Isn't it kind of insane that BA.1 might have infected billions worldwide but BA.2, which emerged from the same host/reservoir a month later or so, is looking like to outcompete all of these BA.1 lineages?

It's also noteworthy that BA.2 is likely a recombinant virus, sharing every mutation past the NTD portion of the spike with BA.1 but being a thing of its own before that spot. It turns out this is a template-switching location and some delta/omicron recombinants from January also split around the same spot.

So the evolutionary history of Omicron is looking like:

1. B.1.1 virus gets in an animal reservoir/immunosupressed person in early 2020, evolves throughout the next 18 months;

2. Said person or reservoir also gets infected with a 'pristine' SARS-CoV-2 mystery lineage;

3. "Ancestral Omicron" (already sharing almost all BA.1 mutations) recombines with mystery lineage at the beginning (BA.3) or middle of the NTD portion of the spike (BA.2) before mystery lineage vanishes;

4. BA.1 emerges from "ancestral Omicron", BA.2 and BA.3 emerge at a later date.

Not surprisingly cases are going back up here since getting rid of mask requirements:
(Plus we've been enduring a cold snap driving people back inside)

https://toronto.ctvnews.ca/ontario-reports-significant-jump-in-covid-19-hospitalizations-nine-new-deaths-1.5839164

Ontario health officials are reporting 790 people in hospital with COVID-19 Tuesday, including 165 patients in intensive care.

Tuesday’s hospitalizations case count marks a considerable increase over the 655 reported on Monday and the 553 reported on Sunday, although not all hospitals report patient data over the weekends.

Of Tuesday’s hospitalizations, 153 patients are unvaccinated and 470 are fully vaccinated. The vaccination status of the remaining patients is unknown.

Wastewater data, provided by Ontario’s COVID-19 Science Table, appears to confirm this slight increase in infection. In nearly every region in the province the concentration of the disease in wastewaters has started to rise.

With 12,302 tests processed in the past 24 hours, the Ministry of Health says the province's positivity rate is about 14.4 per cent.



Quebec is getting a BA.2 wave

https://www.vancouverisawesome.com/coronavirus-covid-19-national-news/experts-say-quebec-has-entered-a-sixth-wave-of-covid-19-propelled-by-ba2-subvariant-5206440

Quebec has already entered a sixth wave of the COVID-19 pandemic driven by the BA.2 subvariant, two experts said Monday, although it's unclear how severe it will be and whether the rest of the country will follow.

Of course it will reach the rest of the country, but it should be more of a ripple than a wave I hope. Anti-bodies should still be high from all the boosters and BA.1 infections.

I suppose the immunocompromised and the elderly will always be at risk.

Which really sucks for them.

For the rest of us, long covid will be a risk. So sad that we couldn't have contained this pandemic early.

It truly is. While Covid itself didn't have too much of an impact to me, the three vaccine shots might have helped with that, I can't smell or taste since four weeks and I'm beginning to think that won't change ever again. Life feels a lot more empty that way and what really annoys me is that it could have been prevented if people wouldn't be so damn stubborn.

On the other hand, I'm starting to drastically lose weight as I have almost zero interest in eating anything, so that's something I guess.

My wife's sense of smell and taste came back eventually, after about 8 months it slowly started improving. She's still having blood pressure issues but whether that's from suspecting to have had covid (never confirmed was in Februari 2020) or something else we don't know. Doctors still don't have time here.

At first everything smelled bad though, will lose your appetite even more :/ But it did come fully back.



They made it official, next wave is here
https://toronto.ctvnews.ca/ontario-has-entered-the-sixth-covid-19-wave-doctors-say-1.5840183

With access to PCR testing limited, the exact number of Ontarians infected with COVID-19 remains elusive. Using viral signals in wastewater, the province’s science advisory table puts the doubling rate at every 9.6 days.


