And Now, here comes COVID-19 version BA.2, BA.4, BA.5,...

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In summary, the BA.2 variant of the Omicron variant of the COVID-19 virus is now nearly a quarter of all COVID cases in the U.S., and is particularly prevalent in the Northeast. However, since the BA.2 variant is more transmissible than the BA.1 variant, many communities can relax since there is no evidence that the BA.2 lineage is more severe than the BA.1 lineage. CDC continues to monitor variants that are circulating both domestically and internationally.f
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Popular article referring to the BA.2 variant:
"It might be, from a human's perspective, a worse virus than BA.1 and might be able to transmit better and cause worse disease," says Dr. Daniel Rhoads, section head of microbiology at the Cleveland Clinic in Ohio. Rhoads reviewed the study but was not involved in the research.

The US Centers for Disease Control and Prevention is keeping close watch on BA.2, said its director, Dr. Rochelle Walensky.

"There is no evidence that the BA.2 lineage is more severe than the BA.1 lineage. CDC continues to monitor variants that are circulating both domestically and internationally," she said Friday. "We will continue to monitor emerging data on disease severity in humans and findings from papers like this conducted in laboratory settings."

Popular article: (many words, little data)

Preprint article referring to the BA.2 variant:
Soon after the emergence and global spread of a new severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) Omicron lineage, BA.1 (ref), another Omicron lineage, BA.2, has initiated outcompeting BA.1. Statistical analysis shows that the effective reproduction number of BA.2 is 1.4-fold higher than that of BA.1. Neutralisation experiments show that the vaccine-induced humoral immunity fails to function against BA.2 like BA.1, and notably, the antigenicity of BA.2 is different from BA.1. Cell culture experiments show that BA.2 is more replicative in human nasal epithelial cells and more fusogenic than BA.1. Furthermore, infection experiments using hamsters show that BA.2 is more 1,2 pathogenic than BA.1. Our multiscale investigations suggest that the risk of BA.2 for global health is potentially higher than that of BA.1.

Preprint article: (At 52 pages, too many words!)

[edited 1hr. after posting: Added preprint Abstract]
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The relative prevalence of BA.2 does seem to be increasing both at the worldwide level (as assessed by sequencing data from GISAID from NextStrain) as well as in the US (as assessed by sequencing data from the US CDC):

Here's the GISAID data from NextStrain, with BA.2 being the darker orange color that has been steadily rising in prevalence from Jan-Feb:

Here's the CDC data showing the increasing prevalence of BA.2 (indicated as the pink color) over the past few weeks:

These data support the idea that it is more transmissible than the original Omicron BA.1 variant. It remains to be seen whether it can cause a new wave of infections or whether it is similar enough to BA.1 that vaccines and prior infections are able to provide sufficient immunity to prevent another major wave of cases.

I remember there being similar concern about the AY.4.2 variant of Delta, where similar data had suggested increased transmissibility over the original Delta strain, but this variant never caused a major wave of infection (mainly because Omicron overtook it and the other Delta variants).
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"Topol says the study’s results mean that many communities can relax. “Instead of thinking that [BA.2] is the new bad variant, I think we can put that aside. I see it as not a worry,” he says."
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March 15, 2022 - CBS News / Omicron BA.2 sub-variant now nearly a quarter of new COVID cases in U.S., CDC estimates
The BA.2 sub-lineage of the Omicron variant now makes up nearly a quarter of new COVID-19 infections nationwide, the Centers for Disease Control and Prevention estimated Tuesday, up from around 1 in 10 new cases just a week prior.

Since January, Omicron has made up virtually all new infections in the U.S. Like in many countries abroad, most cases in the U.S. had been caused by a sub-lineage of Omicron known as BA.1. But while both BA.1 and BA.2 can be traced back to some of the earliest samples gathered of Omicron, BA.2 has only recently begun to climb in prevalence.

