Showing posts with label coronavirus. Show all posts
Showing posts with label coronavirus. Show all posts

Saturday, September 09, 2023

New variant of COVID-19

A new variant is not a new thing, of course, but BA.2.86, known also as Pirola, seems to be causing some concern in the UK and elsewhere.  

It seems a long time ago that I compiled page after page on this blog about COVID-19.   Those pages are still there, all but one are now "archived" and have that word in their title.   The Current resources about COVID-19 is the exception, updated in June 2023.

I wondered if a few resources on this new variant would be useful.   In case I am right, here are some.   I don't know how long this one will be useful for, but will try to keep it updated.   

A PubMed search for BA.2.86 finds a few.   Adding Pirola finds authors called Pirola, and as a consequence a lot of irrelevant things, so for now I have made a search that searches the two terms, plus a term used in the UKHSA risk assessment (V-23AUG-1)  in titles and abstracts:

PubMed search for COVID-19 BA.2.86 (Pirola) variant

This still finds some things discussing papers by Pirola and at least one about PIROLA, plasminogen activator (r-tPA) orolingual angioedema, a complication of stroke treatment.   At the moment anyway, searching BA286 finds one other thing on a different infectious agent.


UK Health Security Agency

Variants update - latest information on variants identified in the UK, the one from 8th September 2023 (at the top of the page at the moment) is about BA.2.86.

Variant surveillance and assessment technical briefing 53 (9th September 2023) - one section is links to published information.

Risk assessment for this variant, 1st September 2023


Other sources

Centers for Disease Control and Prevention risk assessment summary for COVID-19 sublineage BA.2.86, August 2023

Yale Medicine news item, 31st August 2023

Monday, June 19, 2023

Current resources about COVID-19

(Last updated 9th September 2023)

Introduction

During lockdown I maintained a set of blogposts linking to resources about COVID.    I have not updated those for some time, and have now decided that they are no longer needed.  I have added the word "Archived" to the start of each page title, and tried to make it clear that they are no longer updated.   

Of course, COVID-19 has not gone away, and has become one of the infectious diseases that is with us always.   So, I think although those older posts are no longer useful, a current list of resources might be.    So, here is a shorter list, a single blogpost, which I will endeavour to keep up to date.

Here is a link to my new post about the BA.2.86 variant (made on 9th September 2023)

Resources

UK

In the UK at the moment is the UK Covid-19 Enquiry, an enquiry into the UK's response and the impact of the pandemic.

The UK Government still maintains a Coronavirus (COVID-19) page with links to information about testing, vaccination, what to do if you have COVID, travel abroad, and reducing the spread.  There are links to the governments in Wales, Scotland and Northern Ireland.

The UK Government Coronavirus data page is still being updated, with figures for the numbers of cases, vaccinations and deaths, some of it by region or home nation.

The UK Health Security Agency page of COVID guidance, which includes guidance for health professionals and the public.  UK Health Security Agency have a comprehensive list of resources, Finding the Evidence: Coronavirus, including many of interest to health professionals (some resources may not be available to University of Leicester members, who are welcome to contact their library to check. NHS staff should contact their own library to check). 

MHRA Coronavirus pages (information about clinical trials of treatments and vaccines) (last updated in June 2022)

Infectious diseases: UK government, including policy, news, statistics, forms, research and guidance

Results and information about the REACT (Real-time Assessment of Community Transmission study, no new news items since June 2022).

Three UK groups: 

NERVTAG (New and Emerging Respiratory Viruses Threats Advisory Group; SAGE and Independent SAGE.


Outside the UK

COVID-19 END (Evidence Network to support decision making, McMaster University)

World Health Organization - Country and technical guidance ; Global Research on Coronavirus (COVID-19) (scientific literature database)

From the WHO ICTRP launch page you can download lists of COVID-19 trials.   There is also a link to the search portal.   Clinicaltrials.gov is listing at least some COVID-19 related trials including studies from the WHO. There are links to other COVID-19 related trial pages from this one.

NCBI Virus SARS-CoV-2 Data Hub (which replaces the older "resources page" at https://www.ncbi.nlm.nih.gov/sars-cov-2/ from 1 August 2023).   Contains epidemiological and genetic data, and links to information from the CDC and to references in PubMed.


