Wuhan Coronavirus Resource Thread

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Amber G.
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

prasannasimha wrote:Incidentally rapid antigen tests(Lateral Flow tests0 may be negative but RTPCR can be positive. It depends on viral load and test sensitivity. So one need not be surprised that RAT was negative one day and next day it was positive or RAT Negative RTPCR positive9I was RAT negative but RTPCR positive)
Thanks for very useful information.

To add: The quality and sensitivity of RAT tests varies by manufactures but in general and especially for the better (more reputable) ones - see the following:

(For example Abbot's Bionax - which we have been using routinely for several months)

- The false positive rate is *extremely* low - close to zero. (Specificity > 99%). So if the test is done correctly, a positive result implies it is really positive.

- The sensitivity for better RAT's. is also *very* high. More importantly it measures 'contagiousness'. BinaxNOW's sensitivity was 98% ( Nasal swab; ....(Gold standard=PCR w/ Ct<30, ie, infectious) (See < this from recent UCSF actual data >

- This means - If you have symptoms (of a few days after the suspected exposure) the RAT is extremely useful - It is quick, takes 15 minutes and can be done by you at home.

(I have talked about this here in BRF. Many ,(especially doctors in India) put this sensitivity around 70%. But good quality RAT's, and process done correctly (Nose swab etc) will achieve >90 % sensitivity - if you are contagious. (This >90 sensitivity is for good quality RATS - don't know what is available in different part of the world. As said before, quality varies a lot, some have been found to be very un-reliable).

Our (extended) family has used this for last many months - hundreds of test results (along with PCR tests for verification) - In *all* cases there were zero false positives or false negatives. What is more - RAT *gave* the result a day *before* PCR - as PCR result - though taken at the same time - came out later. To be clear - PCR tests are more accurate - especially when viral load is low - but the results take longer time.
RAT tests take only 15 minutes while PCR turn-around in our case is about a day).

One more take away - Nasal swab for RAT (as recommended) is much better than Throat swab (which was found only about 50-60% reliable). I know in some circles - they are using both but it really doesn't improve the result -- apart from gross factor).

---
Another helpful hint for those who are in USA. If you have access to computer with a camera and sealed/approved kit and you are registered etc - you can perform the test at home (for you or any other person) and can get an official vaccine certificate - all through internet within half an hour. (For International travel where PCR test is required, this might not be helpful but for domestic travel - or other places where RAT test is acceptable this is quite convenient).
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

Meanwhile the blue curve continues to follow the orange curve of SUTRA in USA.
Image

US update: Nearly 3,000 new deaths, cases continue to drop.
New cases: 541K (45/50 States Reporting),
- Average: 651,826 (-91,351), - In hospital: 148,681 (-1,117)
- In ICU: 25,744 (+51) - New deaths: 2,997)
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

IITH site now has current Sutra projections. We are at the peak..

Here just for record the values reported by other sites. (The graph is quite close to SUTRA model projection).


Image

Last Two Months:
Image
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Re: Wuhan Coronavirus Resource Thread

Post by Zynda »

prasannasimha wrote:Incidentally rapid antigen tests(Lateral Flow tests0 may be negative but RTPCR can be positive. It depends on viral load and test sensitivity. So one need not be surprised that RAT was negative one day and next day it was positive or RAT Negative RTPCR positive9I was RAT negative but RTPCR positive)
Doc, after onset of symptoms, what is the ideal time for Rt-Pcr test?
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Re: Wuhan Coronavirus Resource Thread

Post by Atmavik »

My 2 ur old’s daycare had an outbreak of omicron and my son was positive. Had fever and runny nose for abt a day and recovered as have all the other kids

The rest of our family had no symptoms. We r all vaccinated and boosted.

Ps: my parents got there booster in hyd yesterday. Very smooth experience
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

Wishing a speedy recovery ..

This wave seems to have caught many people - including EAM Dr. S. Jaishankar, ex DST secretary Dr Agrawal and many people I though who have been extremely careful, have been fully vaccinated (and boosted etc). Virtually all the cases have also been mild - for those who were vaccinated. (Those who were tested positive after someone in the family had symptoms, had extremely mild symptoms - or no symptoms. Vaccines have been extremely effective).