BA.2's prevalence is the highest in the Northeast, according to the CDC's "Nowcast" estimates published Tuesday. In the region spanning New York and New Jersey, the agency estimates 39.0% of circulating viruses are BA.2. In New England, prevalence of BA.2 is at 38.6%.
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I believe most Omicron cases in NZ are the BA.2 variant. Which is the likely variant I caught last week. My self isolation period ends in two days; just a slight cough now and my nose is still stuffy but it isn't runny like before and I'm not sneezing.
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A close family friend has a case of COVID-19, and about 70% chance that it is BA.2, based on current numbers in CDC Region 2. He is double vaccinated + first booster. His wife is procuring the antiviral treatment. His condition was described as 'sounding bad', which I interpret as a bad cold.

Taking a look at New York State, where masks mandates have expired for about a month, and BA.2 is about 71% of cases, and B.1.1.529 is the remainder:

Age group    Cumulative  Jan-Mar '22  1Q22/Cumul.
90 and Over    8,716        1,152      0.1322
80 to 89      14,671        1,732      0.1181
70 to 79      14,248        1,699      0.1192
60 to 69      10,010        1,139      0.1138
50 to 59       4,772          567      0.1188
40 to 49       1,716          213      0.1241
30 to 39         710           85      0.1197
20 to 29         227           36      0.1586
10 to 19          31            9      0.2903
 0 to  9          30           12      0.4000
All ages      55,131        6,644      0.1205
Cumulative is the total since the beginning of March 2020, Jan-Mar '22 is the last three months, and the last (rightmost) column is the ratio of Jan-Mar'22 to Cumulative.

New York State fatalities reported to CDC = 70,251
The confirmed cases = 55,140 = 55,131 + 9 unknown

Note that 40% of the child (ages 0-9 yrs) deaths and 29% of the adolescent deaths occurred during the last 3 months. Nearly 16% of deaths in the young adult (20-29) death occurred in the last 3 months in NY. The last 3 months represents about 12% of the last 25 months, since the beginning of March 2020.

Since March 2020, New York has reported 4,975,747 positive cases, in a population of ~2.020 M, and with a reported 104,592,544 tests, or 5x the population. - updated daily - cumulative database of confirmed cases
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New York state officials this week announced that two new omicron subvariants, dubbed BA.2.12 and BA.2.12.1, have become the dominant forms of the Coronavirus in the central part of the state. For weeks, infection rates in central New York have been at least twice the state average, according to data from the state health department.

The new omicron sublineages in New York have picked up mutations that may help the virus enter cells faster and evade vaccine- and infection-boosted immunity, said Andy Pekosz, a virologist at the Johns Hopkins Bloomberg School of Public Health.
In March, the two subvariants accounted for more than 70% of reported Covid-19 cases in central New York. So far in April, the data show an increase to 90% of all new cases.
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A couple of new kids on the block...
"Working through the weekend, he and his colleagues found that they had. A month earlier — during the first week of March — the BA.4 and BA.5 sequences comprised around 5% of the roughly 500 genomes sequenced in South Africa. By the first week of April, the portion had risen to 50%. That week, an international virus classification group determined that BA.4 and BA.5 were indeed their own separate lineages on the Omicron family tree and gave them their names."

"One thing that makes BA.4 and BA.5 stand out to virologists is an amino acid mutation they share called F486V. It is located on the viruses’ spike protein near where the protein attaches to the ACE2 receptor on cells — an interaction that opens the door to infection. Important antibodies generated in response to COVID-19 vaccines and to prior infections with SARS-CoV-2 neutralize the virus by clinging to this spot."
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Now in April, after falling through March, positive SARS-Cov-2 infections have picked up again in New York State thanks to subvariants BA.2.12 and BA.2.12.1. Daily deaths which had fallen into single digits have returned to double digits and may continue to increase slightly as the rate of infections increase.

The Omicron variant was first confirmed in New York State on December 2, 2021. During the winter Omicron wave that followed, the lineages BA.1 and BA.1.1 were most prevalent, and in February, a rapid growth of BA.2 began.

