Case Update, January 12, 2022; Omicron Update, Omicron now at 98% of COVID cases.

This is a case update. Cases continue be super high in the US. Over the past 2 years, the Sunday numbers are always the lowest of the week, but they also usually predict what will happen to the number in the following week. If you look closely at the case graph for the US, you can easily see the weekend dips in numbers. For this Sunday’s number, the rise in cases is much lower relative to the previous week than the number for the 26th. Because of this, I expect new case numbers in the US to peak this week or next.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, January 12th, 2022
Endcoronavirus State Level Map, January 12th, 2022

All that being said, cases are still extremely high in every state in the US right now, and still rising. Only Washington DC appears to be seeing a drop in cases right now. Deaths have not yet started to increase in the US. Deaths have tended to increase between 2 and 5 weeks after the start of a peak, so it’s still too early to know how high they will be.

California and San Diego County are of course also experiencing extremely high numbers of cases right now. LA County again has the highest number of cases in the US, with a staggering 384,000 active cases right now.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

In Denmark, which has a lot of testing and virus surveillance, deaths are up but at a very moderate rate. At the peak of last year’s Winter surge, the COVID fatality rate was 0.94% (deaths/confirmed cases). For the Omicron wave in Denmark, the rate has been only 0.053%. This rate is very small, but it’s still not zero, so if you have COVID risk factors, continue to take precautions.

From Worldometer.
From Worldometer.

Omicron Update: The CDC recently released an update on variant proportions. Omicron is now 98% of SARS-2 cases for both the US and the Southwest region This is great news.

From the CDC page on Variant Proportions. Accessed January 12th, 2022.
From the CDC page on Variant Proportions. Accessed January 12th, 2022.

Omicron infections are proving to be very mild in most patients. That being said, there are a tremendous number of cases right now. I have lots of friends and family who have had COVID in the last 2 weeks, and several businesses near me have had closures or reduced hours because of under staffing. Additionally, hospitalizations are way up, and doctors and nurses are pretty exhausted taking care of all the sick people.

Hospitalizations, from the CDC website.

Managing COVID right now: Hospitalizations are way up, and lots of people are getting tested, either in a health care setting or with home rapid test a drug store. For this reason, tests are now in short supply everywhere. If you don’t need a test to go back to work or school, please consider NOT testing yourself just to satisfy your curiosity. If you do need to test yourself, please don’t test yourself every day, and try to reduce the number of tests you use. Since current tests are based on the Wuhan strain, there are lots of false negatives right now, especially with the rapid tests, since Omicron is the dominant strain. So a negative test is not very meaningful if you have symptoms. Most people’s Omicron symptoms last between 2 and 5 days.

Although Omicron causes less severe disease in general, there are a huge number of cases right now and some are still severe. If you don’t think you need medical attention, and are just experiencing cold-like symptoms, consider NOT going to the hospital for a test or to be treated. Please keep space open for those with more severe symptoms. However, if you have one of the classic COVID symptoms, like shortness of breath, don’t hesitate to check in with your doctor.Please don’t assume your vaccination, even with booster, will prevent you from getting COVID right now. Many fully vaccinated and boosted people are getting COVID right now because the Omicron variant is so different from the Wuhan strain used to make the vaccines.

Also, I still usually wear a mask indoors. If you choose to wear a mask, wear an N95, KN95, or KF94. Don’t imagine that a blue surgical mask, cloth mask, or neck gator is going to prevent infection. These masks are ineffective against Omicron. Effective medical grade masks are easily available at stores and online right now.

Remember to supplement with Vitamin C, Zinc, and especially Vitamin D! This is for everyone, to prepare your body should you get infected, or if you have Omicron right now.

Omicron scorecard: Here’s my “scorecard” for this week. The new data from South Africa suggests that Omicron infection is “back compatible” with Delta, preventing Delta infection. This is great news and suggests Omicron infection will prevent future infections from other variants. As a reminder, I am not an epidemiologist, I’m a molecular biologist. This is my informed but not expert opinion.

1) Omicron must not use the ADE pathway to produce more severe cases: Looking at the available data so far, Omicron may preferentially infect those who have been previously infected, but cases are still mild, and fatality rates very low. So for now, this criteria is met.

2) Low fatality in older populations: South Africa has a relatively young population, so reports of mild symptoms may not carry over to countries with older populations. The UK data from this week suggests that Omicron deaths will be low, even in older populations. We are seeing a slight drop in deaths already.

3) Displace Delta: Delta has a much higher case fatality rate in the US than Omicron appears to have. For Omicron to end the pandemic, it must displace Delta from the COVID population of strains. Data from the US and UK suggest this is happening!

4) Omicron must not circulate independently from Delta: Related to the above, if Omicron is very different from Delta, it may act as a completely different virus. There’s a chance that Omicron may displace Delta on the short term but still allow Delta to persist. Since Omicron is displacing Delta, it looks like this criteria may be met, but we won’t know for sure until we can see if Delta pops back up after the Omicron wave is over.

5) Omicron infection must immunize against future SARS-2: Since Omicron appears to infect those with immunity to Delta, it may be that it is different enough that it will not provide immunity to Delta or other SARS-2 strains. This criteria is not strictly necessary if Omicron completely displaces other SARS-2 strains (see 3 above), but it would be really nice to have some protection against future strains. We won’t know for sure about this one until a new version of COVID arises. The new data from Denmark suggests this criteria is met!

I believe that the Pandemic is almost over, but there’s one big final push! Continue use your head, but be encouraged!

Don’t fear, but be smart!
Erik

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