Emmanuel Profile picture
Jun 6 โ€ข 17 tweets โ€ข 6 min read โ€ข Read on X
๐™Ž๐˜ผ๐™๐™Ž-๐˜พ๐™Š๐™‘-2 :
๐™๐™๐™š ๐™œ๐™ง๐™š๐™–๐™ฉ ๐˜พ๐™Š๐™‰๐™๐™๐™Ž๐™„๐™Š๐™‰ ๐™—๐™š๐™ฉ๐™ฌ๐™š๐™š๐™ฃ ๐™Ž๐™€๐˜ผ๐™Ž๐™Š๐™‰๐˜ผ๐™‡, ๐˜พ๐™”๐˜พ๐™‡๐™„๐˜พ ๐™–๐™ฃ๐™™ ๐™ˆ๐™€๐™๐™€๐™Š๐™๐™Š๐™‡๐™Š๐™‚๐™„๐˜พ๐˜ผ๐™‡ ๐™›๐™–๐™˜๐™ฉ๐™ค๐™ง๐™จ
(๐˜ฎ๐˜ฆ๐˜จ๐˜ข-๐˜ต๐˜ฉ๐˜ณ๐˜ฆ๐˜ข๐˜ฅ - 1๐˜ด๐˜ต ๐˜ฑ๐˜ข๐˜ณ๐˜ต)
2) SEASONAL DISEASES refer to illnesses or health conditions (flu, common cold, allergies...) that are more prevalent during SPECIFIC seasons of the year (usually winter or spring).
These diseases are influenced by environmental factors and the presence of seasonal pathogens. Image
4) COVID-19 is a PANDEMIC and CYCLIC disease.
Pandemic, as it has spread globally and continues to affect populations worldwide.
Cyclic, because it appeared on average every 3/4 months which could give the false impression that it followed the seasons. Image
5) Like any rule there are exceptions, with cycles which have not taken place in some countries, with generally a more intense cycle afterwards.

Contrary to what some say, they are not linked exclusively ... Image
6) ... to the emergence of new variants, as we have shown for the US ๐Ÿ‘‡
There is a combination of factors, new variants, waning immunity / increase in nb of susceptible people, population movements and changes in modes of transmission (vacations, school breaks, etc.) ... Image
7) What is the contribution of meteorological factors (temperature, humidity) to these cycles?

In less than a month, there have been 3 fascinating studies on this subject which we will develop in a 2nd part, far from clichรฉs or abusive simplifications ๐Ÿ˜Š
8) METEOROLOGICAL FACTORS
(2๐˜ฏ๐˜ฅ ๐˜ฑ๐˜ข๐˜ณ๐˜ต)

1st study :
"A mixture of mobility and meteorological data provides a high correlation with COVID-19 growth in an infection-naive population: a study for Spanish provinces"
frontiersin.org/journals/publiโ€ฆ
Image
9) Analysis of Spanish COVID-19 data reveals high correlations between growth rate and principal components of mobility and meteorological data, with mobility playing a larger role. Correlations are maximal at 2-3 week time lags, consistent with delays between infection ... Image
10) ... symptom onset, and case reporting. Combining mobility and meteorological data improves explanatory power compared to either alone.

2nd study :
COVID-19 dynamics in Hiroshima, Japan, and its association with meteorological factors over 3.5 years.
cureus.com/articles/24332โ€ฆ
Image
11) Wind speed showed the strongest correlation with COVID-19 metrics. SARS-CoV-2 variant distributions, with Alpha, Delta, and Omicron predominant, were also linked to meteorological factors. Image
12) The findings highlight the role of environmental factors in shaping pandemic outcomes and underscore the need for integrated surveillance approaches to mitigate future outbreaks. Image
13) Spearman's correlation coefficient. Image
14) Maybe the most interesting one to end :
"Non-linear effects of meteorological factors on COVID-19: An analysis of 440 counties in the americas"
cell.com/heliyon/fullteโ€ฆ
Image
15) This study analyzed the non-linear effects of meteorological factors (temperature, humidity, solar radiation, surface pressure, precipitation, wind speed) on COVID-19 transmission across 440 counties in the Americas from 2020-2021. The results showed ... Image
16) - Temperature had a positive correlation below 5ยฐC and above 23ยฐC, and a negative correlation between 5-23ยฐC.
- Relative humidity and solar radiation exhibited significant negative correlations, with a rapid decrease in daily new cases above 74% humidity and ... Image
17) ...750 kJ/m2 solar radiation.
โ€ข Surface pressure showed an inverse relationship at 0-10 and 15-21 day lags.
โ€ข Precipitation had no significant associationใ€‚
โ€ข Wind speed had a slightly higher infection risk under low (0-2 m/s) and high (10 day lag) conditions. Image
18) The study provides important insights into the complex, non-linear relationships between meteorological factors and COVID-19 transmission, highlighting the need for regional and latitudinal considerations in understanding pandemic dynamics.

