# Corona Updates October 2020

## Good news

### Masking increases chances of asymptomatic disease by those who wear it
- Masks of any kind filter a substantial amount of virus
- The smaller the inoculum the less severe the disease tends to be. A large part of the disease is caused by the immune reaction of the host, not the virus, and a smaller inoculum seems to lead to more controled immune response
- Several lines of evidence seem to show that universal masking leads to substantial higher rates of asymptomatic cases
- example of cruise ships:
- Diamond Princess: no masks - 18% asymptomatic
- Argentinian cruise ship in March: 81% asymptomatic
- As soon as the first passenger got sick, staff got N95 masks and passengers got surgical masks
- Bonus: asymptomatic transmission seems to lead to robust T-cell immunity
- Expert Monica Ghandi goes as far as to state she would rather be wearing a mask than physically distant in a croud ... Masks should be worn everywhere even outside

refs:
- https://www.ucsf.edu/news/2020/07/418181/one-more-reason-wear-mask-youll-get-less-sick-covid-19
- https://johnshopkinssph.libsyn.com/142-asymptomatic-infection-with-covid-19

### Asymptomatic infection leads to robust T-cell immunity

refs:
- https://johnshopkinssph.libsyn.com/142-asymptomatic-infection-with-covid-19

### The Herd immunity threshold for most European countries is around 15% when variable susceptibility is taken into account
https://www.medrxiv.org/content/10.1101/2020.09.26.20202267v1.full.pdf

### New efficient pooling algorithms
https://myemail.constantcontact.com/COVID-19-Updates---October-9--2020.html?soid=1107826135286&aid=7gSPBbUzCRQ

### 10ish days post symptom onset people most people won't be contagious

source: https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.32.2001483#html_fulltext

### Final IFR will almost certainly be between 0.1% and 0.35%
https://www.cebm.net/covid-19/global-covid-19-case-fatality-rates/

### Portugal might have a slightly lower IFR than comparable countries
https://www.medrxiv.org/content/10.1101/2020.07.23.20160895v6.full.pdf

https://arxiv.org/pdf/2006.02757.pdf

The value above might be an underestimate

### Inverse relation between vitamin D and chance of COVID diagnostic
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0239252
https://www.the-scientist.com/news-opinion/scientists-advice-for-ways-to-ward-off-the-coronavirus-68037

### Large expression study on COVID patients reveals potential drug targets, candidate drugs and reinforces recommendation for Vitamin D
https://elifesciences.org/articles/59177

### Masks are proven to work for Sars-cov-2
https://msphere.asm.org/content/5/5/e00637-20/article-info

### The Surescreen antibody test we run at CCU has a sensitivity of about 70% for infections <10 days after onset
https://www.medrxiv.org/content/10.1101/2020.06.02.20120345v1.full.pdf

### Carrageenan in vivo results with influenza A and comparison to remdesivir in vitro is favorable
https://www.nature.com/articles/s41598-020-80896-9#Sec2

## Bad news

### BCG vaccine doesn't protect against acquiring COVID-19, dying from it or developping more severe disease
A "ecological" study had indicated previously that BCG vaccination seemed to reduce rate of spread in countries that still required it:
- https://advances.sciencemag.org/content/6/32/eabc1463

However, a more detailed study of a swedish cohort of 1M patients seems to not support that, at least for those who have gotten the vaccine at birth and were born prior to 1975
- https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa1223/5896039

There is currently a trial going on:
- https://www.raps.org/news-and-articles/news-articles/2020/3/covid-19-vaccine-tracker

### Acid reflux might worsen COVID-19
- 2-3 fold higher chance of death by covid for patients who were taking PPI

https://www.medrxiv.org/content/10.1101/2020.09.10.20179135v1.full.pdf

### Convalescent plasma doesn't work at least if not first screened for some feaeures
https://www.nature.com/articles/s41577-020-00461-3

### Without UV and at 65% humidity and 20'C the virus can remain infectious for up to weeks in smooth surfaces and on surgical masks up to days
https://virologyj.biomedcentral.com/articles/10.1186/s12985-020-01418-7

### Previous seasonal coronavirus infection doesn't protect against Sars-Cov-2
https://www.medrxiv.org/content/10.1101/2020.10.08.20209650v1.full.pdf

### Average age of hospitalized covid-19 patients in Amadora-Sintra is 53 years old
https://expresso.pt/life_style/beleza/2020-10-25-Hospitais-sob-pressao.-O-Sao-Joao-e-o-Amadora-Sintra-ja-nao-esperam-milagres

