nursing home employees.

Neighboring Austria, which has also been hit by a surge in new cases, announced it would extend a nationwide lockdown to vaccinated people from Monday, and introduce compulsory vaccinations from February.

Such measures are not currently being discussed in Germany, where the outgoing Merkel government and the three-party alliance hoping to replace it are at odds over how to respond to the pandemic.

HAMBURG(AP)–Germany is scrambling to deal with a raging fourth wave of COVID-19 as the country this week recorded its highest number of cases yet amid flatlining vaccination rates, fractured political decision-making, and an increasingly radical anti-vaccine movement.

More than 16 million people aged 12 or above—around a third of the country’s population—remain unvaccinated, according to Robert Koch Institute, Germany’s disease control agency, and health minister Jens Spahn has publicly blamed those people for what he calls a “pandemic of the unvaccinated.”

“There should have been stronger measures taken,” Jonas Schmidt-Chanasit, a virologist at the University of Hamburg, told The Daily Beast. “This rise was expected. But in some states in Germany, prevention was not done with too much enthusiasm and now there’s an overload of ICUs and hospitals. This is a very regional phenomenon.”

The sad political nature of Covid-19 response

In the beginning of this pandemic, and throughout its waves, even continuing into the present, Republicans and Donald Trump as well as his followers have bucked and fought almost every public health directive issued.  They fought masking, distancing, shutdowns, lockdowns, vaccines, and mandates of every ilk, and they still are.

(CNN)— Almost half of the states in the country are reporting rises in Covid-19 cases of late as colder weather drives more people inside and the still-too-high number of unvaccinated Americans continue to get sick and, yes, die.  It’s against that backdrop that a new analysis from the Kaiser Family Foundation has dropped — revealing just how political getting vaccinated has become.

According to the organization’s Vaccine Monitor, unvaccinated Americans are now THREE times as likely to lean Republican as lean Democrat.

“Partisanship stands out as the strongest single identifying predictor of vaccine uptake,” concludes a KFF memo on the findings.

The numbers are startling. Of the 27% of Americans who were still not vaccinated in October, Republicans comprised 6 in every 10. Democrats were just 1 in every 5 of the unvaccinated.

While the unvaccinated have tended to be more Republican since the vaccine emerged earlier this year, the numbers have grown more and more clearly partisan as the year has gone on. In April, for example, 42% of the unvaccinated identified as Republicans while 36% said they were Democrats. By July, more than half of the unvaccinated (51%) were Republicans while 23% were Democrats. As the October numbers show, that trend line has only accelerated as we near the end of the year.

Newsweek–Pastor Robert Smith of the Gospel Light Baptist Church in Amherst, a city in the Canadian province of Nova Scotia, has said, “I followed what God wanted us to do,” when discussing a recent event at his church, which has since been linked to three recent COVID-19 deaths.

At the end of October, the church hosted a multi-day gathering of faith groups across Nova Scotia. Over 100 people attended. They weren’t required to wear face masks or show proof of vaccination beforehand, which violated public health orders.

A guest at the event allegedly caused an outbreak at Rupert House, a local group home for those with intellectual disabilities, in Amherst.  The outbreak led to the death of Victoria Harrison, a 64-year-old vaccinated woman who lived in the house. Harrison died November 10, one week after being diagnosed with COVID-19. At the time of her diagnosis, she was already suffering from pneumonia. The event has also been linked to the COVID-19-related deaths of a man and a woman, both above age 80, in East Cumberland Lodge, a nursing home in Pugwash.

In a recent sermon, Smith reportedly called the deaths “unfortunate.” However, he added, “I followed what God wanted us to do. We had a great week of meetings … A young lady got saved.”

(NYT)–A scientist who has pored over public accounts of early Covid-19 cases in China reported on Thursday that an influential World Health Organization inquiry had most likely gotten the early chronology of the pandemic wrong. The new analysis suggests that the first known patient sickened with the coronavirus was a vendor in a large Wuhan animal market, not an accountant who lived many miles from it.

The report, published on Thursday in the prestigious journal Science, will revive, though certainly not settle, the debate over whether the pandemic started with a spillover from wildlife sold at the market, a leak from a Wuhan virology lab or some other way.