Point of care resources and other clinical resources

NICE have a page with their guidance, advice, and rapid guidelines.

BMJ Best Practice - coronavirus  - material on coronavirus and some comorbidities.  Some material is still free, other material requires NHS access or a subscription.

Evidence Aid - Coronavirus - summaries of research, in English and other languages

DynaMed and UpToDate (these may need subscriptions)

Saturday, November 27, 2021

Archived - Omicron (B.1.1529 COVID variant ) (including "deltacron") (no longer being updated)

Last updated (the sensitive PubMed strategy), 0920 GMT, 15th November 2022.


PubMed to find research articles

Less sensitive strategy (includes deltacron and deltamicron)


More sensitive strategy (includes the less sensitive strategy plus deltakron, deltamikron, XE, and the lineages BA.1, BA.2, BA.3, BA.4, BA.5, BQ.1, BQ.1.1, AY.25, XBB). 
Note: this more sensitive strategy finds any work from the UK postcodes BA1, BA2, BA3, BA4, BA5, from any Dutch postcodes that include the letters XE, and any COVID work involving xenon.


PubMed COVID-19 Clinical Query 
Searching the Omicron terms from the less sensitive search above.  Select aspect (diagnosis, treatment, etc.) from the drop down box.


Preprints

COVID preprints from medRxiv and bioRxiv (sorted by date so newest first).  Note that the PubMed strategies above will also find some preprints.


UK government, SPI-M-O, SAGE, UK academic institutions, REACT

COVID research and statistics - includes scenarios, reports and modelling on Omicron.

Scientific Pandemic Influenza Group on Modelling, Operational Sub-Group (SPI-M-O) consensus statement, 8th December 2021, for SAGE 

SAGE minutes for December 2021  - various papers relating to Omicron.

UK government oral statement, 26 November 2021

Imperial College MRC Centre for Global Infectious Disease Epidemiology reports - report 50 is on hospitalisation risk for Omicron cases in England, report 49 is on growth, population distribution and immune escape of Omicron.

REACT-1 study of coronavirus transmission.   Carried out from 23 November to 14 December, published 23 December, includes some information about Omicron


Scottish Government

Coronavirus daily data for Scotland


UK Health Security Agency

UK Health Security Agency daily overview

UK Health Security Agency SARS-CoV-2 variants of concern and variants under investigation in England, Technical Briefings

Briefings, and technical data.   Briefings from 29 onwards, and some other documents, discuss Omicron.    The UK government coronavirus page has updates on the rule changes and guidance in the light of Omicron.

UK Health Security Agency news item about situation in the UK (issued 1 October 2021 but updated since)


Genomic information

Information from the CoVariants site (using information from GISAID)

GISAID - initiative to share data about all influenza viruses and about SARS-CoV-2.


WHO

South Africa

FAQ from the National Institute for Communicable Diseases, South Africa

Republic of South Africa Health Department Coronavirus portal has this presentation on what is known, and this infographic


European Centre for Disease Prevention and Control (ECDC)

ECDC Threat Assessment Brief

First update (dated 2 December) to the Threat Assessment Brief

ECDC Epidemiological Update


Centers for Disease Control and Prevention (CDC, US)

CDC Statement

CDC - Omicron variant: what you need to know

CDC Potential rapid spread of Omicron variant


Other

GAVI: The Vaccine Alliance

ReliefWeb press release (from the WHO)

The symptoms of Omicron, from the ZOE COVID project.



News sources

BBC Coronavirus

BMJ Coronavirus Hub

CIDRAP Novel Coronavirus Resource Center

The Guardian's Coronavirus Live page

Medical Xpress Diseases, Conditions and Syndromes  

Medscape UK

Nature's news pages (you may need a subscription to read)

STAT: What's known and unknown about Omicron


Other things

Your Local Epidemiologist (Substack, payment may be needed).

Imperial College London Q and A

On Twitter, try #Omicron, #Omikron and #OmikronVariante, and for older information perhaps, #B11529.     Choose carefully, of course.  The two spellings with the -k- do find some tweets in English and some in other European languages.

Saturday, December 05, 2020

Archived - COVID-19: Vaccines (no longer being updated)

Last updated and links checked 27th November 2021.

