Thread by @DanielBanas_sk

Will Slovakia avoid „Czech scenario“?
Health minister #marekkrajčí 16.10. first time publicly compared the second wave COVID-19 trends in Slovakia and Czech republic in a chart showing that Slovakia is following the scenario in Czech republic with a delay of 2~3weeks.:

Trend chart from few days ago (22.10.) was even worse and clearly showing that Slovakia is repeating the Czech scenario:

Somewhere here we should be looking for motivation of the government in Slovakia and prime minister #igormatovič to solve the problem of rising second wave of epidemics and dark vision of collapsing health care by unusual way - #masstesting in combination with limited lockdown.

Despite scepticism in a part of the Slovak scientific community the government, with help of the armed forces, local municipalities and volunteers, organized a #masstesting pilot run in 4 districts and plans to organize later 2 nation wide test runs. The first one this weekend.

There are some signs that the epidemics curve might be turning away from the path to "Czech scenario". Doubling time is now longer than 2 weeks:
5. 10. – 11. 10.: 6863 new cases
12. 10. – 18. 10.: 10340 new cases
19. 10. – 25. 10.: 14460 new cases

Also test positivity rate trend starts to diverge, though it is still too far away from safe levels (~20% now vs. <5%):

One explanation could be that restrictions introduced in Slovakia from the beginning of October are starting to show some results, mobility of iPhone users in Slovakia is close to the first wave lockdown levels:

While in Czech republic the mobility of iPhone users is not yet down to the first wave lockdown levels:

We should also see a slight effect of pilot #masstesting run in next days where the population of the 4 most hit districts was tested. Out of the 140945 people tested, 5594 had a positive test result (quick anti-gen tests were used).

Positive cases from pilot #masstesting run are not accounted in official COVID-19 statistics that includes only results from more precise PCR tests. I will provide some numbers from #masstesting in next days and further development in Slovakia.

God job by Daniel Kerekes from @dennikN by filling a gap in #masstesting information campaign in #Slovakia. He created an interactive map of test sites in capital city Bratislava.
dennikn.sk/2112895/mapa-k…

Slight decrease in number of new positive #COVID19 cases for yesterday in #Slovakia: 2785 new cases out of 14335 PCR tests. Test positivity ratio is still high but below 20% and diverging a bit more from "Czech scenario" trend.

For yesterday a jump in positive #COVID19 cases in #Slovakia to new record 3363 but also new record in number of PCR tests done in one day - 16556. Result is that the test positivity rate sticks to the same level (20,3% yesterday) and it is diverging from #czechscenario:

Optimistic news from #Slovakia. Drop in positive test cases to 2573 and also a record number of PCR tests in one day: 18074. This gives test positivity rate below 15% and confirms diverging from #czechscenario. Reminder: #masstesting in Slovakia this weekend.

I report about #masstesting in #Slovakia in a separate thread.

https://twitter.com/DanielBanas_sk/status/1322278324480204801

Again very optimistic data from #Slovakia for yesterday: again drop in positive cases to 2282, again record in total PCR tests (21949) and again drop in TPR.

Also promising data from the first day of #masstesting in #Slovakia. 2,58mln antigen tests, 25859 were positive and stay home in quarantine. Based on experience in worst hit regions I will not be surprised if total daily PCR positive cases will drop below 500 in about a week.

Sudden rise in number of PCR tests done in #Slovakia is suspicious. It could be caused by higher amount of commercial PCR tests. PCR tests were allowed as alternative to #masstesting campaign antigen tests. We should expect a drop in number of tests and PTR rise in next days.

Data from yesterday's #COVID19 PCR tests in #Slovakia: 1883 positive test cases out of 21477 tests. That is a rise from value 7 days ago (1312) but we have a huge increase of PCR tests (6175 week ago). TPR below 10%. Let's see if this number of PCR tests is sustainable.

Let's see how the test&tracing (normally source of many PCR test indications) will catch up with large number of #COVID19 infections identified by #masstesting antigen tests.

Data from Monday's #COVID19 PCR tests in #Slovakia: 1727 positive test cases out of 18994 tests. That is again a rise from value a week ago (901) but we have a huge increase of PCR tests (5899). TPR below 10%. Still a long way to acceptable 5%. Suspicious data from #Czechia.

Surprise, surprise: 3216 positive cases out of 13337 PCR tests, bump in PCR to 24%! Waiting for more official data or inside info what could be behind this sudden change. By the end of this week (Saturday?) we should see some effect of #masstesting, it was not immediate in pilot.

