Thread by @DevanSinha

Temperature and SARS-COV-2 transmission:

Some seasonality expected for resp viruses, hard to say how much. England had unique circumstance Feb 7-13th.

- week long cold snap across country of similar magnitude
- no change in restrictions
- no increase in daily mobility

1/

Due to variables being reasonably controlled we can estimate how temperature may affect general transmission dynamics.

Note Seasonality: viruses transmit at ALL times of year but climate affects biology and behaviour which impacts on how much transmission occurs.

2/

Cases by specimen date in England showed a marked deceleration in the rate of decline the week after the cold period. From more than -5% per day to less than -2%.

(daily change adjusted for day of the week effect in testing)

3/

Those people testing positive on a given day didn't all catch SARS-COV-2 at the same time

Mean time from exposure to symptoms is 5.5 days + time for getting test (2days). There's a distribution (log-normal best fit) with slightly longer tail. ~8 days from infection to test.

4/

Daily growth rate can then be changed into R.

There's a high degree of correlation with temperature.

Pearson correlation coefficient 0.79

2.2% [1.7-2.6] increase in R per 1C decrease in temp

(humidity correlation coefficient separately 0.46)

5/

As an aside: changes in R affect time from exposure to test specimen. As R<1 weight is behind the right of the probability distribution (old exposures slightly dominant and R marginally too high by spec date). Further decline negligibly changes this until equilibrium.

6/

Anyways correlation ≠ causation. Considering other factors.

In Lockdown mobility increases 2.5% avg week on week despite no change in restrictions instead change in behaviour/adherence.

However that week was low/negative between Feb 9-13. Only time in any lockdown.

7/

Result of snow/ice conditions etc and people staying indoors at home.

Usual caveat applies that mobility!= transmission risk

Therefore expectation would be fall in R considering mobility alone.

8/

Also vaccination removes people from the susceptible population and proportionally reduces effective R.

Using compartmentalised mixing of over 70's and vulnerable groups with conservative 65% efficacy and 3 week till protection we see baseline R should have declined.

9/

Physical attendance in school ~18% nationally is unlikely to have contributed to the rising R in week 6 followed by rapid decline week 7 (half term). Effect on case rate was uniform across ages in both weeks, with no delay to infer secondary transmission via children.

10/

IF change in R with temperature is as indicated by this ecological study we can expect seasonality of 29% [22-35] from peak to trough in England over the year. R0 +/- 16%

Slightly higher than Imperial model (20% peak to trough)

11/

However scope of behavioural change was limited in the study period by lock down restrictions. eg indoor socialising with other households rather than outdoor etc.
Which may underestimate impact.

12/

Biological factors contributing to seasonality:

-virus stability
-humidity and temp affecting transmission dynamics
-mucociliary clearance
-epithelial integrity
-innate immune efficiency

13/

Nice review paper of physiology👇

annualreviews.org/doi/pdf/10.114…

In the context of B117 in England with year average R0=4

This would mean R 4.6 in winter and R 3.4 in summer.

Potential for year round exponential growth and epidemic outbreaks without either pre-existing immunity (vax or prior infxn) or social distancing restrictions.