COVID-19


last update: 5 January 2021

Introduction


The
World Health Organisation has a Coronavirus (COVID-19) Pandemic website, and a dashboard with the latest confirmed cases, new cases, and deaths around the world. They also issue daily 'situation reports'.

Useful sources of information include:-
The US
Centres for Disease Control and Prevention, which has a 'Situation Summary'.
The
European Centre for Disease Prevention and Control has a webpage dedicated to COVID-19.
The US Food & Drug Administration has a
press announcements page, with regular COVID-19 updates
The UK has a "
what you need to know" webpage, and the French government has a Coronavirus information webpage. Every other European country also has a dedicated COVID-19 website, e.g. Luxembourg has a website COVID-19 in English.
Johns Hopkins provides
an up-to-date guide to the Coronavirus COVID-19.
The Pharmaceutical Journal provides "
Everything you should know about the coronavirus outbreak" and they have a Coronavirus (COVID-19) webpage with information updated daily.
The Lancet hosts a
COVIS-19 Resource Centre, and Nature has the COVID-19 Watch.
Oxford University hosts the
Centre for Evidence-Based Medicine, which has a specific Oxford COVID-19 Evidence Service.

In addition Google publishes the
COVID-19 Community Mobility Reports.
World Mapper provides a '
Chronology of a Pandemic', which includes a map animation showing how the virus spread across the world.

Finally several publications make reference to the long-term leadership that the '
One Health Commission' could provided. They are trying to address the fact that nearly 75% of all emerging human infectious diseases in the past three decades originated in animals.