It also shows what I have mentioned some days ago - more than ~15k of PCR daily tests is not yet sustainable for #Slovakia. This affects TPR trend - we need to look at moving average.

Possible reasons for a bit surprising data for #Slovakia today:
- less tracing in past days (preparation for #masstesting), that would mean that the data were not so real
- trying to confirm positive #masstesting antigen tests by PCR
- extended tracing from #masstesting data

#Slovakia is able to carry out ~15k PCR tests on weekdays at sustainable level. When counting with 5% TPR (WHO limit) it gives 750 cases. This is the highest number of cases when we can consider that the situation is under control.

Limit for releasing of some epidemics restrictions is 500 cases and less in 7-day moving median value.

Continuing with up&down data (after #masstesting) from #Slovakia. Yesterday there were 1962 positive tests (down from 2785 week ago) in 12864 tests. Next days could be similar as #masstesting confirmation tests by PCR or extended tracing are going on. TPR down to 15%.

Up&down data again: 2354 positive cases, 11615 tests done. TPR up to 20%, positive cases a bit up from yesterday but down from a week ago (3363). This looks like flattening the curve. Some regions are still "burning", including some hidden areas found by #masstesting.

Flattening the curve: 2579 positive cases, 15767 tests done. TPR down to 16%. Almost same value as a week ago (2573). Next (but reduced to 54% of population of most hit regions) round of #masstesting this weekend.

Another weekly decrease on Saturday: 1828 positive cases (2573 week ago), 15466 tests. TPR down to 12%. Important: decrease in hospitalisations and ICU patients, no reported deaths. Projected collapse of hospitals was the main reasons of #masstesting.

#masstesting is not yet showing off in PCR test results yet dramatically as in some regions from pilot testing but definitely it is visible in number of hospitalised patients. The second #masstesting round shows that each round reduces the number of infections by ~55%.

Time to change the chart - we do not need to compare trends in Slovakia and Czech republic. Let's focus on the effect of #masstesting. With some help of Python, #matplotlib, #pandas and #numpy.

Optimistic Sunday data from #Slovakia: 577 positive cases (1883 week ago) in 4056 tests. TPR at 11,6%. It will be interesting to see how/when (if?) the effects of #masstesting.

Correction: number of tests on Sunday: 4956

Comparison of the first and second wave of SARS-CoV-2 epidemic in Slovakia.
#matplotlib #pandas #numpy

New data from Monday tests: 1051 positive (1727 week ago), 6813 tests done. I have extended the chart to include TPR trend as a "mirror of truth" for PCR test data. I expect some ups in next days due to tracing after #masstesting.
#matplotlib #pandas #numpy

Tuesday data from #Slovakia: 2058 positive (3216 week ago), 12891 tests done. I have extended the chart sheet to include reproduction number and mobility trends. Reproduction number is around 0.75 as calculated by R.Koch Institute formula.
#matplotlib #pandas #numpy

Comparison of the first and the second #SARSCoV2 wave in #Slovakia, including #TPR, #R0 and #mobility trends.
#matplotlib #pandas #numpy

Wednesday data from #Slovakia: 2591 positive test cases (2354 week ago), 12584 tests done. #R0 below 1.0. It may indicate flat curve but also it could be a result of PCR tests indicated from #masstesting as we saw a week ago, higher #TPR could be related. We will see next week.

#SARSCoV2 data for #Slovakia from Thursday: 10736 tests done, 2024 positive cases, hospitalisations down by -32. I have extended the epidemic sheet with #OxCGRT Oxford COVID-19 Government Response Tracker data.

Friday #SARSCoV2 data for #Slovakia: 10742 tests done, 1771 positive cases (2579 week ago), hospitalisations down again. I have extended the epidemic sheet with some healthcare stats. #R0 somewhere between 0.7 and 0.9. Curve is decreasing.

Interesting to see what will next days bring. On Monday churches, cinemas and theatres (all at 50% capacity) and gyms/pools (up to 6 ppl) are opening again. All shops and most of services are open with exception of one week of soft lockdown.

Friday epidemic sheet once again, last bar was missing in charts. It looks like we passed the peak in hospitalisations too.

Saturday #SARSCoV2 data for #Slovakia: 6545 tests done, 1200 positive cases (577 week ago), hospitalisations down again (seems behind peak?). #R0 still somewhere between 0.7 and 0.9.#TPR: perhaps we need to relax conditions for test indication (more tracing).

Sunday #SARSCoV2 data for #Slovakia: 1771 tests done, 509 positive cases (577 week ago). Suspicious: high #TPR / low number of tests, hospitalisations bit up (between Thursday and Friday level). Typical Sunday data - always look at wider context.