### Entrevista a Baltazar Nunes
https://sicnoticias.pt/programas/poligrafo/2020-10-19-Coronavirus-em-Portugal.-Transmissao-da-doenca-esta-mais-elevada
- O crescimento de internados em UCI não está a ser tão rápido como para os pacientes em enfermaria
- A grande maioria dos óbitos é acima dos 70 anos

### Fecal aerosol transmission between flats in an apartment block
https://www.acpjournals.org/doi/10.7326/M20-0928

### Half of recovered patients have lingering fatigue
https://www.cidrap.umn.edu/news-perspective/2020/11/half-recovered-covid-19-patients-report-lingering-fatigue

## Neutral / Mixed news
### S1 or RBD ELISAS are good predictors of neutralizing activity but N ELISAS and quick tests (LFI) are not
- A dilution of 1:16 of peak antibody concentration (1 month after disease) still neutralizes pretty well
https://onlinelibrary.wiley.com/doi/epdf/10.1111/all.14608

### For the other seasonal coronaviruses immunity is only around 45 weeks but there is cross-immunity
https://science.sciencemag.org/content/368/6493/860?te=1&nl=debatable&emc=edit_db_20200910

### For other coronaviruses reinfections have been recorded as close as 6 months after infection

https://www.nature.com/articles/s41591-020-1083-1

### We are likely to not have worse incidence in the Winter compared to the Autumn


Qualitatively something similar to C/H Blue in the figure above is what we will likely have

source: https://science.sciencemag.org/content/368/6493/860/tab-figures-data

Sars-cov-2 is most similar to HKU1 and OC43 from the other coronaviruses. These have a peak around December.


ref:
https://smw.ch/article/doi/smw.2020.20224

### Crowded cities have less peaked but more prolongued epidemic
https://www.nature.com/articles/s41591-020-1104-0#Sec18

### Cities with higher humidity also have lower peaked**ness
https://www.nature.com/articles/s41591-020-1104-0#Sec18

results above were also true for Influenza:


https://science.sciencemag.org/content/362/6410/75both

For Lisbon it seems like we will have a longer but less peaky epidemic

### Good testing program at university scale using only spit and no RNA extraction and immediate innactivation of viruses
https://www.nature.com/articles/d41586-020-02611-y

### A slow drift upward after a jump in new cases is a signature of an inefficient testing and tracing system
https://arxiv.org/pdf/2009.05732.pdf

### Susceptibility is age dependent
https://www.nature.com/articles/s41591-020-0962-9#Fig2

### Safety of air in gyms
https://www.sciencedirect.com/science/article/pii/S0360132320304029

### Serology for just the RBD and not RBD + Spike have a false positive rate of around 1.2%
https://onlinelibrary.wiley.com/doi/10.1002/eji.202048970

### Neutralizing antibodies might last for up to 6 months
https://onlinelibrary.wiley.com/doi/10.1002/eji.202048970

### Covid hospitalization and death calculator
https://qcovid.org/

### Public event limitation and school closures are most efficient measures
https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30785-4/fulltext

### Incubation period (latency to symptoms)

### Secondary attack rate is 35% in household members

https://www.cidrap.umn.edu/news-perspective/2020/10/covid-19-scan-oct-30-2020

### 20% positivity rate in the North of Portugal

### Another age stratified estimate of IFR this time with seroreversion modeled out
https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/2020-10-29-COVID19-Report-34.pdf

### Interesting estimate of uncounted deaths using age stratification
https://arxiv.org/pdf/2006.02757.pdf

### Video showing influence of mask fit on filtration
https://www.youtube.com/watch?v=mJ81IBTMvcU&feature=youtu.be

### Very good paper about mortality and age
https://www.nature.com/articles/s41586-020-2918-0

### Restaurants, churches, gyms, cafes among the biggest superspreaders
https://www.nature.com/articles/s41586-020-2923-3

### Symptoms of covid
https://www.publico.pt/2020/11/10/sociedade/noticia/covid19-investigadores-querem-testes-alargados-dor-cabeca-obstrucao-nasal-1938723

### Deletions in 4 distinct parts of the Spike protein drive immune escape
https://science.sciencemag.org/content/early/2021/02/02/science.abf6950?utm_campaign=SciMag&utm_source=JHubbard&utm_medium=Twitter

### Higher viral load = higher probability of infecting contact & of developing symptoms & of having incubation timed shortened from 7 to 5 days
https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30985-3/fulltext

## Forecasts

### 2020/10/06


### 2020/10/12


### 2020/10/19