Handy-dandy Covid19 Links

            My Covid19 bookmarks folder was getting cumbersomely large, and a friend wheedled at me to share it, so here's my bookmarked links as a web page.  I've organized it a bit and pruned some of the expired resources (waah, I miss epiforecasts) and may or may not update it with future links.  You know how that goes; this is the internet, and stale content is just how we live now.
            How to use this information:
            The first section links to regularly-updated metrics and policies, suitable for keeping informed on the state of the pandemic.  I check on a few of them every week, the others about once a month.
            The second section is reference material, describing medical research findings on specific topics.  Use them to learn more about how the virus spreads, what the vaccines do and do not do, what long covid is and who it inflicts, the behavior of virus-bearing aerosols, and other general information.
            See also my page of upcoming vaccines.
General Resources
Sources to check weekly:
Pandemic Mitigation Collaborative dashboardPMC19
CDC SARS-CoV-2 Sewage Monitoring Dashboard, by stateCDC
CDC SARS-CoV-2 Sewage Monitoring Dashboard, by territory and nationwideCDC
County of Santa Clara SARS-CoV-2 Sewage Monitoring DataSanta Clara County, CA
Sewage coronavirus concentration levels for Los AngelesWasteWaterScan
Sewage coronavirus concentration levels for Santa RosaWasteWaterScan
Monitoring Variant ProportionsCDC
California covid hospitalizationsCovid Act Now
COVID-19 Weather Reports, a folksy-breezy overview of recent pandemic trendsThe People's CDC
The leading strains for the USA's current infection wave, from early June 2024 to present:
    KP.2 variant, a BA.2.86.* descendant (dominant)Cov-Spectrum
    KP.3 variant, a BA.2.86.* descendant (secondary)Cov-Spectrum
    LB.1 variant, a BA.2.86.* descendant (secondary)Cov-Spectrum
    LB.1 variant at Outbreak Info, since Cov-Spectrum doesn't seem to have it yet.Outbreak Info
The leading strains for the USA's infection wave from late October 2023 to mid-February 2024:
    JN.1 variant, a BA.2.86.* descendant (dominant)Cov-Spectrum
    HV.1 variant, an XBB.1.9.* descendant (secondary)Cov-Spectrum
The leading strains for the USA's infection wave from August 2023 to October 2023:
    EG.5.1 variant aka "Eris", an XBB.1.9.* descendant (dominant)Cov-Spectrum
    FL.1.5.1 variant, also an XBB.1.9.* descendant (secondary)Cov-Spectrum
Sources to check monthly (or annually):
Absolutely Maybe blog about vaccines and other medicinePLOS
COVID19 burden estimatesCDC
Tracking COVID Long-Haulers from the CDCCDC
Simple dashboard for USA and World infections and outcomesCoronaboard
Tracking vaccination levels by county across CaliforniaCalifornia Dept of Public Health
Kaiser Permanente's current covid19 policiesKaiser Permanente
California's current covid19 vaccination policiesCalifornia
The top covid19 vaccine myths spreading onlineBritannica
The Microcovid Project, estimating risk for youMicrocovid
Wikipedia: Timeline of the SARS-CoV-2 Omicron variantWikipedia
Nationwide SARS-CoV-2 Sewage Monitoring DataBiobot Analytics
Genomic epidemiology of SARS-CoV-2 with subsampling focused on North America over the past 6 monthsNextstrain
Variants and Genomic Surveillance for SARS-CoV-2CDC
Rates of COVID19 deaths by vaccination statusCDC
Our World In Data -- Coronavirus (COVID-19) CasesOur World In Data
Our World In Data -- Coronavirus (COVID-19) VaccinationsOur World In Data
A highly accessible summary of COVID19 health impactsSHI
Another list of COVID19-related medical research publications, maintained by u/aQuiMieuxMieuxGDocs
Sewage coronavirus trackers for all USA states and territoriesReddit
SARS-CoV-2 Airborne Decay CalculatorDHS
Medical Publication and News Articles
2024-04-10SARS-CoV-2 infects cells lining the blood-retinal barrier and induces a hyperinflammatory immune response in the retina via systemic exposure -- and related news articlePLOS
2024-02-28 Mounting research shows that COVID-19 leaves its mark on the brain, including with significant drops in IQ scores -- an article rather than a research publication, but references several medical studies and ties them together nicelyThe Conversation
2024-02-21COVID-19's neurological effects linked to immune response, not direct viral attackNews Medical
2024-01-24Respiratory distress in SARS-CoV-2 exposed uninfected neonates followed in the COVID Outcomes in Mother-Infant Pairs (COMP) StudyNature
2024-01-19Microstructural brain abnormalities, fatigue, and cognitive dysfunction after mild COVID-19Nature
2024-01-17SARS-CoV-2 infection causes dopaminergic neuron senescenceCell
2023-12-14Long-term outcomes following hospital admission for COVID-19 versus seasonal influenza: a cohort studyLancet