On April 13, 2022, the Department announced the emergence of two recently-identified Omicron subvariants in New York State, BA.2.12 and BA.2.12.1. Both subvariants are sub-lineages of BA.2, and at that time, were estimated to have a 23% – 27% growth advantage above the original BA.2 variant. BA.2.12.1 has been noted to be of higher concern, given additional mutations.

For samples of SARS-CoV-2 collected between March 27, 2022 -- April 9, 2022 from New York that are sequenced and uploaded into GISAID, 100% were the Omicron variant. During this time period 0.8% of Omicron sequences were lineage BA.1, 7.0% were BA.1.1, 57.4% were BA.2, 9.5% were BA.2.12, and 25.4% were BA.2.12.1.

Between April 10 and April 16, 2022 CDC’s program for HHS Region 2 (New York, New Jersey, Virgin Islands, Puerto Rico) estimated 100% of samples were the Omicron variant. During this time period 2.1% of Omicron sequences were lineage BA.1, 45.7% were BA.2/BA.2.12 and 52.3% were BA.2.12.1.

Monitoring Omicron BA.2.12.1
For more information on the emergence of BA.2.12.1 in New York State, the graph below presents the percent of sequences in GISAID, with additional patient location information from laboratory databases, classified as BA.2.12.1 in each region over the past three months.

In the Central New York region, which has experienced the most elevated case rates in New York State since March 2022, BA.2.12.1 was first detected in February 2022 and rose to 77% of sequences by April 2022. Furthermore, in April BA.2.12.1 also represented >50% of sequences in the Finger Lakes region, and >25% of sequences in Capital Region, Mohawk Valley, and Southern Tier regions, based on sequences through April 20, 2022.
The most vulnerable are those 65 and older, but there are occasional deaths in the 30-, 40- and 50-somthing populations, and once in a while in the 20-something population.
Reinfections also seem to be trending with new positive cases.
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These graphs can get tidied up but with those two large peaks at 650 and rolling 7 day average at 240 deaths per day by April 22nd these numbers are still high.

Considering we appear to be at the “living with it” stage.

Another poster pointed out we cannot relay on cases data anymore as we are not testing anywhere near previous levels.

With all restrictions lifted here the virus will find its way to the old, whose immune response to the vaccine will not be as effective, the unvaccinated (plenty of them) and immune suppressed.

A very stressful situation for a family with a child with leukaemia, auto immune or grandparents over 75.

Total isolation the only real protection?
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Total isolation the only real protection?
That would be optimum... but realistically difficult to put into practice based on personal experience. My wife is immunosuppressed so we both spent about two years in hermit mode, that worked up until last January, then it didn't. (Vaccinated, boosted, etc.) and still managed to get the virus. Fortunately with the Vaccinations it amounted to sever Flu symptoms rather than something worse. I highly recommend vaccination.
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Reports of new cases were nearly flat in the U.S. at the beginning of April, but as the month draws to a close, they are increasing in all but three states, signaling a wave that is increasingly national in scope.

Hospitalizations are also on the rise nationwide, after plummeting early this month to their lowest point since March 2020. More than 30 states and territories have seen their hospitalization rates tick up in the past two weeks, and in much of the Northeast, the number of people hospitalized with the Coronavirus has increased since mid-month by 40% or more.

“It’s not over yet,” Toner said Friday. “It may be a mistake to relax all of our protective measures too quickly.”

And according to the NY Times, "new data from the Centers for Disease Control and Prevention shows that more than 60% of Americans have been infected with the Coronavirus at least once, . . . " I expect this is based on some analysis or projection. For example, NY State has reported 5151200, or about a quarter of the population has had a positive test in the last two years, but the actual number could be greater, but to don't believe 2.33 times greater. NY State has conducted slightly more than 107.8 million tests, for people with symptoms or those who were exposed, and some more frequently because of health care concerns, or someone needs a negative test in order to travel or perform duties. Of course, there are many who may have been exposed and were asymptomatic, or had very mild symptoms, but they may not have been tested.