Thanks and nice weather to you ๐Ÿ˜Š Image

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More from @ejustin46

Jun 8
๐™๐™‰๐™Ž๐™๐™Š๐™‹๐™‹๐˜ผ๐˜ฝ๐™‡๐™€!
๐™Ž๐˜ผ๐™๐™Ž-๐˜พ๐™Š๐™‘-2, ๐™„๐™ฃ๐™›๐™ก๐™ช๐™š๐™ฃ๐™ฏ๐™– ๐˜ผ, ๐™„๐™ฃ๐™›๐™ก๐™ช๐™š๐™ฃ๐™ฏ๐™– ๐˜ฝ, ๐™๐™ช๐™ข๐™–๐™ฃ ๐™ง๐™š๐™จ๐™ฅ๐™ž๐™ง๐™–๐™ฉ๐™ค๐™ง๐™ฎ ๐™จ๐™ฎ๐™ฃ๐™˜๐™ฎ๐™ฉ๐™ž๐™–๐™ก ๐™ซ๐™ž๐™ง๐™ช๐™จ, ...

respiratory-research.biomedcentral.com/articles/10.11โ€ฆ
2) This study assessed the performance of a multiplex respiratory panel detecting SARS-CoV-2, influenza A/B, and respiratory syncytial virus (RSV) in two time periods. In early 2022, SARS-CoV-2 infections dominated (66.1%), but influenza A (1.6%), RSV (0.7%), and ... Image
3) ...influenza B (0.1%) were also detected. In the 2022/23 season, SARS-CoV-2 positivity decreased to 9.6%, while influenza A (3.5%), RSV (2.8%), and influenza B (0.6%) increased. Co-detections remained around 1-2% across both periods. Image
Read 4 tweets
Jun 8
๐™Ž๐˜ผ๐™๐™Ž-๐˜พ๐™Š๐™‘-2 ๐™€๐™‘๐™Š๐™‡๐™๐™๐™„๐™Š๐™‰,
๐™—๐™š๐™ฉ๐™ฌ๐™š๐™š๐™ฃ ๐™๐™„๐˜พ๐™๐™„๐™Š๐™‰ ๐™–๐™ฃ๐™™ ๐™๐™€๐˜ผ๐™‡๐™„๐™๐™”
(3rd and last part)

In this very interesting study ๐Ÿ‘ published in 2024, they explores the eco-evolutionary dynamics between rapidly evolving pathogens, like influenza and SARS-CoV-2 ... Image
2) ...and the immune responses of their hosts.ย 

As pathogens spread, host immunity builds up, creating selective pressures that drive the pathogens to rapidly evolve immune-evading variants. arxiv.org/abs/2402.07252
Image
3) However, host immunity also adapts, limiting the growth advantage of new variants. They use a (SIR) model to simulate this co-evolutionary process, showing that depending on factors like cross-immunity between strains and durability of immune responses ... Image
Read 8 tweets
Jun 8
๐™Ž๐˜ผ๐™๐™Ž-๐˜พ๐™Š๐™‘-2 ๐™€๐™‘๐™Š๐™‡๐™๐™๐™„๐™Š๐™‰,
๐™—๐™š๐™ฉ๐™ฌ๐™š๐™š๐™ฃ ๐™๐™„๐˜พ๐™๐™„๐™Š๐™‰ ๐™–๐™ฃ๐™™ ๐™๐™€๐˜ผ๐™‡๐™„๐™๐™”
(2nd part)

In another study with @jbloom_lab , they showed that the Omicron mutation spectrum is more similar to the long-term evolutionary spectrum of other sarbecoviruses ... Image
2) ...hinting that SARS-CoV-2 may be trending back towards a bat-like mutation profile after adapting to humans.