Good ventilation, masking and isolation when a family member tested positive prevented it from spreading to others.

Stay safe.
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

Meanwhile in the news (from mainstream media and scientific journals)
-Israel's advisory group recommends 4th shot for all adults.
- Both Moderna and Pfizer are running trials for Omicron specific variants.
- The remarkable, consistent 99% reduction of mortality with vaccination and booster in Switzerland and the United States ((and many other countries).
- For ages 5+, ~95% of hospitalization could be prevented.
-(Remarkable 90% and durable protection (>3 months) with booster vs Omicron vs hospital admission, the 1st US data, confirms in one study Link: https://papers.ssrn.com/sol3/papers.cfm ... id=4011905)
- US >99% is now Omicron. (With sub variants appearing in many states).
****
Almost 10 Billion doses of vaccines have been administered in the world in just one year
- But still about 3 billions have not gotten a single shot!
- In India about 94% (~937M) of eligible people have at least one shot while 70% (~698M) of eligible adults have two shots. (For the total population these numbers are about 67% and 50% respectively).
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Re: Wuhan Coronavirus Resource Thread

Post by putnanja »

Amber G.
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

SinghS wrote:
Sutra in omicron is like Pedro's arrows.
... SUTRA makes sense and it is not like Pedro's arrow.
Not at all ..Speaking of SUTRA ..India recognizes their talents .. Was happy to read the recent news:
Image

Congratulations to Lt Gen Madhuri Kanitkar on being conferred the Param Vishisht Seva Medal. Lt Gen Kanitkar is the Vice-chancellor at MUHS, Maharashtra and Member, prime Minister's STI Advisory Council.

Lt Gen Kanitkar is the third leading member of SUTRA team - Along with Prof. Manindra Agrawal (Padma Sri) and Prof. Vidyasagar.
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Re: Wuhan Coronavirus Resource Thread

Post by Pratyush »

Bharat Biotech nasal booster vaccine for COVID 19 is approved.
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Re: Wuhan Coronavirus Resource Thread

Post by Sonugn »

Active case load is going down.

Now, scientists have given a warning for a new virus - "NeoCov"

1 in 3 Die': Wuhan Scientists Warn of New Coronavirus 'NeoCov' With High Death, Infection Rate, Says Report
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

Sonugn wrote:Active case load is going down.

Now, scientists have given a warning for a new virus - "NeoCov"

1 in 3 Die': Wuhan Scientists Warn of New Coronavirus 'NeoCov' With High Death, Infection Rate, Says Report
Active case load is following what was expected - thats good - (*** see my separate post below ***

FWIW - Yes I see there is a lot of hype about this 'new' Neo Cov but:

- NeoCov is an old virus closely related to MERS Cov which enter cells via DPP4 receptors
- What's new : Neo cov can use ace2 receptors of bats but they can't use human ace2 receptor unless a new mutation occurs.

(Take all the news with usual careful scrutiny).
Last edited by Amber G. on 28 Jan 2022 21:54, edited 2 times in total.
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

Pratyush wrote:Bharat Biotech nasal booster vaccine for COVID 19 is approved.
Covaxin Maker Bharat Biotech's Nasal Booster Dose Trials Get Approval
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

Some more comments - (Technical discussion - Please ignore if you so chose)

-While the phase is stable enough for SUTRA model to make some more reliable points.
- Sutra consortium has (https://sutra-consortium.in/) latest graphs and trajectories for various states and locations captured by the model.