UK Health Security Agency: Coronavirus has a section on vaccines

The Green Book, chapter 14a, from Public Health England contains vaccination information for health professionals.

COVID-19 testing and vaccines. Useful looking ebook from Biotechniques (free registration may be required)


Department of Health and Social Care - scroll for various items on vaccinations


European Medicines Agency - COVID-19 vaccines

Medicines and Healthcare products Regulatory Agency - Coronavirus - Vaccines

NHS - Coronavirus vaccines

UK Health Security Agency - COVID19 vaccination programme.

UK Health Security Agency's Public Health Matters blogpost about the role of the MHRA and Joint Committee for Vaccination and Immunisations. 


Find the latest research with this 
PubMed search (sorted by best match) 

For discussion about global access to the vaccine, look at information from Global Justice Now and Medecins sans Frontieres. 

Friday, December 04, 2020

Archived - COVID-19: Long COVID (no longer being updated)

Links checked 27th November 2021


My (6 line) Ovid Medline search strategy for Long Covid (may need updating)

COVID-19 NICE rapid guideline: managing the long-term effects of COVID-19, developed by NICE, SIGN and the RCGP.  

NICE's search strategies are available (PDF)  including a more detailed Ovid Medline strategy, and strategies for other databases.


Resources 




Articles (all are open access) (I will add some more recent items)

Viewpoint (review article), Long-term health consequences of COVID-19, Journal of the American Medical Association (October 2020)

Feature, COVID-19: what do we know about long COVID: British Medical Journal (July 2020)

Rapid review, Short- and potential long-term adverse health outcomes of COVID-19, Emerging Microbes and Infections (October 2020)

Saturday, June 27, 2020

Archived - COVID-19 resources (no longer being updated)

This post is no longer being updated and neither are any of the pages linked from it.

Links were last checked on 1st February 2022.    

**For information relating to Leicester, please see this information from Leicester City Council.**

Some collections of information are listed at the end of this post.   I have also collected information sources about COVID-19 in these separate posts:


Other collections of information


Knowledge for Healthcare (HEE): COVID-19/Coronavirus - (Health Education England).  For Knowledge and Library Service staff in the NHS.   Use the link in the menu bar to access resources, including those for patients.

Compass: COVID-19 resources for social and behavior change - material relating to some African nations or Pakistan.  

Evidence Aid Coronavirus Resources Information Hub - systematic reviews, guidelines, journal and publisher resources, and information in languages other than English.

Finding the Evidence: Coronavirus (UK Health Security Agency).    Resources listed that require an OpenAthens login may be restricted to UKHSA staff, but University of Leicester undergraduate health students can ask their library (librarians@le.ac.uk) and NHS staff their library for advice.

WHO EPI-WiN   Information from the WHO Information Network for Epidemics.
To search for information relevant to the NHS and patients, search NICE Evidence Search

Archived - COVID-19: information for health and care professionals (no longer being updated)

Links checked 2nd July 2022.

On this page, evidence summaries, guidelines and government and related information for practitioners.

See also the epidemiology and genetics and current awareness pages.  There is a page of journal and database publishers making content available free (although I suspect this is out of date).


REACT
Findings from the Real-time Assessment of Community Transmission study

A collection of articles (you may need a subscription to read the full articles, but your Library may be set up with QxMD to allow access - ask your Librarian).

Resources from Royal Colleges (list maintained by HEE)

Clinical Trials

The WHO ICTRP indexes trials from a number of sources, including the US and EU registries.  From the launch page you can download lists of COVID-19 trials.   There is also a link to the search portal.   Clinicaltrials.gov is listing at least some COVID-19 related trials including studies from the WHO. There is a separate Clinicaltrials.gov page (linked from this one) about trials related to SARS-CoV-2.

NCBI SARS-CoV resources includes clinical trials


UK government information



MHRA Coronavirus pages (information about clinical trials of treatments and vaccines)

Infectious diseases: UK government, including policy, news, statistics, forms, research and guidance

Coronavirus data  - numbers of cases and deaths



Other UK information

King's Fund - leadership support and analysis on COVID-19


Nursing and Midwifery Council : Coronavirus information and advice

NICE - all NICE guidelines, including rapid guidelines, and advice on COVID-19.