I had a look into detailed data. There was a Sunday burst reported in one small district - Vranov nad Topľou had 136 cases alone. In all other days of November it was 454 cases. Looks like local hot spot. I hope that it is included in hot spot testing round next weekend.

Sadly, these cases were in one spot - large pensioner house. Article by @denniksme in Slovak:
presov.korzar.sme.sk/c/22535944/obr…

Monday #SARSCoV2 data for #Slovakia: 7837 tests done, 1326 positive cases (1051 week ago). TPR back to better numbers but hospitalisations up again.

Tuesday #SARSCoV2 data for #Slovakia: 5833 tests done, 1311 positive cases (2058 week ago). TPR up, hospitalisations down this time. Is higher TPR during declining phase common for countries with high infection (see Belgium, Czechia, ...)?

Another question is when (and where) was the peak of positive cases. Peak in hospitalisations usually follows the peak in positive cases by 6-8days. I think that this deserves the separate thread as the stats were obscured by masstesting effects.

Hospitalisation numbers were updated bit up on official page so here is the epidemic sheet with updated Tuesday data.

Wednesday #SARSCoV2 data for #Slovakia: 7913 tests done, 1665 positive cases (2591 week ago). TPR bit down, hospitalisations down. I have added LOWESS local regression to add trend approximation that does not lag (hint by @oliverbeige).

Regarding lower number of tests: official stats included PCR tests only so far (according to ECDC standards). There is a large number of places now where people can daily get free antigen tests, even without medical indication, with instant results. They reduce PCR test counts.

There is a plan to make stats for these antigen tests public but probably in a separate field. I will then include that in my sheet.

Thursday #SARSCoV2 data for #Slovakia: 9836 PCR tests done, 1818 positive cases (2024 week ago). Both TPR and hospitalisations bit down. We have daily antigen test data for the first time: 15103 tests done yesterday, 635 positive cases. I will include them in chart in next days.

Friday #SARSCoV2 data for #Slovakia: 10554 PCR tests done, 1861 positive cases (1771 week ago). Both TPR and hospitalisations bit down again. Antigen test data: 12139 tests done yesterday, 369 positive cases.

I do not have historical PCR+Ag data so I share at least chart with 7-day trend of positive PCR+Ag tests (blue line) published by the government yesterday.

I have extended the test number chart with Friday data with total test numbers, TPR still calculated from PCR only.

In addition to free daily antigen tests that people can get in 118 test sites there is another round of massive antigen tests in 458 small cities or villages with more than 1% of positive cases in previous round.

Saturday #SARSCoV2 data for #Slovakia: 5691 PCR tests done, 984 positive cases (1200 week ago). Antigen test data: 6898 tests done yesterday, 247 positive cases. In addition to that mass antigen tests in some hot spots: 68888 tests, 1366 positive cases.

I have extended the sheet with chart about deaths. I did not want to do that in the past but people are discussing it. So here it is for context. Slovakia tries to confirm all COVID-19 deaths by autopsy, at least of lungs. According to WHO standards.

Interview with Slovak pathologist: "If we hadn't done a detailed investigation, we would have had significantly more deaths in Covid-19," in Slovak, postoj.sk/65044/mnohe-ob… via @PostoJ.sk

Sunday #SARSCoV2 data for #Slovakia: 1773 PCR tests done (Sunday low but this time very low), 231 positive cases (509 week ago). Antigen tests: 1850 tests done, 55 positive cases. Mass antigen tests in hot spots yesterday (incomplete data): 14529 tests, 380 positive cases.

As you can see that COVID-19 hospitalisations now oscillate around 1.5k for a bit longer time. That could be a sign of the fact that we lost the peak of the wave in fog of mass testing and PCR tests provide slightly different picture than before.

Monday #SARSCoV2 data for #Slovakia: 6545 PCR tests done, 1021 positive cases (1326 week ago). Antigen daily tests: 44769!!! tests done, 919 positive cases. I am not sure what this huge number of daily antigen tests mean. Some previous daily antigen test data are not yet public.

Positives from antigen tests are very valuable because if we exclude false positives we get people that are infectious now and instantly. PCR detects a lot of asymptomatic people after being infectious (31%-52% before and 61%-80% after peak via @michaelmina_lab ) and with a lag.

High number of daily antigen tests is an overlooked strategy in disputes between mass-testing and tracing via PCR tests. In longer term and with sufficient amount (free tests in many test sites, regular tests in hospitals, nursing homes, ...) it could be the best one.