Pandemic relevant papers
This is mostly scientific papers relevant to the pandemic - there are a few official data sources included as well. Inclusion is not necessarily endorsement (particularly I include a couple under misinformation that I would not endorse but think are relevant to understanding the pandemic).
We made a flu strain go extinct via COVID control measures
Influenza lineage extinction during the COVID-19 pandemic? | Nature Reviews Microbiology
Responses to a pandemic
Highlighting COVID-19 racial disparities can reduce support for safety precautions among White U.S. residents - ScienceDirect | Social Science & Medicine - this should be read in conjunction with The Misperception of Racial Economic Inequality - Michael W. Kraus, Ivuoma N. Onyeador, Natalie M. Daumeyer, Julian M. Rucker, Jennifer A. Richeson, 2019 which discusses motivated reasoning in people thinking the racial wealth gap is less bad than it is.
Longterm effects of COVID inc. Long COVID
Long-term cardiovascular outcomes of COVID-19 | Nature Medicine
Long-term neurologic outcomes of COVID-19 | Nature Medicine
Long COVID after breakthrough SARS-CoV-2 infection | Nature Medicine - this has an excess burden at 6 mnths of 120 per 1000 people for those with any symptom compared to controls. Suggesting that even when vaccinated Long COVID rate might be 12% (120 per 1000).
https://www.researchsquare.com/article/rs-1749502/v1 - this is a preprint - but has now passed peer-review to become Acute and postacute sequelae associated with SARS-CoV-2 reinfection | Nature Medicine and has Ziyad Al Aly as an author like the 3 papers above - unsurprisingly is another study of US veterans (like 3 above). My understanding is the design does not permit us to know whether the consequences of reinfection are due to those having it worse on first infection are more likely to get reinfected - or whether among those who had mild first infections a second infection may extract a greater toll. What the paper does indicate is that in either case reinfection should be avoided as those twice infected are likely to have bad outcomes.
CDC Household Pulse Survey (referenced in this 22nd June 2022 press release) - has a high incidence of Long COVID among those who ever experienced COVID - but as technical note on page mentions the proportion in survey saying they have had COVID is smaller than seroprevalence studies suggest so the denominator and hence the true incidence of Long COVID may be lower (Pulse Survey puts it at over 30% - compare to paper directly above : though that is in vaccinated people).
SARS-CoV-2 is associated with changes in brain structure in UK Biobank | Nature
Cardiovascular disease and mortality sequelae of COVID-19 in the UK Biobank - another Biobank study. See Table 2 - non hospitalised COVID-19 cases have a hazard ration of 2.74 relative to controls for venous thromboembolism (VTE) (I think this increased VTE risk is seen in other studies so not a “torture the data until you get a significant result” problem of multiple comparisons). In Table 2 the control rate per 1000 person-years is 1.41 and for non-hospitalised cases is 3.94. So, particularly with a hazard ratio for all cause death among non-hospitalised cases of 10.23, COVID-19 is definitely to be avoided - but the base rate of VTE among the non-hospitalised is low in absolute terms so the nearly threefold increase in risk does not mean a large absolute increase in VTE among the non-hospitalised.
Immune boosting by B.1.1.529 (Omicron) depends on previous SARS-CoV-2 exposure
Vaccine papers
Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine | NEJM
Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom | Nature Medicine
Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II): protocol for an observational study using linked Scottish national data | BMJ Open - using Scottish data to estimate impact of pandemic and effectiveness of treatments & vaccines (used in preceding link re: first vaccine dose effectiveness).
Delayed Second Dose versus Standard Regimen for Covid-19 Vaccination | NEJM
Covid-19: Researcher blows the whistle on data integrity issues in Pfizer’s vaccine trial | The BMJ (note this is not a peer-reviewed scientific paper as most links on here are - it is more investigative report) - my impression of this is some of the issues it touches on are the kind that affect patient care and some are the kind that might affect the scientific integrity of the trial. The point is if you read the papers in this section overall - rather than just this - there are a number of post rollout vaccination studies that agree on the positive effects of the vaccine. So I do not think a balanced reading sees this as negating the value of vaccines - but rather emphasises a better regulatory regime to raise some standards.
Masking papers
School Masking Policies and Secondary SARS-CoV-2 Transmission
Impact of community masking on COVID-19: A cluster-randomized trial in Bangladesh | Science
Efficacy of FFP3 respirators for prevention of SARS-CoV-2 infection in healthcare workers | eLife
Sources of healthcare workers’ COVID‑19 infections and related safety guidelines
An upper bound on one-to-one exposure to infectious human respiratory particles | PNAS
Overall impact of pandemic
Years of life lost to COVID-19 in 81 countries | Scientific Reports
Misinfo
This: Vaccines | Free Full-Text | The Safety of COVID-19 Vaccinations—We Should Rethink the Policy is a retracted paper that prompted this “Journal retracts paper claiming COVID-19 vaccines kill | Science” coverage - here is the data source as archived on the Wayback Machine and if you translate “Overlijden ná vaccinatie betekent niet dat een bijwerking van het vaccin de oorzaak is van het overlijden.” which you will find clearly - right above the figures misused by that paper - then you can verify trivially for yourself that the paper is untrustworthy.