Image

- The trajectory continued to peak about 23rd Jan. (Actual peak from reported data seem to be around 25th Jan. Hopefully it will start to decline now)
- According to the model, the reason for lower peak is not change in testing strategy.
(Sorry ignorant/bigoted experts of NYT etc - who claim the actual numbers are much higher). Trajectory change around the first week of January shows reduction in β (contact rate). May be people became more careful - more use of masks and less crowds.) Highly contagious Omicron increased β by about a factor of 3 but then it looks like it was reduced by a factor of about ~2/3).
- As can be seen the predicted future decline is less steep than rise. If the decline is indeed less steep, it would strongly support the hypothesis of β going down.
- (Technical point - reduction in epsilon (ratio of 'tested' vs actual infected) may change the height (obviously) but it does not change the slope -- this is how we can estimate this ratio even if testing strategy changes if we have historic data).
- This "less steep" decline is from data of places that peaked a while ago. Let us see what future tells us about other places. While Mumbai, Delhi, Kolkata may be declining as per prediction, the whole country's curve depends on when the peak occurs in various places. If there is a longer gap between the state/city level peaks than predicted, the national curve should become flatter.
- Hope people's use of masks etc will win against any BA2 lineage spread.

(I will try to answer genuine questions - will ignore trolls).
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

Dr. Anurag Agrawal, director of Institute of Genomics and Integrative Biology, is also a member of the SUTRA Consortium. Sharing his views regarding the next steps on COVID for India in Indian Express.
He makes a strong argument for the reopening of schools, at least in areas where the Covid curve has begun to go down.
Open schools, all-India wave dip early February...
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Re: Wuhan Coronavirus Resource Thread

Post by uddu »

Amber G. wrote:
Sonugn wrote:Active case load is going down.

Now, scientists have given a warning for a new virus - "NeoCov"

1 in 3 Die': Wuhan Scientists Warn of New Coronavirus 'NeoCov' With High Death, Infection Rate, Says Report
Active case load is following what was expected - thats good - (*** see my separate post below ***

FWIW - Yes I see there is a lot of hype about this 'new' Neo Cov but:

- NeoCov is an old virus closely related to MERS Cov which enter cells via DPP4 receptors
- What's new : Neo cov can use ace2 receptors of bats but they can't use human ace2 receptor unless a new mutation occurs.

(Take all the news with usual careful scrutiny).
Very much possible the CCP is wargaming by locking people and stringent lockdown of cities. When NeoCov mutates one find day, no one else is prepared to deal with it in the way possible.
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Re: Wuhan Coronavirus Resource Thread

Post by Deans »

Amber G. wrote: Congratulations to Lt Gen Madhuri Kanitkar on being conferred the Param Vishisht Seva Medal. Lt Gen Kanitkar is the Vice-chancellor at MUHS, Maharashtra and Member, prime Minister's STI Advisory Council.

Lt Gen Kanitkar is the third leading member of SUTRA team - Along with Prof. Manindra Agrawal (Padma Sri) and Prof. Vidyasagar.
Lt Gen Kanitkar is also the Dy Chief of the Integrated General staff. Senior most lady officer in the forces.
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Re: Wuhan Coronavirus Resource Thread

Post by nandakumar »

Lt. Gen. Ms Kanitkar was also the driving force behind setting up innumerable Army Referral Units for treating Covid cases at the height of the Second Wave.
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Re: Wuhan Coronavirus Resource Thread

Post by Mort Walker »

For all of India, SUTRA projection is on the mark, but for states, with the exception of KL, it seems off. Over and underestimates of actual data.

What would explain this?
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Re: Wuhan Coronavirus Resource Thread

Post by Pratyush »

https://timesofindia.indiatimes.com/ind ... 230703.cms

Covid-19: 3 shots okayed last year still not part of vaccination drive
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Re: Wuhan Coronavirus Resource Thread

Post by vijayk »

https://www.reuters.com/business/health ... 022-01-31/
Ivermectin shows ‘antiviral effect’ against COVID, Japanese company says
The company, which has been working with Tokyo's Kitasato University on testing the drug as a potential treatment for COVID-19, did not provide further details. The original Reuters story misstated that ivermectin was "effective" against Omicron in Phase III clinical trials, which are conducted in humans.
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