Useful articles and publications


2021.01.11 Houriiyah Tegally,
et.al., "Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa"
2020.12.31 Fernando P. Polack,
et.al., "Safety and Efficacy of the BNT162b2 mRNA Covid-10 Vaccine"
2020.12.18 Andrew Rambaut,
et.al., "Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations"
2020.12.17 Edward E. Walsh,
et.al., "Safety and Immunogenicity of Two RNA-Based Covid-19 Vaccine Candidates"
2020.11.18 Sanjay Mishra, "
How mRNS vaccines from Pfizer and Moderna work, why they're a breakthrough and why they need to be kept so cold"
2020.11.09 David A. Kennedy and Andrew F. Read, "
Monitor for COVID-19 vaccine resistance evolution during clinical trials"
2020.10.30 Jeffrey Shaman and Marta Galanti, "
Will SARS-CoV-2 become endemic?"
2020.10.30 Michael Worobey,
et.al., "The emergence of SARS-CoV-2 in Europe and North America"
2020.10.28 Ania Wajnberg,
et.al., "Robust neutralising antibodies to SARS-CoV-2 infection persist for months"
2020.10.27 James Gallagher, "
Covid: Antibodies 'fall rapidly after infection'"
2020.10.23 Jordan Cates, ,
et.al., "Risk for In-Hospital Complications Associated with COVID-19 and Influenza"
2020.10.23 Eric J. Topol, "
COVID-19 can affect the heart"
2020.10.23 Elizabeth C. Lee,
et.al., "The engines of SARS-CoV-2 spread"
2020.10.23 David B. Beck and Ivona Aksentijevich, "
Susceptibility to severe COVID-19"
2020.10.23 Paul Bastard,
et.al., "Autoantibodies against type I IFNs in patients with life-threatening COVID-19"
2020.10.22 James Gallagher, "
Covid: Why is coronavirus such a threat?"
2020.10.21 Marc Lipsitch and Natalie E. Dean, "
Understanding COVID-19 vaccine efficacy"
2020.10.20 Sandhya Bangaru,
et.al., "Structural analysis of full-length SARS-CoV-2 spike protein form an advanced vaccine candidate"
2020.10.20 Natasha Hinde, "
Covid-19 has 7 Key Strains. Here's What You Need to Know"
2020.10.12 Steven H. Woolf,
et.al., "Excess Deaths From COVID-19 and Other Causes, March-July 2020"
2020.10.09 Jeremy Rossman, "
COVID-19: Is the virus imitating?"
2020.10.09 Alexandra I. Wells and Carolyn B. Coyne, "
Inhibiting Ebola virus and SARS-CoV-2 entry"
2020.10.01 Takuya Sekine,
et.al., "Robust T cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19"
2020.09.30 Ugur Sahin,
et.al., "COVID-19 vaccine BNT162b1 elicits human antibody and TH1T cell responses"
2020.09.30 Debanjali Bose, "
How 11 of the world's most momentous pandemics changed the course of human history"
2020.09.21 Chadi M. Saad-Roy,
et.al., "Immune life history, vaccination, and the dynamics of SARS-CoV-2 over the next 5 years"
2020.09.03 David M. Morens and Antony S. Fauci, "
Emerging Pandemic Diseases: How We Got to COVID-19"
2020.09.02 Emma P. Fischer,
et.al., "Low-cost measurement of face mask efficacy for filtering expelled droplets during speech"
2020.09.01 Thomas Smith, "
A Supercomputer Analysed Covid-19, and an Interesting New Theory has Emerged"
2020.08.19 Sebastian Duchene,
et.al., "Temporal signal and the phylodynamic threshold of SARS-CoV-2"
2020.08.11 Ugur Sahin,
et.al., "Individualised vaccines for cancer" (US Patent).
2020.08.05 Megan Molteni, "
Front-Runners Emerge in the Race for a Covid-19 Vaccine"
2020.08.11 Anna R. Yousaf,
et.al., "A prospective cohort study in non-hospitalised household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time"
2020.07.31 Nicholas J. Matheson and Paul J. Lehner, "
How does SARS-CoV-2 cause COVID-19?
2020.07.24 Angus Liu, "
Columbia team pinpoints potent antibody cocktail for COVID-19"
2020.07.21 Matt Reynolds, "
How does the trial Oxford coronavirus vaccine work?"
2020.07.20 Zaria Gorvett, "
The people with hidden immunity against Covid-19"
2020.07.17 Nicola Davis, "
Coronavirus symptoms fall into six different groupings, study finds"
2020.07.14 John T. Brooks,
et.al., "Universal Masking to Prevent SARS-CoV-2 Transmission - The Time is Now"
2020.07.14 Andrea M. Lemer,
et.al., "The COVID-19 Serology Studies Workshop: Recommendations and Challenges"
2020.07.13 Polly Hayes, "
Here's how scientists know the coronavirus came from bats and wasn't made is a lab"
2020.07.07 Gregory Barber, "
A Mathematicians Guide to How Contagion Spreads"
2020.07.01 Muhammad Adnan Shereen,
et.al., "COVID-19 infection: origin, transmission, and characteristics of human coronaviruses"
2020.06.26 Victoria Turk, "
These four coronavirus vaccines are the closest to becoming reality"
2020.06-26 Kimberly A. Prather,
et.al., "Reducing transmission of SARS-CoV-2"
2020.06.25 Golzar Hossain,
et.al., "SARS-CoV-2 host diversity: An update of natural infections and experimental evidence"
2020.06.25 Jim Morrison, "
A Virus Study You're Never Heard of Helped Us Understand COVID-19"
2020.06.15 Christopher Giles,
et.al., "Coronavirus: Fact-checking claims it might have started in August 2019"
2020.06.12 Edward A. Belongia and Michael T. Osterholm, "
COVID-19 and flu, a perfect storm"
2020.06.10 James Gallagher, "
Coronavirus came to UK on at least 1,300 separate occasions"
2020.06.08 Kaitlyn Folmer and Josh Margolin, "
Satellite data suggests coronavirus may have hit China earlier"
2020.06.04 Lois Parshley, "
How long does the coronavirus last inside the body?"
2020.06.03 Giovanni Salvatori,
et.al., "SARS-CoV-2 Spike Protein: an optical immunological target for vaccines"
2020.06.02 Kelly Servick and Martin Enserink, "
A mysterious company's coronavirus papers tin top medical journals may be unraveling" (this is related to tests on the antimalarial drug hydroxychloroquine)
2020.06.01 Megan Molteni, "
Meet ACE2, the Enzyme at the Centre of the Covid-19 Mystery"
2020.05.28 Jeremy Rossman, "
Herd immunity in Europe - are we close?"
2020.05.28 Adam Rogers, "
To Beat Covid-19, You Have to Know How A Virus Moves"
2020.05.28 Sotiris Georganas, "
Mobile data shows which European countries took lockdown seriously"
2020.05.21 Nicole Lurie,
et.al., "Developing Covid-19 Vaccines at Pandemic Speed"
2020.05.20 Ahmed S. Abdel-Moneim and Elsayed M. Abdelwhab, "
Evidence for SARS-CoV-2 Infection of Animal Hosts"
2020.05.15 Inayat Singh, "
The coronavirus is mutating - and that can help us track it"
2020.05.07 Kate Kelland, "
A study reveals that coronavirus had spread around the world by late 2019"
2020.05.05 "
Statement on essential principles and practices for COVID-19 contact tracing applications"
2020.04.29 Tara C. Smith, "
What other coronaviruses tell us about SARS-CoV-2"
2020.04.16 Ana Sandoiu, "
COVID-19: how long is this likely to last?"
2020.04.16 Wildlife Watch, "
Wet markets likely launched the coronavirus, here's what you need to know"
2020.04.16 Rachel Donadio, "
I can't stop thinking about patient one"
2020.04.14 Fatima Amanat and Florian Krammer, "
SARS-CoV-2 Vaccines: Status Report"
2020.03.30 Adam Rogers and Megan Molteni, "
The mathematics of predicting the course of the coronavirus"
2020.03.21 Roy M. Anderson,
et.al., "How will country-based mitigation measures influence the course of the COVID-19 epidemic?"
2020.03.20 Own Jarus, "
20 of the worst epidemics and pandemics in history"
2020.03.17 Kristian G. Andersen,
et.al., "The proximal origin of SARS-CoV-2"
2020.03.15 Jun Kheng, "
SARS-CoV-2: an emerging coronavirus that causes a global threat"
2020.03.14 Nicholas LePan, "
Visualising the history of pandemics"
2020.03.09 Shengjie Lai,
et.al., "Assessing spread risk of Wuhan novel coronavirus within and beyond China, January-April 2020: a travel network-based modelling study"
2020.02.25 Tara C. Smith, "
The animal origins of coronavirus and flu"
2020.02.16 Botao Xiao, "
The possible origins of 2019-nCoV coronavirus"
2020.02.03 Peng Zhou,
et.al., "A pneumonia outbreak associated with a new coronavirus of probable bat origin"
2020.01.21 Nsikan Akpan, "
New coronavirus can spread between humans - but it started in a wildlife market"
2020.01.03 "
China pneumonia outbreak: Mystery virus probed in Wuhan"
2018.12.10 Jie Cui,
et.al., "Origin and evolution of pathogenic coronaviruses"
2018.08.10 "
Past Pandemics"
2016.11.16 "
Coronaviridae" in Fenner's Veterinary Virology (fifth edition)
2016.10.12 Diego Forni,
et.al., "Molecular evolution of human coronavirus genomes"
2015.04.01 Andrew J. Broadbent,
et.al., "Respiratory virus vaccines"
2012.06.20 Sandrine Belouzard,
et.al., "Mechanisms of Coronavirus Cell Entry Mediated by the Viral Spike Protein"
2011.06.15 Yonggun He,
et.al., "Emerging Vaccine Informatics"