And yep, the immunocompromised and elderly are double screwed now in flu season

https://www.ctvnews.ca/health/coronavirus/risk-of-death-more-than-doubles-with-covid-19-and-flu-co-infection-study-suggests-1.5839815

Researchers from the University of Edinburgh, University of Liverpool, Leiden University and Imperial College London studied more than 305,000 hospitalized COVID-19 patients and published their findings in The Lancet on Friday. Of the patients studied, nearly 7,000 had respiratory viral co-infections with 227 of these patients simultaneously having seasonal influenza and COVID-19.

According to the study, patients with a co-infection of SARS-CoV-2, the virus that causes COVID-19, and influenza viruses were four times more likely to need ventilation during their hospital stay. The study also suggested these patients were 2.4 times more likely to die than patients hospitalized with just COVID-19.

At least from those numbers, the risk of co-infection is pretty small. Yet that study was done when the seasonal flu was still held back by all the Covid measures.

Do symptom presentation or viral load correlate with chance of reinfection? Some might be asking this considering Omicron.

According to data from the ONS, it kind of does, but the difference is nowhere as dramatic as you might be led to believe: the asymptomatic have a 22% higher chance of reinfection compared to the symptomatic, and most viral loads are within 10% of the average reinfection risk. Only those with very low viral loads (Ct above 30 in a PCR test ) have a meaningfully higher chance of reinfection (13% to 61% higher than the average risk).

So while Omicron might be somewhat less immunogenic overall due to prefering closed RBD loops, like the endemic coronaviruses, it should not be so due to its intrinsic mildness. The odd BA.2 reinfection should be possible since it has six different mutations in the RBD compared to BA.1, though rare since these are mostly at minor epitopes.

Weekly update, living with Covid, reported cases staying mostly level but at least reported deaths keep going down.

In total 10.2 million new cases were reported last week (down from 11.6 million) to a total of 489,706,743
Also another 28,399 deaths were reported last week (down from 49,074 yet that was with corrections, 36,036 2 weeks ago) to a total of 6,170,829

Europe mostly staying level, USA heading back up slightly, deaths still declining.

The continents

Same thing, leveling off across the board.

Corners of the world

South Korea on top with 2.2 million new cases last week (down from 2.5 million) and 2,296 more deaths (down from 2,512), peaked.
Canada and Australia are creeping back up, India still declining.
Iran might be getting another wave or a ripple.

Europe in detail

The field spread out some more while slowly going down over all.
Reporting is getting less and less frequent and accurate though, the 'real' numbers are just a guess.

Here they're warning about a resurgence while talking about a second booster shot.

Hong Kong and Shanghai are struggling under lockdowns
https://www.ctvnews.ca/health/coronavirus/hong-kong-urges-testing-shanghai-struggles-under-lockdown-1.5845656

Now in flu season? It's spring time flu season is winter.

Surprised to see China still pushing for Zero-covid19 policies, I wonder if their failure of a vaccine is the reason for this.

Living with covid19 is going well in the UK.

That's a matter of perspective though, their are still on avg 160 people dying every day in the UK of Covid-19 and close to 2 million currently infected. But the draconian measures in China are not sustainable. (Over 165K deaths in the UK, 4,600 in China)

China is 86% fully vaccinated vs UK 73%. It's not a failure of a vaccine, it's just a different mindset. 50K daily new cases is the new normal in UK, China locks cities down after a couple dozen cases.

Shanghai recorded another 13,354 cases on Monday -- the vast majority of them asymptomatic -- bringing the city's total to more than 73,000 since the latest wave of infections began last month. No deaths have been ascribed to the outbreak driven by the omicron BA.2 variant, which is much more infectious but also less lethal than the previous delta strain.

A separate outbreak continues to rage in the northeastern province of Jilin and the capital Beijing also saw an additional nine cases, just one of them asymptomatic. Workers shut down an entire shopping center in the city where a case had been detected.


But yes, their vaccine is seen as weaker and they have the problem that the vulnerable won't get vaccinated, doh

While China's vaccination rate hovers around 90%, its domestically produced inactivated virus vaccines are seen as weaker than the mRNA vaccines such as those produced by Pfizer-BioNTech and Moderna that are used abroad, as well as in the Chinese territories of Hong Kong and Macao. Vaccination rates among the elderly are also much lower than the population at large, with only around half of those over 80 fully vaccinated.