2023-11-22Covid-19 vaccine effectiveness against post-covid-19 condition among 589,722 individuals in Sweden: population based cohort studyBMJ
2023-09-28The New Normal: Delayed Peak Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Viral Loads Relative to Symptom Onset and Implications for Coronavirus Disease 2019 (COVID-19) Testing ProgramsClinical Infectious Diseases
2023-09-18Severe COVID-19 may lead to long-term innate immune system changesNIH News Advisory
2023-08-28Assessment of Hospital-Onset SARS-CoV-2 Infection Rates and Testing Practices in the US, 2020-2022JAMA Network
2023-08-28Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deerNature
2023-08-21Incidence of New-Onset Hypertension Post-COVID-19: Comparison With Influenza (and related article)Hypertension
2023-08-21Postacute sequelae of COVID-19 at 2 yearsNature
2023-08-19Acquired Immune Deficiency Syndrome correlation with SARS-CoV-2 N genotypesBiomedical Journal
2023-08-18Severe COVID-19 Can Alter Long-term Immune System Response (news article)Weill Cornell Medicine
2023-08-16Risk of autoimmune diseases following COVID-19 and the potential protective effect from vaccination: a population-based cohort studyLancet
2023-08-13Severe COVID-19 may lead to long-term innate immune system changes (news release)NIH
2023-07-21A Systematic Review of Persistent Clinical Features After SARS-CoV-2 in the Pediatric PopulationAAP
2023-07-11The Immunology of Long CovidNature
2023-06-27Divergence of wastewater SARS-CoV-2 and reported laboratory-confirmed COVID-19 incident case data coincident with wide-spread availability of at-home COVID-19 antigen testsPeerJ
2023-06-26Viral persistence in children infected with SARS-CoV-2: current evidence and future research strategiesLancet
2023-06-23Trends in Laboratory-Confirmed SARS-CoV-2 Reinfections and Associated Hospitalizations and Deaths Among Adults Aged >=18 Years -- 18 U.S. Jurisdictions, September 2021 to December 2022CDC
2023-05-25No, the COVID-19 Pandemic Isn't OverCleveland Clinic
2023-05-04A bivalent ChAd nasal vaccine protects against SARS-CoV-2 BQ.1.1 and XBB.1.5 infection and disease in mice and hamstersbioRxiv
2023-04-23Viral reactivations and co-infections in COVID-19 patients: a systematic reviewNIH
2023-04-22Assessing COVID-19 pandemic policies and behaviours and their economic and educational trade-offs across US states from Jan 1, 2020, to July 31, 2022: an observational analysisLancet
2023-04-17A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primatesNCBI
2023-04-15Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: A longitudinal cohort studyJCV
2023-03-15Robust T cell responses to Pfizer/BioNTech vaccine compared to infection and evidence of attenuated peripheral CD8+T cell responses due to COVID-19Cell
2023-03-08Long-Term Adverse Effects of Mild COVID-19 Disease on Arterial Stiffness, and Systemic and Central Hemodynamics: A Pre-Post StudyJCM
2023-03-03Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: A longitudinal cohort studyJCV
2023-02-27Excess cardiovascular mortality across multiple COVID-19 waves in the United States from March 2020 to March 2022Nature
2023-01-13Long COVID: major findings, mechanisms and recommendationsNature
2023-01-11Long covid outcomes at one year after mild SARS-CoV-2 infectionBMJ
2023-01-10Risk of autoimmune diseases in patients with COVID-19: A retrospective cohort studyNIH
2023-01-06SARS-CoV-2 infection and multi-organ system damage: A reviewNIH
2023-01-05Association between COVID-19 and consistent mask wearing during contact with others outside the householdInfluenza and Other Respiratory Viruses 2022
2022-12-31Autopsies Show COVID-19 Virus in Brain and Elsewhere in BodyNeuroscience News
2022-12-27Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariantsbioRxiv
2022-12-07Post COVID-19 condition diagnosis: A population-based cohort study of occurrence, associated factors, and healthcare use by severity of acute infectionJIM
2022-12-03Estimated SARS-CoV-2 antibody seroprevalence trends and relationship to reported case prevalence from a repeated, cross-sectional study in the 50 states and the District of Columbia, United States -- October 25, 2020 - February 26, 2022Lancet
2022-12-01The prevalence and long-term health effects of Long Covid among hospitalised and non-hospitalised populations: a systematic review and meta-analysisLancet
2022-11-10Acute and postacute sequelae associated with SARS-CoV-2 reinfectionNature
2022-11-07Nirmatrelvir and the Risk of Post-Acute Sequelae of COVID-19MedRxiv
2022-11-07Viral load dynamics of SARS-CoV-2 Delta and Omicron variants following multiple vaccine doses and previous infectionNature
2022-11-06Doctor Claire Taylor on COVID and Long COVIDThreadreaderapp
2022-11-06Study finds no evidence of major SARS-CoV-2 spread among wild rodentsMedical Life Sciences
2022-11-04Size distribution of exhaled aerosol particles containing SARS-CoV-2 RNATaylor & Francis