Cases are certainly increasing as NY has lifted the mask mandates and social distancing, but they are still in place in government offices and some businesses at the owner/operators discretion. Cases have increased following the Easter holiday, and the daily death toll has begun to increase from mostly single digits to double digits, mostly between 10 - 21 so far. Although there have been a few deaths in the 20-60 year range, those 65 and older are still the most vulnerable and account for the majority of deaths.

NY State has reported 218554 reinfections so far.
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ABC News reports "COVID-19 hospital admissions, deaths forecasted to rise in the US for first time in months"

In New York State, infections are on the rise with BA.2, BA.2.12 and BA.2.12.1. The numbers for BA.4 and BA.5 have not been reported yet.

The forecast now predicts that approximately 5,000 deaths will occur over the next two weeks, with Ohio, New York, and New Jersey projected to see the largest totals of daily deaths in the weeks to come.

On average, more than 2,200 virus-positive Americans are entering the hospital each day -- a total that has increased by 20% in the last week, the CDC reports. This also marks the highest number of patients requiring care since mid-March.

Overall, there are about 18,300 patients with confirmed cases of COVID-19 in hospitals across the country, up by 18% in the last two weeks, the Department of Health and Human Services reports.
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Coming out of a holiday so numbers not necessarily 100%
This where the UK is now. Those big spikes in April (650 deaths) have not been adjusted as yet.


This from the ONS

Some take aways from that link.

The number of deaths involving COVID-19 in the UK increased from 1,152 to 1,185 in the latest week (ending 22 April 2022).

Deaths involving COVID-19 accounted for 9.7% of all deaths in the latest week; a decrease from 10.2% in the previous week.

The number of deaths involving COVID-19 in England increased or remained the same for those aged 45 years and over but decreased or remained at zero for those in age groups under 45 years in the latest week.

Also, I mentioned ethnicity before but I do not think male and female death rates have been discussed that much?

A a lot of variation with the error bars??
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New York State reported its first day with over 10k cases since mid January, and 21 deaths. In the past several days, there have been three deaths in the age group 30-39 years, and one death in 20-29 age group, so Omicron is affecting younger people. In April, there was one death of a child in the 0-9 age group. It is expected that cases will increase in the near term, and likely the mortality rate.
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In the past several days, there have been three deaths in the age group 30-39 years, and one death in 20-29 age group, so Omicron is affecting younger people.
Any information on vaccination status and any corbidities in the above four ?
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The Coronavirus mutant that is now dominant in the United States is a member of the omicron family but scientists say it spreads faster than its omicron predecessors, is adept at escaping immunity and might possibly cause more serious disease.

A genetic trait that harkens back to the pandemic’s past, known as a “delta mutation,” appears to allow the virus “to escape pre-existing immunity from vaccination and prior infection, especially if you were infected in the omicron wave,” said Dr. Wesley Long, a pathologist at Houston Methodist in Texas. That’s because the original omicron strain that swept the world didn’t have the mutation.
The omicron “subvariant” gaining ground in the U.S. — known as BA.2.12.1 and responsible for 58% of U.S. COVID-19 cases last week — isn’t the only one affected by the delta mutation.

Although most people don’t know for sure which [Omicron] variant caused their illness, the original omicron caused a giant wave of cases late last year and early this year.
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The omicron variant of Covid-19 has branched out into more transmissible and evasive versions.
Treatments have also hit some snags. The mutations in omicron have rendered several monoclonal antibody treatments ineffective. Some doctors have also reported that Covid-19 symptoms in patients rebounded after completing a course of the antiviral drug Paxlovid.

All the while, another wave of Covid-19 cases is poised to wash over the US as summer heat forces people back indoors, creating more opportunities to spread the virus. Many parts of the country have also lifted face mask requirements and social distancing rules. Covid-19 cases number around 100,000 per day, but the rise of at-home testing means the official tallies are, if people bother to get tested at all.