UK Health Security Agency have a comprehensive list of resources, Finding the Evidence: Coronavirus, including many of interest to health professionals (some resources may not be available to University of Leicester members, who are welcome to contact their library to check. NHS staff should contact their own library to check). 




If you are in practice or placement in the NHS, or have placement students in your care, please look for advice from your Trust.

Elearning

BMJ Learning -  learning related to COVID-19 and wellbeing. Some is free to access, some not.

COVID-19 Critical Care (University of Edinburgh / Royal College of Physicians of Edinburgh - limited access unless you pay)

eLfH Coronavirus (for use in UK.   Available outside UK as eIntegrity Coronavirus e-Learning Programme 

eLearning resources (HEE)

Evidence based summaries

BMJ Best Practice - coronavirus  - material on coronavirus and some comorbidities.  Some material is free, other material requires NHS access or a subscription.

DynaMed - coronavirus (a subscription may be needed)

Evidence Aid - Coronavirus - summaries of research, in English and other languages

UpToDate (a subscription may be needed)

Other information for health and care professionals

Contact your library if you need something related to a particular specialty not listed here.

Lots of publishers are (or were) making journal content available for free and these are listed on a separate page.   


COVID-19 END (Evidence Network to support decision making, McMaster University)

Department of Health and Social Care (UK)  - advice for health professionals.  

Elsevier COVID-19 Information Hub - materials from Elsevier sources including Clinical Key

Evidence Aid Coronavirus Information Portal - systematic reviews, guidelines, journal and publisher resources, and information in languages other than English.

Genetic Engineering and Biotechnology News includes information on drug treatments in development.

Information from the The Faculty of Intensive Care Medicine, Intensive Care Society, Association of Anaesthetists and Royal College of Anaesthetists 


Office for Health Improvement and Disparities: Wider Impact of COVID-19 on Health (WICH) Monitoring Toolublic Health England Wider impacts of COVID-19 on health monitoring tool (WICH)

Royal College of Obstetricians and Gynaecologists, coronavirus (COVID-19), pregnancy and women's health

Royal College of Physicians (of London) Ethical dimensions of COVID-19 for frontline staff.

Relief Central - collection from Unbound Medicine, containing guidelines and information for the public. Information from the WHO and CDC and other sources.

Social Care Institute for Excellence, Coronavirus (COVID-19) advice for social care. Advice for councils and other organisations providing social or residential care, or supported living.

World Health Organization - Country and technical guidance ; Global Research on Coronavirus (COVID-19) (scientific literature database)


I have posts covering other aspects of COVID-19. Links are on the page here.

Archived - COVID-19: journal, books and databases with some freely available content (no longer being updated)

This was a list of journals, books and databases that were made available for free when the COVID-19 pandemic started.

I checked the links in December 2021 and kept those which still seemed to allow free access.  

At the start of the pandemic, some publishers pledged to make COVID-19 related content freely available, including for some in PubMed Central - they are asterisked on this list from the Wellcome.

GIDIF-RBM (an Italian association for health librarians) have a list (in Italian, dated March 2020) of freely available resources

Here are publishers that were (and possibly still are) making coronavirus related content available for free, or publishing it open access.

American Academy of Pediatrics - Critical updates and resources for paediatricians.

American College of Physicians - A collection of Annals of Internal Medicine articles related to coronavirus is freely available.

American Medical Association - JAMA Network COVID-19 information collection

American Psychiatric Association Publishing - Resources for Psychiatrists and on Coping with the Outbreak

American Society for Microbiology - research articles about COVID-19, and a toolkit to help spread information.

American Society of Civil Engineers - Resources for working from home.

Annual Reviews Coronavirus article collection


BioOne - articles in journals hosted in BioOne.

Coronavirus Hub - research, guidance and updates.  Includes articles from other journals published by BMJ.

CABI Global Health - 
Free access to coronavirus resources in this public and global health resource.   Click Login, Redeem a voucher, then register (or login) to be able to use the code
CV4Y85D5JG9.  (Code still valid December 2021). Searches also include animal coronavirus references from CAB Abstracts.

Cambridge University Press: Coronavirus Free Access Collection.  Still a free access collection December 2021.

Clarivate - A range of resources, including Cortellis Drug Discovery Intelligence.  Request access on this page.  There is also a Disease Briefing (Disease Insight).   Note the dashboard seems not to cover periods of time after January 2021.


