We recently published a research letter on SARS-CoV-2 re-infection rates in JAMA Open Network. While working on the problem I realised that obtaining valid estimates was more complex than I had anticipated. Some thoughts on SARS-CoV-2 epidemiology (1/9) jamanetwork.com/journals/jaman… 2/9 Obvious questions to ask with re-infection rates are: i) does time from initial infection effect rates? ii) does vaccine status and time from last vaccine dose effect rates? iii) what are the rates by age group?

Hér má nálgast skýrslu sem inniheldur frumgreiningu á innlögnum eftir bólusetningarstöðu frá september til byrjun janúars 2022. Mikið enn ógert, m.a. ítarleg greining á forsendum, tenging við eldri gögn. Líta skal á þróun frekar en punktmöt drive.google.com/file/d/11WHrWh… Það sem skín í gegn er að bólusetning skiptir sköpum. Áhætta allra aldurshópa á alvarlegum veikindum (gróflega skilgreint sem þörf á spítalainnlögn eða flutning á gjörgæslu) hefur lækkað verulega síðustu 30-45 daga

Ákvörðunin sem lá/liggur fyrir byggir gróflega á eftirfarandi forsendum:
1) kallar núverandi ástand á inngrip?
2) er líklegt að inngripið beri árangur?
3) hvað kostar inngripið?
4) er hlutfall 2)/3) ásættanlegt?

Öfunda ekki þá sem þurfa að ákveða en skil samt ekki ákvörðunina Svarið við 1) er augljóslega já. Það er ekki hægt að keyra á velvilja starfsfólks gjörgæslunnar, legudeilda og göngudeildarinnar endalaust. Fjöldi yfirvinnutíma fyrir þorra starfsfólks er að nálgast ígildi auka 100% starfs. 50% allra aðgerða hefur verið frestað sl. vikur

Nú mun sami farsi hefjast eins og í hverri bylgju Covid-19 hingað til. Sóttvarnalæknir mun benda á að bylgjan er í vexti og við þurfum að hefja aðgerðir til að verja spítalakerfið gegn hruni. Fólk mun þá hrópa: "En sjáið hvað eru fáir inniliggjandi!" Þeir sem greinast leggjast inn á spítala að miðgildi 7 dögum seinna (IQR 6-10) og á gjörgæslu að miðgildi 10 dögum seinna (IQR 9-15). Jafnvel ef við brygðumst við núna mun bylgjan halda áfram að vaxa í einhverjar vikur, mynstur sem er hreinlega eðli smitsjúkdóma

Iceland is unfortunately experiencing the beginning of its fifth wave of Covid-19. An interesting anecdote is the large gap in infections among 13-17 year olds, who recently become eligible for vaccination (august-september) of whom roughly 70% accepted In fact, no vaccinated child has been diagnosed with Covid-19 during the 4th and, now likely 5th, wave of infections in Iceland. This is in keeping the notion that vaccines protect maximally against infection soon after vaccination

Hefði verið gagnlegt að setja 4144 tilkynningar um aukaverkanir í samhengi. Það voru gefnir 556302 skammtar, svo 4144/556302 = 0.7%. Til samanburðar eru ~1% líkur á "nýrnakvillar sem geta valdið bjúgmyndun, bólgur í nýrum og nýrnabilun" við töku íbúfens visir.is/g/20212173262d… Þess utan voru algengustu tilkynningarnar höfuðverkur, hiti, vöðvaverkir og þreyta. lyfjastofnun.is/covid-19/aukav…

Is anyone interested in studying the policy impact of coupling state funding to diagnosis-related groups (DRG) on diagnostic coding? An interesting natural experiment will be occurring in Iceland during the New Year #epitwitter Landspitali-The National University Hospital of Iceland and Akureyri Hospital will be moving from a fixed state budget to being funded based on DRGs. Primary Care Centres will however remain on a fixed budget system

Hugely interesting study! Before I read the result I obtained the questionnaire from the supplementary data and answered. I highly recommend this as an exercise. Of course I was primed by reading the first tweet in this thread

https://twitter.com/dr_dmorgan/status/1424761171031117826

I answered using absolute estimates but as the discussed, relative risks were tempting. The fact that clinicians were not told to use absolute rather than relative risks make the results harder to interpret, though I realize this is a result in & of itself. My answers:

Vaccines are the most important tool we have to combat SARS-CoV-2. Whilst I stand by my original point that vaccines alone are unlikely to result in herd immunity, they do protect against illness. With huge caveats, the Icelandic data also do suggest that they reduce transmission In the above figures created by @hjalli_is, the crude incidence of SARS-CoV-2-infection is shown among vaccinated (green) and unvaccinated (yellow). The curves largely diverge, suggesting a protection against infection/transmission. More details: grid.is/@hjalli/covid-…

I hate to be the bearer of bad news, but Iceland (93% of the population 16 years of age or older vaccinated) is experiencing its largest wave of Covid-19 yet. At this point, I think it is unreasonable to assume that increased vaccine coverage will result in herd immunity On the bright side, a much larger proportion of those infected have minimal or no symptoms, and fewer patients with Covid-19 are being admitted.

Detailed vaccine data: covid.is/statistical-in…

Detailed incidence data: covid.is/data

Við erum að nálgast veruleika þar sem heilbrigðiskerfið þolir ekki álagið þrátt fyrir mátt bólusetninga. Ef það greinast ~150 á dag, og miðgildi bráðra veikinda er ~10 dagar þá verða á hverjum tíma 1500 með virka sýkingu. Ef um 2% leggjast inn þá verða ~30 á spítala Sem læknir á LSH get ég fullyrt 100% að LSH þolir ekki slíkt álag til lengdar. En þetta eru algjörlega marklausir reikningar því að miðgildi veikindatíma hjá þeim sem leggjast inn á spítala nálgast ~30 daga, þar af ~15 dagar inn á spítalanum sjálfum og það er óhjákvæmilegt...

Have you ever wondered what proportion of patients with COVID-19 have specific symptoms when prospectively followed with repeated structured interviews in a population-based sample? Wonder no more! Our preprint is finally up. medrxiv.org/content/10.110… Iceland introduced an early, robust test & trace approach with broad access to free, same-day-result PCR, and open-invitation & random population screening. As a result, we detected milder disease, the majority (67.5%) having only mild symptoms throughout their disease course.

At @Landspitali (Iceland's largest and only tertiary hospital) we have an awesome team of inhouse engineers and programmers that develop EMR software in close collaboration with physicians and nurses. I have never seen a better EMR, its almost perfect cnbc.com/2018/12/27/doc… Specifically, the important difference is that our EMR is not built for billing/coding. It is built to optimise the presentation of clinical information and avoid unnecessary clicks. Large interdisciplinary meetings are held regularly to decide what solutions will be implemented

The writing phase of my PhD has begun. I am writing it in @rstudio using @xieyihui excellent #bookdown package. I am hosting it live on eliaseythorsson.github.io/phd_thesis/ as I write. Any and all criticisms, tips and encouragements are appreciated. Daily commits. Here goes nothing. Next step is to sort out citation issues, and figure out how to keep protected data off github while still being able to use it in the bookdown rendering