I was just listening to an interview with an epidemiologist who mentioned that with the Omicron variants, a more people are getting reinfected, and it may happen more than once or twice. Look for the episode, "How often can you get Covid?"
Vox Today Explained asked a researcher who has been studying omicron reinfections.
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I talked with a Canadian friend and colleague today via FaceTime. He apologized for a persistent cough then mentioned that he had tested positive for SARS-Cov2. He apparently contracted SARS-Cov2 from exposure to his son, who caught it from a teacher at school. Although his son wears a mask (N95) at school, the teacher and most other students do not. Of course, the student must remove his mask to drink and eat. So SARS-Cov2 (most probably a variant or subvariant of Omicron) is circulating in the schools in Ontario.

My friend (in his 30s) has had the two Pfizer vaccinations last year, and more recently a booster with Moderna, but I don't know how long ago. His COVID-19 symptoms are mild.

He thought his symptoms were allergies acting up, but his allergy medications didn't affect the symptoms. He then did a home test, which indicated positive. I don't know if he did a PCR test. He is isolating at home.
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I think there needs to be some international coordination to get cases right down. NZ managed to go many months without any detected cases, though we had our borders closed. It won't be easy, and is probably too delusional to think it is viable.
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Update on BA.4 and BA.5 now becoming dominant.

'The worst version' of COVID SARS-Cov2 is spreading.​
For anyone who hasn’t been paying attention, the Omicron strain that triggered last winter’s massive COVID wave (BA.1) is now extinct. In March, it was supplanted by the even more transmissible BA.2 … which was supplanted in May by the even more transmissible BA.2.12.1 … which is now being supplanted by the (you guessed it) even more transmissible BA.4 and BA.5.

Experts say BA.5 is the one to worry about: “The worst version of the virus that we’ve seen,” as Dr. Eric Topol, the founder of Scripps Research Translational Institute, recently put it. Together, the closely related BA.4 and BA.5 now account for the majority of new U.S. COVID cases, according to the latest data from the Centers for Disease Control and Prevention — but BA.5 (36.6%) is spreading a lot faster than BA.4 (15.7%). By early July, it will be the dominant strain in the U.S.

A.4 and BA.5 Omicron: How worried should we be?​

Omicron - B.1.1.529, BA.1, BA.1.1, BA.2, BA.3, BA.4 and BA.5​

First identified: South Africa

BA.4 and BA.5 are spreading in NY and CDC region 2 during June, and are expected to spread during July.


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'The worst version' of COVID is spreading. Can we update our vaccines in time?​

Andrew Romano
Andrew Romano
·West Coast Correspondent
Thu, June 30, 2022 at 9:19 AM

For anyone who hasn’t been paying attention, the Omicron strain that triggered last winter’s massive COVID wave (BA.1) is now extinct. In March, it was supplanted by the even more transmissible BA.2 … which was supplanted in May by the even more transmissible BA.2.12.1 … which is now being supplanted by the (you guessed it) even more transmissible BA.4 and BA.5.

Experts say BA.5 is the one to worry about: “The worst version of the virus that we’ve seen,” as Dr. Eric Topol, the founder of Scripps Research Translational Institute, recently put it.
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Global COVID cases rise as BA.4 and BA.5 expand​

COVID-19 cases jumped 18% last week and are at their highest levels since April, and the increase comes as the more transmissible Omicron BA.4 and BA.5 subvariants cause most infections, the World Health Organization (WHO) said today in its latest update.

BA.4, BA.5 make up 55% of global samples​

Four of the six WHO regions saw rises last week: the Eastern Mediterranean, Europe, Southeast Asia, and the Americas. Globally, deaths stayed level, but were up in the Eastern Mediterranean, Southeast Asian, and Americas regions.

About 4.1 million cases were reported to the WHO last week, likely an undercount given reduced testing in many countries. The United States, Germany, Brazil, Italy, and China reported the most cases.

The Hill - New omicron subvariant BA.5 now a majority of US COVID-19 cases

Pediatric COVID-19 cases rising for 1st time since May​

Last week, nearly 76,000 children tested positive for the virus.