Elsevier - Novel coronavirus information center - guidance and clinical information, some specially written.  Access to research articles in Elsevier journals.  Some information from China, including some in Chinese, from sources including the Chinese Center for Disease Control and Prevention.  Also includes official guidance from a number of countries.  

Emerald: Free content related to coronavirus and the management of epidemics.

Future Science Group (Infectious Diseases Hub) - COVID-19 Hub

Health Service Journal - free access to HSJ coronavirus content (registration required)

JSTOR Public Health journals.  Access possible to institutions that have some access already to JSTOR, until June 2022.

Karger: Topic articles Coronavirus (COVID-19).  

The Lancet - Coronavirus Hub


Mary Ann Liebert - Free articles from the journal Health Security


MEDBOX - a collection of resources for humanitarian and aid workers, now includes coronavirus resources.


Microbiology Society - articles. 


MIT Press - Articles on understanding pandemics and epidemiology.  Free access may have ended in August 2020.

National Academy of Sciences COVID-19 Responses and resources

NEJM - Coronavirus (COVID-19) - Collection of articles and other resources.  

Open Book Publishers - blog post giving details of resources being made free by a number of publishers (scroll down).

Ovid: tools and resources for clinicians.  Request access to GIDEON, access to records in Ovid Medline and Journals@Ovid, and to articles in American Heart Association and other journals hosted by Ovid.

Oxford University Press: Free access to OUP resources on coronavirus and related topics.

Proceedings of the National Academy of Sciences - Sharing research data and findings relevant to the novel coronavirus (COVID-19) outbreak.

ProQuest Coronavirus Research Database.  Searches open access content and preprints. Login needed - search for your institution (worked for mine, can't guarantee it will work for yours!)

Royal Society - research data and findings relevant to the novel coronavirus outbreak.

Royal Society of Chemistry - Coronavirus articles - free to access collection

SAGE journals - medical, social and behavioural articles

Society of Industrial and Applied Mathematics - free access to the SIAM Epidemiology Collection.

Springer Nature - Novel coronavirus - research articles, and a live blog


Thieme: Specialist Information on the Coronavirus: 

Wiley - coronavirus research articles.



I have posts covering other aspects of COVID-19.   Links are on the page here.

Archived - COVID-19: Current awareness and literature searching (no longer being updated)

Last updated 3rd February 2022.


To keep up to date with new scientific literature about COVID-19, use one of the searches or curated lists below.

Archived - COVID-19: news (no longer being updated)

For news for health professionals, look at the BMJ or New England Journal of Medicine.   You may need a subscription or access through a library to read the items.   University of Leicester students and staff can login here first.

Links checked and updated 27th November 2021

NICE

NICE guidelines on COVID-19



WHO 

WHO situation reports

WHO news releases (on all topics - use the filters to find coronavirus related ones) .

WHO health topics: coronavirus. 

World Health Organization emergencies: nCoV



UK

Coronavirus data (DHSC), updated daily.



News sites

BBC: coronavirus outbreak

The Guardian: coronavirus.  The Guardian have a weekly email newsletter.

The New Humanitarian: Infectious diseases  (The New Humanitarian is an independent source of news on humanitarian crises and gives a perspective from low and middle income countries)



Specialist news sources and items

BMJ news.   BMJ's content about the virus is all available for free.

CIDRAP - Center for Infectious Diseases Research and Policy, University of Missouri

Nature - infection.   Scroll down to read news items.   Some are free to read.   For those that are not, University of Leicester members can use this link instead: Nature - infection.


STATNews (infectious diseases)



I have posts covering other aspects of COVID-19.   Links are on the page here.

Archived - COVID-19: epidemiology, genetics and data (no longer being updated)

Links last checked 3rd February 2022.  Item labelled NEW was added 27th June 2022


How many cases?
See the WHO dashboard or the Johns Hopkins CSSE map.   JHU CSSE shows number of cases, recoveries and deaths.   

Official UK government COVID data - cases, testing, deaths, healthcare.  Scroll down to search for data for a specific geographical area.  Go to the cases, deaths, healthcare or testing pages to find data for a nation, region or local authority area.