^^^ ( You may like to edit/correct the post)..
vijayk wrote:https://www.reuters.com/business/health ... 022-01-31/
Ivermectin shows ‘antiviral effect’ against COVID, Japanese company says
The company, which has been working with Tokyo's Kitasato University on testing the drug as a potential treatment for COVID-19, did not provide further details. The original Reuters story misstated that ivermectin was "effective" against Omicron in Phase III clinical trials, which are conducted in humans.
^^^^ Ugh Reuters messed up bad. The new Ivermectin study did **NOT** show it is effective in humans. Reuters hastily misread a press release based on only Omicron *lab results*, but confused thinking it was in humans They corrected the story after damage was already done.. Unfortunately old Reuters headline is now all over right wing websites.
Image

On top of that even in corrected story -- is not corrected fully ... The phase III clinical trial was fake & not even clinical data at all. (That's Reuter for you - they have published many fake stories about India's 10x deaths and some other absolute junk)
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Re: Wuhan Coronavirus Resource Thread

Post by chetak »

Bharat Biotech manufactured Nasal vaccine could be a game changer if it provides mucosal immunity: AIIMS Doctor.
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

When all is said and done - Bottom line - this is typically true in general per all reports..

Latest 3-shot vaccine effectiveness data vs omicron, summarized:
✓ ~50% against infections
✓ ~90% against hospitalizations
✓ ~95% against deaths


Here is one typical report from CDC:
>>> From: SARS-CoV-2 Infection and Hospitalization Among Adults Aged ≥18 Years, by Vaccination Status, Before and During SARS-CoV-2 B.1.1.529 (Omicron) Variant Predominance — Los Angeles County, California, November 7, 2021–January 8, 2022

Report for Omicron wave
Vaccination + booster: 96% reduced hospitalization
Vaccination, w/o booster: 81% reduced hospitalization
Compared with unvaccinated, 8 January 2022,

(the largest US county)
Image
Last edited by Amber G. on 02 Feb 2022 06:16, edited 2 times in total.
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

Also - in US it looks like vaccines to children 6 months and above will be available soon - within next month -- per many newspaper reports.

Update on US: Cases dropping in all but 2 states, deaths continue to rise.
Average: 450K (-34K), In hospital: 126K (-4,518), In ICU: 23K, (-591)
New deaths: 3,600..
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Re: Wuhan Coronavirus Resource Thread

Post by Mort Walker »

The 3 shot mRNA vaccine effectiveness after 16 weeks is not clear at this time. Those who became fully vaccinated by January 2021 and then received booster dose by August 2021, may now be at risk.

Moral of the story, try to reduce risk by avoiding contact in large public places, continue mask wearing and hand washing. Long term vaccine efficacy past 12 months is unknown.
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Re: Wuhan Coronavirus Resource Thread

Post by vijayk »

The vaccination numbers have been dropping.

There is new news of variant of Omricon is coming.

May be time to reduce booster shot gap and encourage people to get 3rd shot
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Re: Wuhan Coronavirus Resource Thread

Post by VinodTK »

India crosses 170 crore vaccination mark
New Delhi: India’s vaccination drive against Covid-19 achieved another milestone as it crossed 170 crore mark on Monday.:
:
:
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Re: Wuhan Coronavirus Resource Thread

Post by vijayk »

Hyderabad news from doctors I know - Omricon is going down. Hospitals are lightly loaded. Most doctors go and recovered. So far pretty mild.
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

vijayk wrote:Hyderabad news from doctors I know - Omricon is going down. Hospitals are lightly loaded. Most doctors go and recovered. So far pretty mild.
Here is Sutra, latest for Andhrapradesh
Image
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

Let me also post the latest SUTRA graphs - The parameters and graphs are not much different than I posted a few weeks/(or a month) ago here.

Now the wave is on the way down - some thoughts - but first, let me post the latest graphs for India. (The old graphs and analysis is still here in BRF - So we can see how the model performed with actual data etc)

*** Starting with current graphs:

(Model Credit - SUTRA Team - some graphs posted in this and few of the following posts are plotted/computed/adjusted by me - if there is an error fault is mine - but the the graphs are same (or computed from same data and parameters) as posted on their web site)

Here is India: (Data up to now, computed from parameters on Feb 1)
Image

Zoomed in Version (for last few months) :
Image
Cont .. (Some analysis on next post...)
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

At present I am keenly looking at South Africa's BA2 Variant and it's effect on trajectory..but the Omicron wave is on downward trajectory both in India and USA - so here are some thoughts - mainly on the modeling.