As more infectious COVID-19 variants become dominant in the U.S., there are renewed signs that COVID-19 cases may be back on the rise across parts of the country.
The national resurgence comes as the number of children testing positive for the virus also sees an increase again.
New infections among children had been on the decline since May, however, for the first time in nearly two months, there has been an uptick in the weekly total of pediatric COVID-19 cases.
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My daughter's roommate has tested positive for SARS-Cov2 infection, which she probably contracted on a flight from Europe to US about a week ago. Roommate's mother, who is not vaccinated (antivaxxer), also tested positive. The roommate has had a strong cough and fever, although the fever is down today. She got a prescription for Paxlovid. Other symptoms included losing sense of taste and diarrhea.

Both my daughter and her roommate are vaccinated and boosted, and my daughter has so far tested negative, and shows no symptoms.

I suspect the roommate has BA.4 or BA.5, or some other Omicron subvariant. Waiting for more information and to see if my daughter comes down with it.
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Vox - The omicron subvariant is tuned to evade immunity, even from previous omicron infections.

Florida records 146,069 new COVID-19 cases, 771 deaths in 2 weeks (that's more than 10K/day cases, and > 55 deaths/day over a 14 day period. Numbers may be high due to lag in reporting deaths over holidays.

I also read a story about some patient with 3 unknown (as yet unidentified) SARS-Cov2 subvariants, but I don't know how recent the article, since I misplaced it.

Some notes from last week (July 13) from the NY Times Coronavirus page

  • The daily case average grew to more than 129,000 on Tuesday, and cases are rising in more than 40 states. Since cases have always been an undercount, it is likely that the true number of cases is far higher — particularly since test positivity rates are also increasing sharply nationwide.
  • These increases come as the BA.5 variant, believed to be the most transmissable variant yet of the coronavirus, is emerging as the country's dominant virus strain.
  • Hospitalizations are also rising in the U.S. That pattern is similar to hospitalization surges seen earlier this summer in countries where BA.5 first began to circulate. More than 37,000 people are in American hospitals with the Coronavirus on an average day, an increase of 17 percent since the start of the month.
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Reuters, Fri, July 22, 2022 - New Zealand COVID-19 death rate at record levels
Deaths from the virus reached 151 in the seven days to July 16, compared with 115 in the worst week of the previous wave, in March, according to Health Ministry data. In the latest 24 hours, 26 people died from COVID, all aged over 60, the ministry said in a statement on Friday.

The Omicron BA.5 sub-variant is driving the current wave in New Zealand, which has 5.1 million people. There have been 64,780 active cases in the past seven days, although authorities say many infections are unreported.

Subvariant BA.5 seems to be running amok around the world.
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I just learned that my brother, his wife and my nearly 93-year old father has Covid-19. All three were quite ill for 5 days. They are currently testing negative. That may explain my dad's cognitive issues.

One of my daughter's friends had Covid-19 a few weeks ago, and while the friend (under 30) 'recovered', she has had breathing issues since. So recovery is not necessarily a full recovery, and there may be permanent damage to lungs and circulatory system.
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I hope things are OK, but it shows that Covid continues to be a real issue. It's worth remembering that a full recovery can take some weeks, so hopefully these issues should resolve.

I thought people might be interested in some of the latest developments and ideas, though you need Medscape membership (free) to access the article.
We had a spike but seem to be on the way down again.
We got to 16,000 from 5000 in a few weeks in hospital.
  • #35
I got both my flu shot and COVID Pfizer booster today (the one with targeted Omicron protection).

I previously got Moderna only, so this was a switch up (only b/c Sam's Club didn't offer Moderna yet).

Will there be a BA.xxxxxx booster coming out anytime. Does the Omicron version help with the BA.xxxxxxx one at all?

And if more and more variants come out, how many targeted boosters do you think we'll ultimately get. Would this go the way of flu shots, where they target 3 or 4 expected strains each year?

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