Weekly coronavirus-related chat, questions, and minor updates - week of March 21

I'm not going to do my own summary this time because Your Local Epidemiologist covers it well. Here are some highlights:

State of Affairs: March 21

In general, there are four Omicron wave shapes:

1. No large BA.1 or BA.2 wave: There are countries, like India and Bangladesh, in which we know BA.1 and BA.2 arrived, but cases have been eerily minimal compared to other countries. At least for now.

2. Large BA.1 and no BA.2: The best example of this is South Africa. [...]

3. Small BA.1 and large BA.2: This is best portrayed by Denmark [...]

4. Double hump wave: And then there are countries, mostly in Europe, which are seeing two humps in their Omicron case pattern. One from BA.1 and the other from BA.2. Overall, cases are still rising across Europe, but have slowed down. Germany, Greece, and Switzerland are losing momentum. The Netherlands peaked.

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BA.2 now makes up 23% of cases in the U.S. and we expect this to increase to 100% over time. We don’t know what BA.2 will look like in the U.S. We could see a second hump, like Europe, or no overall increase, like South Africa. Or, perhaps we may see an increase in only some states. (This is exactly what happened with Alpha and has my vote.)

BA.2 makes up the highest proportion of cases in the Northeast (see pie charts below; pink=BA.2; purple=BA.1). So, if we do see an uptick in cases, it would be in the Northeast first.

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On a national level, case trends have been declining but are starting to lose momentum and plateau. New York is the only state that has an increasing case trend, with a 15% increase in the past 14 days. It’s an increase from a very small number to another small number, but we should keep an eye on it.

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Even though cases in the rest of the U.S. are declining/plateauing, there are still pockets of high transmission.

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Because cases continue to decline, national hospitalizations are declining fast and the trend is looking really good. In fact, we’re close to reaching our lowest recorded COVID hospitalizations since the pandemic began.

Deaths also continue to decline slowly but surely. Unfortunately, today, we’re still loosing 1,100 Americans per day to COVID19.

One in five South Koreans have had Covid, as latest wave sees deaths surge

Cases began rising in February, driven by the highly transmissible Omicron variant. The country is now seeing hundreds of thousands of new cases each day -- some of the highest daily averages in the world.

Authorities reported 395,598 new cases on Thursday, pushing the total caseload to 10.8 million, according to the Korea Disease Control and Prevention Agency. That makes up about 20% of the national population -- meaning roughly one out of every five South Koreans have now been infected at some stage of the pandemic.

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And Wednesday saw the country's deadliest day so far, with 470 new Covid deaths -- the highest daily coronavirus death toll since the virus was first detected in South Korea, according to data released Thursday.

But with almost 87% of South Korea's 52 million residents fully vaccinated and 63% of residents having now received booster shots, the country's infection and death rate is still far lower than many other nations.

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Despite the surge, South Korea is easing its Covid-19 restrictions, and public opinion appears to support those moves.

On Monday, the cap on private gatherings was upped from six to eight people; other relaxations include scrapping the seven-day quarantine for fully vaccinated international arrivals, except for those coming from "high-risk countries" including Pakistan, Uzbekistan, Ukraine and Myanmar. The government has also stopped enforcing vaccine passes and scaled back its once-aggressive system of contact tracing and quarantine.

"We see this could be the last major crisis in our Covid responses, and if we overcome this crisis, it would bring us nearer to normal lives," Son, the health official, said in a briefing last week.

From Our World In Data, the seven-day average for cases in South Korea is highest in the world at 687 per 100k. It seems to have peaked.

The death rate is 4x lower than Hong Kong at 7 per million, but it lags cases and it's still rising.

Latest version of omicron accounts for most new infections in many parts of the U.S., genomics testing shows (Washington Post)

The recently emerged version of the coronavirus called BA.2 that has driven a wave of cases in Europe now accounts for as much as 70 percent of new infections in many parts of the United States, according to an estimate from the genomics company Helix that could signal a new chapter in the third year of the pandemic.

The estimate from Helix, which conducts genomic sequencing on virus samples, comes amid concerns that Europe’s surge in infections will be replicated in coming weeks in the United States, where caseloads have often trailed those in Europe by roughly a month.

It’s clear BA.2, officially considered a subvariant of omicron, is gaining traction as the previously dominant lineage of omicron subsides. In two or three weeks, “everything in the Northeast is going to be BA.2,” predicted Jeremy Luban, a virologist at the University of Massachusetts Medical School.

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The Centers for Disease Control and Prevention on Tuesday reported that BA.2 accounts for 35 percent of coronavirus infections nationally, up from 22 percent a week ago. In New England, the CDC reported, BA.2 accounts for 55 percent of new infections, compared with 39 percent last week. The Helix data is more up to date and includes samples from many states, including California, Florida, Pennsylvania, Massachusetts, Michigan and Texas, Helix chief scientist Will Lee said.

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So far, no broad surge of new cases has emerged in the United States. There are so many variables at work when it comes to coronavirus transmission — including human behavior, perhaps the hardest factor to predict or measure — that disease experts cannot say with confidence whether and when a new wave will materialize.