Case Update: January 18, 2022; Omicron now 99.5% of cases, Infection rate by Delta and Omicron, new CDC mask guidance

This is a case update. I’ll also give an update on the state of Omicron in the US, and show some data from a great new paper from California. I’ll also comment on the new mask guidance by the CDC.

New cases have apparently peaked in the US over the past week, reaching a high of 1.5 million cases in 1 day. Cases are now declining for the US as a whole, driven by declines in several Eastern states like New York, New Jersey, and Florida. Cases have not yet declined in most US states, although many may be peaking right now as new cases have slowed. So far, deaths are only slightly up for the US. Hospitalizations appear to have peaked as well.

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 17th, 2022
Endcoronavirus State Level Map, January 18th, 2022
Hospitalizations, from the CDC website.
Endcoronavirus State Level Map, January 18th, 2022
Endcoronavirus State Level Map, January 18th, 2022

California and San Diego County new cases appears to be still going up, but new cases have slowed, and I suspect will start declining soon, maybe this week. Again, deaths have not yet started to increase. Deaths usually follow cases by between 2 and 4 weeks.

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.

Omicron Update: Omicron infections now represent 99.6% of infections in the US. Omicron has now almost completely eliminated Delta in the US. It continues to appear that Omicron represents the end of the pandemic, although it will go out with a bang!

From the CDC page on Variant Proportions. Accessed January 18th, 2022.
From the CDC page on Variant Proportions. Accessed January 18th, 2022.

I finally got COVID!: Last Friday I tested positive for COVID! I almost certainly got it while in a “gray area” situation that had some risk, but might have been OK with a previous variant. Most symptoms have been very mild, but I was super achy for a day. I’m still not feeling strong and I nap a lot. No loss of taste and smell, or shortness of breath, but I did have a fever during my achy day. As of yesterday, I still test positive, so my body is still fighting.

Omicron much milder than Delta, but evades vaccines much more: As I’ve stated before, it’s a little scandalous how few useful papers have come out of the US this last year. But a UC Berkley lab has a great new paper in pre-print right now. They had the foresight to collect data for a time period in December when both Delta and Omicron were present in the population. The paper is a little opaque because much of the information is in dense tables, with less than useful headings (SGTF = Omicron, non-SGTF = Delta) but has some great information nonetheless.

Table S10 is the most interesting to me. I’ve turned some of the data into graphs to make the meaning more clear. The table compares the number of infections by Delta or Omicron in unvaccinated persons, those with differing levels of vaccination, and with documented previous infection (natural immunity). Vaccination definitely helps prevent infection by the Delta variant, but Delta still infects vaccinated individuals. This may be because vaccine efficacy goes down over time, the Delta variant is too different to be completely stopped by the Wuhan based vaccines, or some combination of both.

Graph is by me, from data in Lewnard et al, Table S10. Cases with Natural Immunity were multiplied by 6 to normalize for the number of documented infected individuals in the population. In San Diego County, there are roughly 500,000 documented COVID-19 cases, out of a population of approximately 3 million in the county.
Graph is by me, from data in Lewnard et al, Table S10. Cases with Natural Immunity were multiplied by 6 to normalize for the number of documented infected individuals in the population. In San Diego County, there are roughly 500,000 documented COVID-19 cases, out of a population of approximately 3 million in the county.

Omicron is far more infectious in general, and also is far more infectious in vaccinated individuals. In fact, more people in this study were infected by Omicron if they had 2 doses of the Pfizer or Moderna vaccines. Since a majority of Southern Californians are vaccinated, it this does not necessarily mean that vaccination made it more likely to be infected by Omicron, but it’s a striking result. Yes, Antibody Dependent Enhancement may play a role in this result, although the exact reasons are likely a complicated combination of factors.

Another interesting result is that infections are far lower among those with previous infections. For the graphs I include, I’ve even normalized this number for the proportion of people who have been infected by multiplying the given number by 6 (see graph for details). In spite of this, infections are FAR lower in those previously infected. This is consistent with the data from Israel suggesting that natural immunity is far better than vaccination at preventing future infection.

Most European countries and Israel include previous infection in immunity requirements. The US still does not accept previous infection as prove of immunity. As we continue to argue about vaccine mandates, it would be wise to include previous infection as proof of immunity.

See a video by Dr. Mobeen Syed for a detailed analysis of this paper.

Better super late than never I suppose: After many months of treating all masks as essentially equal, the CDC released new guidelines regarding masks that points out that simple cloth masks are not as effective as medical grade respirators like N95s, KN95s, and KF94s. They still don’t go far enough in my opinion, since they still promote surgical masks as effective. Blue surgical masks are loose fitting on the side and allow air to enter and exit without being filtered. If you wear a mask, wear a medical grade respirator, not a blue surgical mask.

I believe we are a few weeks away from the end of the pandemic! As for me, I’m really looking forward to eating indoors at a restaurant again!

I know a lot of this post is dense and complicated. Your questions will help me be more clear.

Don’t fear, but be smart,
Erik

3 thoughts on “Case Update: January 18, 2022; Omicron now 99.5% of cases, Infection rate by Delta and Omicron, new CDC mask guidance

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