A place for an
alternative perspective
2020.12.01 Annalisa Merelli, "
How drug companies will profit from making Covid-19 vaccines"
2020.06.03 Samuel Cohn and Mona O'Brien "
Contact tracing: how physicians used it 500 years ago to control bubonic plague"
2020.05.27 Benjamin Strick,
et.al., "Coronavirus: Inside the pro-China network targeting the US, HK and an exile tycoon"
2020.04.26 Jean-Dominique Michel, "
Anatomie d'un désastre" (video), plus a blog
2020.04.24 Beth Mole, "
Experts demolish studies suggesting COVID-19 is no worse than flu"
2020.04.02 Amanda Glassman,
et.al., "Does one size fit all? Realistic alternatives for COVID-19 response in low-income countries"
2020.03.28 Charles F. Manski, "
COVID-19 policy must take all impacts into account"
2020.03.27 Richard Baldwin, "
Coronavirus: An economist's view of the epidemiological curve"
2020.03.17 John P.A. Ioannidis, "
A fiasco in the making: As the coronavirus pandemic takes hold, we are making decisions without reliable data"
2020.03.16 Philip Ball, "
Coronavirus: Why scientists are divided over the effectiveness of the UK's strategy"
2020.03.10 "
COVID-19: How does coronavirus compare to other outbreaks?"
2020.02.21 Catherine Offord, "
How COVID-19 is spread"



Archive - Sections that could be useful, but might now be out of date



One of the most impressive national efforts concerning prevention, detection, and documentation of COVID-19 is in Iceland. They have a
multi-lingual website and have tested more citizens per capita than any other country in the world. Possibly the most important result is "about half of all those who tested positive are non-symptomatic" (i.e. asymptomatic). That means that they do not have symptoms, would usually not be in self-quarantine, but could still be spreading the virus. Previous to this data there were no reliable studies on the percentage of asymptotics, i.e. figures ranged for 5% to 80%.

