updated list of COVID-19 Research Resources: Databases, chest CT images.

please suggest or send me a message, if you have idea of any other link , i will update the list.

• please follow WHO https://www.who.int/ and your official country website , for Latest Coronavirus (Covid-19 ) updates.
• Please do not submit any personal information on any website.

List of Open source dataset (chest CT Images, X-ray Images, )

Corona Tracker

https://www.mohfw.gov.in/ (for Indians)

Aarogya Setu (Android App for Indians)

https://play.google.com/store/apps/details?id=nic.goi.aarogyasetu&hl=en

https://www.worldometers.info/coronavirus/

https://www.coronatracker.com/analytics

https://www.bing.com/covid

https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

https://github.com/CSSEGISandData/COVID-19/issues/576

Coronavirus (covid-19) Hackathon :

https://samhar-covid19hackathon.cdac.in/

https://ultrahack.org/covid-19datahack

https://www.codevscovid19.org/

https://codevscovid19.devpost.com/submissions

https://www.teensinai.com/hackathons/covid-19-hackathon/

https://hackingcovid19.fr/en/

https://joinup.ec.europa.eu/collection/digital-response-covid-19/hackathons-and-events

https://samhar-covid19hackathon.cdac.in/

https://hackathon.common.vc/

Additional Resources

Chinese Bats May Be Carrying the Next SARS Pandemic

https://www.wired.com/2013/10/bats-next-sars-pandemic/

https://www.sciencemag.org/news/2013/10/bats-may-be-carrying-next-sars-pandemic

Bat Coronaviruses in China

https://www.mdpi.com/1999-4915/11/3/210

COVID-19 Research Database (provided by the WHO)

https://www.who.int/emergencies/diseases/novel-coronavirus-2019/global-research-on-novel-coronavirus-2019-ncov

LitCOVID (provided by the NIH)

https://www.ncbi.nlm.nih.gov/research/coronavirus/

COVID-19 Resource Page (provided by Microsoft Academic) 

https://www.microsoft.com/en-us/research/project/academic/articles/microsoft-academic-resources-and-their-application-to-covid-19-research/

COVID-19 Research Export File (provided by Dimensions)

https://docs.google.com/spreadsheets/d/1-kTZJZ1GAhJ2m4GAIhw1ZdlgO46JpvX0ZQa232VWRmw/edit#gid=2034285255

Blog Post: Computer Scientists Are Building Algorithms to Tackle COVID-19

https://onezero.medium.com/amp/p/f4ec40acdba0

Article Correlation of Chest CT and RT-PCR Testing for Coronavirus D...

Emerging 2019 Novel Coronavirus (2019-nCoV) Pneumonia

Article Emerging Coronavirus 2019-nCoV Pneumonia

Cell Press Coronavirus Resource Hub

https://www.cell.com/2019-nCOV

An initiative from the scientific community to put all available resources at the service of the fight against COVID-19.

https://crowdfightcovid19.org/

COVID-19 Datasets for Machine Learning

https://docs.google.com/document/d/1Wkvbf2t2Da87NtNvMJf_PRqv9zLHyqqtRitBIGGKKNM/edit?ts=5e78bf6d#heading=h.m7aq1vqtpegc

Reverse engineering the coronavirus (SARS-CoV-2)

https://github.com/geohot/corona

I found https://github.com/geohot/corona very informative, you can also check.

Open questions

How do the researchers know (guess?) where orf1ab cleaves?

nsp3 and nsp5 do it -- https://www.pnas.org/content/pnas/103/15/5717.full.pdf

Which protein is the immune system responding to?

"spike" and "nucleocapsid" -- http://www.cmi.ustc.edu.cn/1/3/193.pdf

Are some people already immune from exposure to other coronavirus?

Find the "furin cleavage site" in the "spike glycoprotein"

https://www.sciencedirect.com/science/article/pii/S0166354220300528

How similar are the other coronaviruses?

(causes colds, not either SARS or MERS)

alpha

https://en.wikipedia.org/wiki/Human_coronavirus_229E (simpler, though targets APN)

https://en.wikipedia.org/wiki/Human_coronavirus_NL63 (targets ACE2!)

https://www.ncbi.nlm.nih.gov/nuccore/MG772808

beta

https://en.wikipedia.org/wiki/Human_coronavirus_OC43 (targets Neu5Ac)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2095096/pdf/JIDMM17330.pdf

Specifically, how similar is the N protein OC43, SARS v1, and SARS v2?

https://en.wikipedia.org/wiki/Human_coronavirus_HKU1 (targets Neu5Ac)

MERS-CoV

SARS-CoV

SARS-CoV-2

Testing

How tests work

• All based on https://en.wikipedia.org/wiki/Reverse_transcription_polymerase_chain_reaction
• USA -- https://www.fda.gov/media/134922/download
  • selected from regions of the virus nucleocapsid (N) gene
  • 28286---28308--28332---28358
  • 29163---29187--29210---29230
  • https://biosearchtech.a.bigcontent.io/v1/static/coa_KIT-NCOV-PP1-1000_Lot-No-143503
• South Korea -- http://www.kogene.co.kr/eng/about_us/news/listbody.php?h_gcode=board&h_code=7&po_no=288
  • E gene detection (same for all coronavirus)
  • specific RdRp detection

Homemade test?

Isolation of viral RNA (no matter what)

• https://www.qiagen.com/us/products/diagnostics-and-clinical-research/sample-processing/qiaamp-viral-rna-mini-kit/#orderinginformation

Primers and probes (to detect SARS-CoV-2)

• https://www.biosearchtech.com/products/pcr-kits-and-reagents/pathogen-detection/2019-ncov-cdc-probe-and-primer-kit-for-sars-cov-2
• Wouldn't need if using a nanopore sequencer (nanopore MinION)

RT-qPCR Master Mix (to PCR)

• https://www.thermofisher.com/order/catalog/product/A15300#/A15300
• Probably wouldn't need if using a nanopore sequencer

All in one?

• https://www.chaibio.com/coronavirus
• Open qPCR, understand https://www.chaibio.com/openqpcr
• FAM and HEX fluorophores?

Possible treatments and prophylactics

Disclaimer: The information in this repository is for informational purposes only. It is not medical advice.

Hydroxychloroquine + zinc

• Zinc blocks RdRp
• https://jvi.asm.org/content/91/21/e00754-17 -- how similar is Hep E RdRp?
• https://www.ncbi.nlm.nih.gov/pubmed/21079686
• Chloroquine Is a Zinc Ionophore (allows zinc into the cell)
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4182877/

RdRP inhibitors

• Favipiravir (prodrug for favipiravir-RTP)
• Adenosine Analog
  • Remdesivir (prodrug for GS-441524)
  • Galidesivir

Homemade DNA vaccine

• https://siasky.net/bACLKGmcmX4NCp47WwOOJf0lU666VLeT5HRWpWVtqZPjEA
• Based on injecting DNA (plasmid) that expresses the spike protein

Resources

Coronavirus-related publications

• Chapter 4 - Coronavirus Pathogenesis -- https://www.sciencedirect.com/science/article/pii/B9780123858856000092
• https://www.futuremedicine.com/doi/pdf/10.2217/fvl-2018-0008
• https://www.sciencedirect.com/science/article/pii/S2095177920302045
• http://korkinlab.org/wuhan

Thanks