Real-Time Assessment of Community Transmission (REACT) 

For up to date information relevant to the NHS, look at NHS Evidence Search (this service closes on 31 March 2022).

Research data

COVID-19 data portal
Sequence data for the virus and host, biochemical data, expression and protein data.  And a search facility for EuropePMC.   Maintained by EMBL-EBI.

Epidemiological information

China Center for Disease Control and Prevention: Tracking the Epidemic (in English).  Numbers of cases and deaths.

ProMedMail for reports of cases.

HealthMap.  Displays ProMedMail data in graphical form. Use Your Location at the top of the screen to display data for a specific country or city.   Current alerts will be shown to the left.


Centers for Disease Control and Prevention (USA)


European Centre for Disease Prevention and Control

UK Health Security Agency / DHSC


Genetic and related information


SARS-CoV-2 Variants Overview.   From the National Library of Medicine, aggregates data from GenBank and the Sequence Read Archive.

COVID-19 Genomics UK Consortium (COG-UK) Group of NHS, academic and other institutions undertaking virus sequencing.   


Rapid access to SARS-CoV-2 data (NCBI Insight)

NCBI SARS-CoV resources
Literature, sequence and protein sequence data, clinical trials

There are multiple sequences in the NCBI Virus SARS-CoV-2 Data Hub.

There are multiple sequences in the GISAID database (registration required)



I have posts covering other aspects of COVID-19.   Links are on the page here.

Archived - COVID-19: information for the public (no longer being updated)

Links were checked on 2nd July 2022.

UK COVID-19 Enquiry



Archived - COVID-19: global aspects (no longer being updated)

Coronavirus is having an impact all over the world and in some countries is raising issues that are not so much of an issue in the UK.   So on this post I shall collect resources that look at the impact of the pandemic on lower and middle income countries and on the world as a whole.  To start with here are two:

Global Justice podcasts - some are about coronavirus.

The New Humanitarian's Coronavirus coverage includes discussion of the impact on aid and migration, and a newsletter.  The New Humanitarian also has a piece about other infectious diseases, which have not gone away.

GAVI: The Vaccine Alliance.   Not just COVID vaccines, of course.  Linked to GAVI is COVAX,  the vaccines part of the WHO's Access to COVID-19 Tools Accelerator.

World Health Organization.  A global view of the pandemic, 

Wednesday, March 18, 2020

Philosophical considerations about COVID-19

And the third.

For some algorithmic reason, my phone alerted me to one of these pieces on the Daily Nous, "information and news for and about the philosophy profession".

They are about some of the philosophical issues raised by the pandemic, including reflections on reactions to it, discussion of how we count things, and the need for transparency in data.    




Further Philosophical Considerations about Covid-19:Why We Need Transparency

While you in the Daily Nous, you might look for the piece discussing what academic journals need to do in this time of pandemic, not in terms of allowing free access, but in terms of facilitating the process of publication.

Plague paintings

My second trip beyond the medical and health science of epidemics.

Here is an interesting Guardian article by Jonathan Jones, about paintings that depict plague.   Along with portrayals of victims, saints, and the Apocalypse, there is a lovely portrait by Rembrandt of Hendrickje Stoffels.  She was his partner in business and also in life.

She died of the plague when a ship from Algiers brought the plague to Amsterdam....  even then there were ways for disease to make long journeys.


I think the portrait is this one in the National Gallery in London (closed from tomorrow because of the current coronavirus outbreak...).


Albert Camus' The plague

First of three epidemic/pandemic related posts, but going beyond the medical and health science.

As it happens, I was reading this book when the current coronavirus outbreak started.  

There is an interesting piece about the book, written at the end of last week, on Literary Hub.

The novel describes a fictional outbreak of bubonic plague in the town of Oran in Algeria, people's reactions to it, and each other, and the decisions that had to be taken.

I am not (and neither is the author of the piece) comparing COVID-19 to bubonic plague but reading the story now does make some of those issues take on a certain relevance.

Wednesday, March 11, 2020

What's new in midwifery - 11th March 2020

University and College Union industrial action is disrupting my blogposts at the moment, but I thought this one could not wait...


RCOG guidance on managing coronavirus in pregnancy


News item

RCOG guidance on COVID-19 and pregnancy

RCOG information for pregnant women and their families