The Pfizer/BioNTech vaccine


On
9 November 2020 Pfizer and BioNTech announced that they had a candidate vaccine with a more than 90% effectiveness. The core technology comes from a German company called BioNTech working on patient-specify approaches to immunotherapy. e.g. using messenger RNA (mRNA) for personalised cancer treatment and more generally as vaccines. The Wikipedia articles and the BioNTech website offer a collection of useful background reading, however you might want to also checkout the following:-
2020.09.30 Ugur Sahin,
et.al., "COVID-19 vaccine BNT162b1 elicits human antibody and TH1T cell responses"
2020.08.11 Ugur Sahin,
et.al., "Individualised vaccines for cancer" (US Patent).

There are a number of questions raised by this announcement, for example:-
What is the situation concerning vaccine development? On the World Heath Organisation website there is a "What we know about COVID-19 vaccine development" dated 2020.10.06. A more technical overview "SARS-CoV-2 immunity: review and applications to phase 3 vaccine candidates" was published on 2020.11.14.
What do these vaccines do? A valuable overview is "Will COVID-19 vaccines save lives? Current trials aren't designed to tell us", published 2020.10.21.
How would a vaccination program work? Probably the best overview is that of the US CDC who have a "COVID-19 Vaccination Program Interim Playbook for Jurisdiction Operations", dated 2020.10.29. The European Commission has a much lighter overview "Preparedness for COVID-19 vaccination strategies and vaccine deployment", dated 2020.10.15.
How has industry approached the need for vaccines? The US FDA provides a decent starting point for defining what is expected from industry "Development and Licensure of Vaccines to Prevent COVID-19: Guidance for Industry", published June 2020.
What exactly are the Pfizer/BioNTech trials? Pfizer has published "A Phase 1/2/3, Placebo-Controlled, Randomised, Observer-Blind, Dose-Finding Study to Evaluate the Safety, Tolerability, Immunogenicity, and Efficacy of SARS-CoV-2 RNA Vaccine Candidates against COVID-19 in Healthy Individuals". The clinical trial protocol was first published on 2020.04.30 and was last updated on 2020.11.13. The start date of the trials was 2020.04.29 with a primary completion date of 2021.06.13, and with the final completion planned for 2022.12.11.
What about misinformation? The World Heath Organisation maintains a 'Mythbusters' webpage, covering topics from bleach, garlic, masks to supplements.

COVID-19 Travel Options


The most recent thing I checked out were COVID-19-related travel options. Clearly the best option is to stay at home. If you travel, focus on remote and outdoor locations, and avoid public transport and crowded areas. If you must travel, or want to travel for a holiday, remember:-
  • Always wear a mask on any form of public transport and in transport hubs

  • The risks increase rapidly with the size of your 'holiday' population (e.g. in a large resort hotel, etc.)

  • The more varied your 'holiday' population (e.g. people coming from many places, etc.) the higher the risk

  • Indoor gatherings involve a higher risk than outdoor gatherings

  • If you stay in a hotel look for ways to reduce contact with others, e.g. take meals in your room, etc.

  • Interestingly, there is no evidence that handling food or eating is associated with directly spreading Covid-19, but avoid touching food, packaging, and utensils, and prefer places that serve food and avoid buffets, salad bars, and drink stations

  • Air travel involves waiting in line with people and touching a lot of different surfaces, but viruses and germs don't spread easily inside aircraft because of the way air circulates and is filtered

  • Prefer flights with blocked middle seats and where passengers must always wear masks, however Covid-19 transmission on planes is considered low

  • Advice is don't remove masks and don't eat and drink on planes, carry lots of disinfecting wipes, and consider wearing a face screen when boarding and deplaning

  • When driving, stops for fuel, food, and bathroom breaks increases the risk of contamination (when outside the car always wear a mask and gloves and dump them before re-entering the car)

  • Travelling by car is the safest option, in part because you don't travel with other people (i.e. don't share breathing space) and in part because you control better the scope for contamination

  • Always use hotels that have high levels of Covid-19 safety procedures, but evidence so far is that hotels and motels don't present a high risk

  • The reality is that Covid-19 risks associated with any form of travelling are considered lower than the risk of a road accident

  • After travelling, take extra precautions for 14 days, and get tested.


There is a
'reopen' website that tries to collect the latest news about travelling within the EU.

I found it useful to check the
'travel corridors' on the UK government website, which list the places that that you can return from without having to self-isolate back at home (i.e. places that have a lower risk than your home location).

Recent Emerging Infectious Diseases

Unfortunately it looks as if you can't really travel anymore without first checking for emerging or re-emerging viruses, etc. Above we can see the different types of infectious diseases, defined as newly emerging (e.g. HIV/AIDS, SARS, MERS, COVID-19), re-emerging (historical known but re-appear in new locations or new resistant forms) and 'deliberately' emerging (e.g. bioterrorism). Check out this ref.