Thread by @miamalan

[Thread] 1. When will SA's #Omicron wave end?

@ProfAbdoolKarim:
1. If cases continue 2 decline @ the current rate, the wave will end in +/- 10-11 days
2. How will we know it's the end?
@nicd_sa uses 30 cases/100,000 in the past 7 days for the beginning/end of a wave

2. If the #Omicron wave does end in +/-10-11 days, it will have been just over half the length of previous waves:
1. Wave 1, 2, 3: About 75 days long
2. Wave 4 (Omicron) likely to be 40-50 days long

3. Can SA expect a next #COVID19 wave?
@ProfAbdoolKarim:
1. Given the consistent 3 month gap we get in SA between waves, the 5th wave can be expected, if it is going to occur, in May this year
2. Of course, a new variant may throw this estimation out the window

4. How #Omicron took over: What proportion of genomes sequenced in SA = #Omicron?

1. December (latest data): 98.4%
2. November: 82.5% (#Delta = 13%)
3. October: 0.26% (Delta = 84.6%)

Source: bit.ly/3qNhoKE

5. What's SA's #COVID19 reproduction rate (how many other people 1 infected person = likely 2 infect)?

By Jan 2, the R value had declined from about 2.2 at the peak of the #Omicron wave to =+/- 0.8 (below 1 = good)

@nicd_sa R reports (up to 21 Dec): bit.ly/3G7BmGK

6. What's happening with #Omicron hospitalisations?

1. Past 14 days (up until Jan 1):
- Daily admissions decreased in all provinces except for EC, NC, WC

2. Past 7 days (up until Jan1):
- Admissions declined in all provinces

@nicd_sa hospital report: bit.ly/3qRLj4A

7. @Netcare_Limited (private hospital group with 49 hospitals) published hospital admission stats in JAMA for the 1st 3 weeks of Wave 4 (#Omicron) and compared it to similar periods of Wave 1 (ancestral), 2 (Beta), 3 (#Delta): bit.ly/3G6mV5s

8. Netcare study:
1. % of #COVID19 patients presenting @ emergency rooms = admitted: 68-69% (Wave 1,2,3) vs 41% (Wave 4)
2. % of patients with acute respiratory conditions @ admission: 72-91% (Wave 1,2,3) vs 31% (Wave 4)
3. Admissions (Wave 4):
- Vaxxed: 24%
- Unvaxxed : 66%

9. Netcare study:
1. % of #COVID19 admissions needing oxygen: 74 - 82% (Wave 1,2,3) vs 17% (Wave 4)
2. % of #COVID admissions needing ventilation: 8-16% (Wave 1,2,3) vs. 1.6% (Wave 4)

10. Netcare study:

1. % of #COVID19 hospitalisations admitted to ICU: 30-42% (Wave 1,2,3) vs 18% (Wave 4)
2. Length of stay: 8-9 days (Wave 1,2,3) vs 3 days (Wave 4)
3. Deaths: 20-29% (Wave 1,2,3) vs 2.7% (Wave 4)

11. Does Netcare's data line up with admission data from other SA studies?

Yes:
1. This Lancet preprint also found smaller % of Omicron patients got admitted and they got less sick:

https://twitter.com/miamalan/status/1476535934359326723

2. @nicd_sa data shows similar trends:

https://twitter.com/miamalan/status/1473635481397215236

12. Have #Omicron hospitalisations peaked? (thanks @Dr_Groome + @tomtom_m 4 helping me with this):
1. Likely yes, because of the sustained decline in the 7 day moving average
2. But we need to wait another week or so to be sure. Why? (answer in next tweet)

13. Why do we need 2 wait another week or so 2 be sure that SA's #Omicron's hospitalisations have peaked? (so far, we've got data up until 1 Jan)

1. There are delays with the reporting of data
2. Right now, more 50+ people (who are more likely to be hospitalised) = testing +

14. What's happening with #Omicron deaths?

1. Past 14 days:
- Daily deaths increased in all provinces

2. Past 7 days:
- Daily deaths decreased in all provinces except EC, FS, WC (biggest dip = GP, where SA's outbreak started + most time = lapsed since the start of infections)

15. In SA, trends in excess deaths are reassuring. We're not seeing the large rises in excess deaths during the #Omicron wave like we saw in past waves.

For excellent analysis on excess deaths via @tomtom_m: bit.ly/3F7IHoa

16. SA's data, so far, shows:
- The numbers of #Omicron hospitalisations + deaths = lower than in Wave 1,2,3
- The decrease in deaths (for #Omicron, compared to other waves) = more dramatic than the decline in admissions

https://twitter.com/tomtom_m/status/1478795238978248713

17. Why is #Omicron leading 2 milder disease?
@ProfAbdoolKarim:
1. We have accumulating evidence that shows Omicron causes little lung infection, so respiratory distress/multi-organ disease = uncommon
2. The main reason 4 the lower severity seems 2 be a less virulent virus

18. Studies that show #Omicron may cause less severe disease than other variants as infection is mostly confined to the upper airway (nose, throat, windpipe) and therefore causes less damage 2 the lungs via @EricTopol.

Eric Topol's original tweet: bit.ly/32TF5t9

19. What are the other reasons for #Omicron causing milder disease?
@ProfAbdoolKarim:
1. Vaccines show substantial impact in preventing severe disease (without boosters)
2. Prior natural immunity may also be making some contribution (SA's natural immunity = between 60-80%).

Here are the tables with the names of the provinces, I accidentally cut off the names when I cropped the images: