Thread by @miamalan

[Thread] 1. How fast is BA.2 (a subvariant of the #Omicron variant) spreading in SA and is it making people sicker than BA.1 (the original form of #Omicron)?

Cheryl Cohen, @nicd_sa:

2. What is BA.2?
1. It is a new form (scientists call it a sub-variant or new lineage) of the #Omicron variant
2. BA.2 has been detected in 145 countries
3. Data from the UK and Denmark suggest BA.2 is more transmissible than BA.1 (so it spreads faster)

3. How widely has BA.2 spread in SA?
1. BA.2 (one of the new forms of #Omicron) has taken over from BA.1 (original form of #Omicron)
2. Look at the graph:
- Light orange = BA.1
- Dark orange = BA.2

4. BA.2 in SA: Close to 100% of the genomes analysed in SA are now BA. 2 via @Tuliodna:

https://twitter.com/Tuliodna/status/1491483399265075202

5. Is BA.2 linked 2 an increased nr of #COVID19 cases in SA?
1. Not a sustained increase, only a slight, brief uptick in cases among school kids (schools opened). The increase = not spilled over 2 older people
2. BA.2 = linked 2 a slower rate of decline in cases vs. other waves

6. BA.2 likely spreads faster than BA.1. But does it make people sicker than BA.1?
1. A new preprint with SA data = released 2day (at an @nicd_sa presser, medRxiv link = not yet up when I sent out this thread)
2. Main finding = No, BA.2 doesn't make people in SA sicker than BA.1

7. How did scientists know who was infected with BA.1 + BA.2?
1. Test samples collected = when 99% of #COVID19 infections in SA = #Omicron
2. BA.1 = S-gene target failure on TaqPath PCR tests, so the S-gene isn't detected
3. BA.2 = no S-gene failure, so S gene = picked up

8. What counted for severe #COVID19 disease?
1. If a patient = in ICU, needed oxygen, had fluid on the lungs (ARDS), died
2. Where did hospital data come from? SA's DATVOC national hospital surveillance system

9. Data used in the study showed how rapidly BA.2 replaced BA.1 in SA.

How did scientists know this? The proportion of PCR #COVID19 tests without S-gene target failures (BA.2) became much larger than those with S-gene failures (BA.1) between Dec 5 (3%) and Jan 29 (80%).

10.
1. How many + #COVID19 test samples were collected? 95,470
2. Was there a difference between people infected with BA.1 and BA.2's likelihood of getting hospitalised? No, their odds = the same:
- BA.1 (3.6% of cases = admitted)
- BA.2 (3.4% of cases = admitted)

11. Once hospitalised, were people infected with BA.2 more likely to fall very ill with #COVID19 than those infected with BA.1?

No.

Overall, severe disease = less common in:
- Kids (5-11)
- Females
- Vaxxed people

12. Study limitations:
1. Only test results of the TaqPath PCR test = used (it picks up S-gene deletions), so only test results from labs using that test = included
2. 3 weeks = waiting period after test results (4 people 2 fall ill), but there could be a lag in severe outcomes

13. Will BA.2 also cause less severe disease in other countries?

We don't have enough data 2 know. Diffs between SA + Europe: most #COVID19 immunity in SA = from natural infection (60-80%), in Europe = most immunity from vaxx. What's the potential implication? (next tweet)

14. Cohen:
BA.2 = not big impact on #COVID19 case nrs in SA (only school kids nrs briefly increased). In some European countries, BA.2 = linked 2 larger increases. Hypothetically natural immunity (most common imm in SA) could provide better protection @ BA.2 infection than vaxx.

15. Want to read the entire study? Here are screen grabs of the text. Tables with data + references will be included in the MedRxiv preprint when it goes live.