 (As an addendum to the above: Manikin-Based Performance Evaluation of N95 Filtering-Facepiece Respirators Challenged with Nanoparticles) 
2022-10-06Risk assessment for long- and short-range airborne transmission of SARS-CoV-2, indoors and outdoorsPNAS
2022-09-29Excess risk for acute myocardial infarction mortality during the COVID-19 pandemicJMV (needs download)
2022-09-16High-Frequency, High-Throughput Quantification of SARS-CoV-2 RNA in Wastewater Settled Solids at Eight Publicly Owned Treatment Works in Northern California Shows Strong Association with COVID-19 IncidencemSystems, ASM
2022-09-11SARS-CoV-2 infection causes immunodeficiency in recovered patients by downregulating CD19 expression in B cells via enhancing B-cell metabolismNature
2022-08-18Onset and window of SARS-CoV-2 infectiousness and temporal correlation with symptom onset: a prospective, longitudinal, community cohort studyLancet
2022-08-17Neurological and psychiatric risk trajectories after SARS-CoV-2 infection: an analysis of 2-year retrospective cohort studies including 1,284,437 patientsLancet
2022-07-14Face masks for DEFCONSubstack
2022-07-05Mosaic RBD nanoparticles protect against challenge by diverse sarbecoviruses in animal modelsScience
2022-06-18Risk of long COVID associated with delta versus omicron variants of SARS-CoV-2Lancet
2022-06-07SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations post recoveryScience Magazine
2022-05-26SARS-CoV-2 Omicron BA.2.12.1, BA.4, and BA.5 subvariants evolved to extend antibody evasionBiorxiv
2022-05-27Post-COVID Conditions Among Adult COVID-19 Survivors Aged 18 to 64 and >=65 Years -- United States, March 2020 - November 2021CDC
2022-05-01New CDC study shows 1 in 5 adults may suffer from long COVID symptomsKTSP
2022-04-13Changes in Life Expectancy Between 2019 and 2020 in the US and 21 Peer CountriesJAMA Network
2022-04-13Pandemic cut US life span almost 2 years, more than any peer nationUMN
2022-04-12Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infectionCell
2022-03-10Estimating excess mortality due to the COVID-19 pandemic: a systematic analysis of COVID-19-related mortality, 2020 to 2021Lancet
2022-03-02Living in a COVID-19 Pandemic While ImmunocompromisedUtah University
2022-03-01Fatigue and cognitive impairment in Post-COVID-19 Syndrome: A systematic review and meta-analysisScience Direct
2022-02-23Intracellular Reverse Transcription of Pfizer BioNTech COVID-19 mRNA Vaccine BNT162b2 In Vitro in Human Liver Cell LineMDPI
2022-02-07Long-term cardiovascular outcomes of COVID-19Nature
2022-01-28Effectiveness of a Third Dose of mRNA Vaccines Against COVID-19 Associated Emergency Department and Urgent Care Encounters and Hospitalizations Among Adults During Periods of Delta and Omicron Variant PredominanceCDC
2022-01-13Immunological dysfunction persists for 8 months following initial mild-to-moderate SARS-CoV-2 infectionNature
2022-01-06A Randomized, Double-Blind, Multi-Center Study to Evaluate the Efficacy and Safety of Ethyl Lauroyl Arginate Hydrochloride (LAEH) Forumulation Versus a Matching Placebo Formulation Administered as a Nasal Spray to Reduce Viral Load From Nasal Area of Subjects with Coronavirus Disease 2019 (COVID-19) -- ethyl lauroyl arginate hydrochloride, aka "Covixyl"clinicaltrials.gov
2021-12-06COVID-19: the case for aerosol transmissionRoyal Society Publishing
2021-11-15Global Prevalence of Post-Acute Sequelae of COVID-19 (PASC) or Long COVID: A Meta-Analysis and Systematic ReviewMedrxiv
2021-11-12Burdens of post-acute sequelae of COVID-19 ("long covid") by severity of acute infection, demographics and health statusNature Communications
2021-08-25Durability of antibody responses elicited by a single dose of Ad26.COV2.S and substantial increase following late boostingMedrxiv
2021-08-19Effect of Vaccination on Household Transmission of SARS-CoV-2 in EnglandNEJM
2021-07-29An outbreak caused by the SARS-CoV-2 Delta variant (B.1.617.2) in a secondary care hospital in Finland, May 2021Euro Surveillance
2021-07-23How We Know That the COVID-19 Vaccines WorkMcGill
2021-06-30Predicting the Delta waveTwitter
2021-05-18Assessing the effect of beard hair lengths on face masks used as personal protective equipment during the COVID-19 pandemicNature
2021-05-01The true death toll of COVID-19: Estimating global excess mortalityWHO
2021-03-30Studies show long-haul COVID-19 afflicts 1 in 4 COVID-19 patients, regardless of severityUC Davis
2021-01-08The Dynamics of SARS-CoV-2 Infectivity with Changes in Aerosol MicroenvironmentBristol University
2020-11-10Mobility network models of COVID-19 explain inequities and inform reopeningNature
2020-09-28Immune dysfunction following COVID-19, especially in severe patientsNature
2020-08-18Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction\u2013Based SARS-CoV-2 Tests by Time Since ExposureACP Journals