(CNN)A rare storm in Egypt has sparked flash floods that killed at least three people and washed swarms of scorpions into people’s homes.  More than 500 people were stung by scorpions who sought refuge from thunderstorms and torrential rainfall in the southern Egyptian city of Aswan over the weekend. Wounded Aswan residents were transferred to hospitals to receive anti-venom injections, Egypt’s state-run Al Ahram newspaper said.

The Aswan area normally receives around 1 millimeter of rainfall per year, making the heavy thunder and hail storms on Friday a rare event. Egypt’s fat-tailed scorpions, which normally dwell in the desert, are among the deadliest in the world. Without treatment, people can die within an hour of being stung.

Andrew Paul–A swarm of “deathstalker” scorpions surfed the waves of a flash flood into an Egyptian desert town on the eve of the Glasgow Climate Pact last week.  According to the New York Times, least 503 people were stung Friday evening as thousands of Leiurus quinquestriatus scorpions were driven from their mountain abodes following unheard-of torrential downpours that flooded the town of Aswan, destroyed homes, and killed three locals.

Although residents are reportedly “just used to” the occasional deathstalker — who’s sting usually entails severe bite site pain, fever, sweating, vomiting, and diarrhea—the sharp increase in victims had local medical authorities depleting their anti-venom caches and scrounging for backup treatments.

Egypt falls within a region that is being hit particularly hard by our rapidly warming planet, and local meteorologists and climate change scientists were quick to attribute the absurdly Biblical events to our ongoing crisis.  It’s hard to think of something more on-the-nose than “flood of deathstalkers at our literal doorstep,” but it’s also terrifying to try imagining something more on-the-nose.

What America looked like last time the Earth was Ice free

(CNN)-Heavy rains and atmospheric flooding in Washington State over the past few days has caused widespread power outages, displaced hundreds of people and inundated 14 counties with floodwater.

Washington State Gov. Jay Inslee (D) declared a state of emergency on Nov. 15 as a severe storm moved into the Pacific Northwest on Nov. 12, bringing wind gusts above 60 mph and several inches of rainfall across the state.

“The severe storm with floods, landslides, mudslides, and the potential for straight-line winds is causing road closures, the need to establish alternate transportation routes, evacuations, impacts to local utility services including significant power outages, localized reductions in available drinking water, and damage to homes and other public and private property and infrastructure,” the governor said in the proclamation.

“These storms are causing hazardous conditions,” he added.

Three out of every four homes in the Washington town of Sumas have been damaged by floodwaters, officials said Tuesday.  Sumas Mayor Kyle Christensen said his 1,600 residents have been without power for more than 24 hours. City officials said later on Facebook workers were still trying to restore power to a few parts of the city and said crews were “having issues getting to the areas” that still need the power back on. Climate change is causing the Earth’s atmosphere to swell, which could have implications beyond just the health of the planet, a new study suggests.

(AP)-on Friday, the zoo announced that the leopards — Everest, Makalu and Ranney — had died of complications from covid-19, about one month after the animals had tested positive for the coronavirus. While scientists are still studying the effects of the virus on animals, members of several species have been infected and died in zoos around the world. Snow leopards are considered vulnerable to extinction, with just a few thousand estimated to be living in the wild.

(Daily Mail) — Climate change is causing the Earth’s atmosphere to swell, which could have implications beyond just the health of the planet, a new study suggests. Researchers at the National Center for Atmospheric Research have found that the lowest level of the atmosphere, known as the troposphere, has inflated roughly 174 feet per decade between 2001 and 2020.

At this point, it’s unclear how a rising tropopause will impact the planet’s climate or weather, but it could result in planes flying higher to avoid turbulence, Live Science reports. The expansion of the troposphere is directly linked to warming temperatures near Earth’s surface and is important, given that it extends from sea level to ‘about 5 miles above Earth’s surface at the poles to 10 miles at the equator, depending on the season.

As I worked on this record in my hilltop retreat another 50,171 of my fellow humans died of Covid-19, of those 8,040 were my fellow Americans, and of those 41 were my fellow Mainers.

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