1. Model has been fairly (excellent in my view as far as most models are concerned) successful in predicting the timing of the peak in states (and localities) in India. This was of high priority as the information can be very useful and planning the resources. For India - for all states:

- Average gap was about 1 day between predicted and actual peak.
- 19 (out of 25) states the difference was less than 3 days.
- Maximum difference was 7 days (for Kerala) and 5-6 days (in Rajasthan, Gujarat)

2 - Model was less successful (But imo, still very well - as we physicists some time deal with 'order of magnitude') in estimating the height of the peak. In most cases, the height was lower - or *much* lower, than 'predicted' . (by a factor of 2 some times - which is okay as far as such models are concerned).

- Many of us thought that this may be due to changing in "testing" strategy" where less number of cases are being detected - or "reported" cases were lower than 'actual' cases. But the model - given enough time - is able to estimate ε (ratio of reported vs actual cases) and after waiting for weeks of more data - the model was still computing higher number than actual. This may lead to new refinement in model itself. But that is the name of the game in science. Since we have detail past data, it would be helpful in refinement - we will see.

3 - Though there is lot of different trajectories in different states (not surprisingly - people and habits are different), *overall* for whole India it seems:

- β increased by a factor of 2 ( some states about 5.5 like UP - some places it was same). β is the contact parameter - depends on infectiousness of the virus as well as people's habit / lockdowns etc). β went up significantly everywhere, but also reduced significantly due to restriction measures some states took. (quite visible in graphs).

- ε remained almost the same (about .03). The value varies from place to place but it did not vary with respect to time. ε is the ratio of 'detected' vs 'actual' cases - which depends on testing strategy etc.
- ρ increased by about 10% overall - some states it remained almost the same. (Not surprising as fully vaccinated percentages varied from state to state). ρ is "reach" of pandemic - this depends on (among other things) vaccinations.

- Loss of immunity was what experts thought - but it seems that some states had very high loss of immunity while others did not.

Edited later: The latest graphs for each states are now up on the website: https://sutra-consortium.in/
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Re: Wuhan Coronavirus Resource Thread

Post by Mort Walker »

The US now has nearly 945,000 dead and even as cases are coming down, it seems deaths are still 1500-2000 per day. States are dropping mask mandates, just when cases are declining. Neither federal or state authorities have ever provided quantifiable numbers and rationale why voluntary masks and social distancing are necessary based on active case loads. If it wasn’t so sad, it would be funny.
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Re: Wuhan Coronavirus Resource Thread

Post by Sonugn »

Excellent. Active case load has dropped below 500000.

Do we have information about the next wave as of yet? Timing/Peak counts etc.
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Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

^^^ Per the model ( chart posted above), By the end of this month, the new cases will be below 20,000 (By March 7th, it is likely to be about 10K)... Active cases is likely to be quite below 200K.

(The confidence in the model is quite high - for next 5-6 weeks the actual numbers are estimated to be within 10% of the projected. What one can *not* predict is what/when/how_bad the next variant will be,

For Omicron, looking at SA data (and UK etc too) some of us ran some scenerios for India. At present, obviously, we are monitoring other emerging variants (#BA2 particularly) - nothing looks too much concerning (In my opinion) at this time - as far as India is concerned. In March, vaccinations for 12 and above will start so the numbers for India will be coming in comfortable range. At present about 96% of eligible adults (70% of total population) are vaccinated. 75+% of eligible adults are with two shots).
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Re: Wuhan Coronavirus Resource Thread

Post by Cain Marko »

Amber G. wrote:^^^ Per the model ( chart posted above), By the end of this month, the new cases will be below 20,000 (By March 7th, it is likely to be about 10K)... Active cases is likely to be quite below 200K.