In this study, examining changes in the mutational spectrum of SARS-CoV-2 over time, they focused on the relative rates of ... biorxiv.org/content/10.110โ€ฆ
Image
3) ... different single nucleotide mutations at four-fold degenerate sites (where mutations are expected to be neutral). They found clear shifts in the mutation spectrum across different SARS-CoV-2 clades, with the most striking change being a ~2-fold decrease ... Image
Read 6 tweets
Jun 8
๐™Ž๐˜ผ๐™๐™Ž-๐˜พ๐™Š๐™‘-2 ๐™€๐™‘๐™Š๐™‡๐™๐™๐™„๐™Š๐™‰,
๐™—๐™š๐™ฉ๐™ฌ๐™š๐™š๐™ฃ ๐™๐™„๐˜พ๐™๐™„๐™Š๐™‰ ๐™–๐™ฃ๐™™ ๐™๐™€๐˜ผ๐™‡๐™„๐™๐™”
(1st part)

An example to start.
BA.2.86, the "father" of the JN.1*, was presented as THE VARIANT which suddenly emerged at the end of 2023. However, BA.2.86 had existed since early 2022 ! Image
2) Alex Sigal @sigallab explained it perfectly, in a post from September 8, 2023, with a variant which has gradually gained its "mutations without spreading because it was either a long infection in someone immunosuppressed or in an animal reservoir."
Image
Image
3) Far from the fictions, which are there above all to make noise, there is a virus which is evolving in an interesting way, and we would like to approach this subject, drawing in particular on the remarkable work of Richard Neher @richardneher
Read 9 tweets
Jun 7
๐™ˆ๐™ค๐™™๐™š๐™ก๐™ž๐™ฃ๐™œ ๐™ฅ๐™ค๐™ฅ๐™ช๐™ก๐™–๐™ฉ๐™ž๐™ค๐™ฃ ๐™ข๐™ค๐™ซ๐™š๐™ข๐™š๐™ฃ๐™ฉ๐™จ ๐™›๐™ค๐™ง ๐™ช๐™ฃ๐™™๐™š๐™ง๐™จ๐™ฉ๐™–๐™ฃ๐™™๐™ž๐™ฃ๐™œ ๐˜พ๐™Š๐™‘๐™„๐˜ฟ-19 ๐™™๐™ฎ๐™ฃ๐™–๐™ข๐™ž๐™˜๐™จ

Forgive me for the lightness of the statement but "a virus has no legs".
It is its hosts that allow its transmission.
medrxiv.org/content/10.110โ€ฆ
Image
2) In this study, they developed a metapopulation SEIR model to simulate COVID-19 transmission across the North American region, including Canada, the United States, and Mexico.
The model-inference system uses the Ensemble Adjustment Kalman Filter to estimate time-varying ... Image
3) ...transmission rates, ascertainment rates, and reproductive numbers for each location based on reported case data. The results highlight important differences in COVID-19 dynamics among the three countries.

Why modeling population movements is so important ? Image
Read 9 tweets
Jun 7
๐™ƒ๐™ž๐™œ๐™ ๐™ก๐™š๐™ซ๐™š๐™ก ๐™ค๐™› ๐™ฃ๐™š๐™ช๐™ฉ๐™ง๐™–๐™ก๐™ž๐™ฏ๐™ž๐™ฃ๐™œ ๐™–๐™ฃ๐™ฉ๐™ž๐™—๐™ค๐™™๐™ž๐™š๐™จ = ๐™๐™ž๐™œ๐™ ๐™ก๐™š๐™ซ๐™š๐™ก ๐™ค๐™› ๐™ฅ๐™ง๐™ค๐™ฉ๐™š๐™˜๐™ฉ๐™ž๐™ค๐™ฃ ๐™–๐™œ๐™–๐™ž๐™ฃ๐™จ๐™ฉ ๐™ž๐™ฃ๐™›๐™š๐™˜๐™ฉ๐™ž๐™ค๐™ฃ

๐™’๐™๐™–๐™ฉ, ๐™ž๐™› ๐™ž๐™ฉ ๐™ฌ๐™–๐™จ๐™ฃ'๐™ฉ ๐™ฉ๐™๐™–๐™ฉ ๐™จ๐™ž๐™ข๐™ฅ๐™ก๐™š?
wwwnc.cdc.gov/eid/article/29โ€ฆ
Image
2) Several studies have shown that higher levels of neutralizing antibodies are associated with immune protection from symptomatic SARS-CoV-2 infection. However, the estimated relationship between neutralizing antibody levels and protection has varied between studies.
3) The authors reconciled these differences by normalizing the antibody titers across studies. They found that the study results converge on a consistent relationship between antibody levels and protection from COVID-19. This can be useful for planning future vaccine use ... Image
Read 8 tweets

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