(The confidence in the model is quite high - for next 5-6 weeks the actual numbers are estimated to be within 10% of the projected. What one can *not* predict is what/when/how_bad the next variant will be,

For Omicron, looking at SA data (and UK etc too) some of us ran some scenerios for India. At present, obviously, we are monitoring other emerging variants (#BA2 particularly) - nothing looks too much concerning (In my opinion) at this time - as far as India is concerned. In March, vaccinations for 12 and above will start so the numbers for India will be coming in comfortable range. At present about 96% of eligible adults (70% of total population) are vaccinated. 75+% of eligible adults are with two shots).
Amberji, can you give a similar concise analysis for US? TBH for aam Abdul like me anything heavier, like many of your posts, are bouncer like :oops:
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Re: Wuhan Coronavirus Resource Thread

Post by sajo »

Despite almost two years of almost militant precautions, the Wuhan virus came knocking to my doors last week of Jan. My whole fever episode lasted about 18 hours with about 101F being the max it would be. SHQ had mild fever for about 6 hours in total. But poor kiddo (3.25 years) was hardest, with fever levels spiking to the levels we had not observed in the past. The pediatrician (a well known neonatal intensivist in Pune), was unfazed and asked use to hold out for 48 hours after which he was confident things would normalize. And they did. Maybe us being vaccinated with covishield cushioned us, kid being not vaccinated was affected the most. We had tested ourselves for antibodies sometime in Oct, and I had over 30x the minimum level of binding antibody titres. Looks like they were in Hindu voter mode (ie, scattered, bored, indifferent) when the Covidullahs began invading, before being jolted into action.
However, the recovery for me hasnt been fun. Post fever, had mild sore throat for somedays, for which the doc prescribed antibiotics. Even then 10 days past since I tested negative, climbing up just two flights of stairs, a bit of running behind the kid, squatting to retrieve stuff which invariably rolls to inaccessible places etc leaves with the wind knocked out of me. I am mostly tired all day long as well. And then there is the brain fog. Dang.. During my illness I would hold the medicine strips in my hand unable to recall whether I had just taken the medicine and keeping it back or yet to take. Used to ask SHQ to count the pills left to come to the right conclusion. Things got a bit worse when I started working after a 5 day leave, and would go blank mid-sentence when in calls with our customers. Still affected by it to some extent.
This summarizes my experience with the WuFlu.
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Re: Wuhan Coronavirus Resource Thread

Post by Cyrano »

Bon courage Sajo ji. Glad you all came out of it OK, hope the lingering effects will subside over time.

Are there any studies being done on such long term effects of Covid? If any knowledgeable member can post a link or two of such studies, it will help.

Thank you.
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Re: Wuhan Coronavirus Resource Thread

Post by sajo »

Cyrano wrote:Bon courage Sajo ji. Glad you all came out of it OK, hope the lingering effects will subside over time.

Are there any studies being done on such long term effects of Covid? If any knowledgeable member can post a link or two of such studies, it will help.

Thank you.
Thank you Cyrano ji. For some reason, though I am not very out of shape (though far far far out from being athletic), not prone to falling ill often, yet seem to be taking the longest to recover. Some days are fine, but rest I wake up absolutely tired and with a heavy head. These are the long (~10 days) symptoms I am observing in myself.
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Location: Ohio, USA

Re: Wuhan Coronavirus Resource Thread

Post by Amber G. »

Sajo - Wishing you and your family a fast and complete recovery.

Last weekend, 4 year old daughter of Dr Murthy (USA's surgeon general) has come out with the virus. He shared:
Parenting during the pandemic has been one of the hardest jobs I could have imagined. I have immense respect for the millions of parents who are grappling with the daily, exhausting decision-making that goes into protecting our kids’ health and their education.

The experience of the last few days has reminded me that despite our varied opinions about the pandemic, we all largely want the same thing: to keep ourselves and our loved ones safe. I hope to remember this the next time I encounter someone with a different point of view. Until then, hold your kids and your loved ones close. That’s what we will do with our daughter until she’s better and for as long as possible thereafter.


As many of parents all over the world are wishing .. hope the vaccinations for *all* children start as soon as possible.
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