Reverse engineering the Coronavirus

See corona.py

Open questions

• How is orf1ab cleaved into polypeptides? Can we predict this from the sequence?
• 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"
  • It might be at the "PRRA" -- https://www.sciencedirect.com/science/article/pii/S0166354220300528
  • Use ProP or PiTou to predict? -- https://en.wikipedia.org/wiki/Furin
• 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
• What adds the phosphate group to the N protein? Kinase?

Work to be done

• Automatic extraction of genes from different coronaviruses
• Good multisequence compare tool
• Molecular dynamics?
• Secondary Structure prediction on orf1a?

Homemade Vaccine

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

Bio vs IDA

• Each letter in genome is a "byte at address x"
• Translation = Disassembly, it's a 3 byte wide instruction set with arbitrary "reading frames"
• Protein ~ Function. polyprotein = Function with multiple pieces
• Proteins appear to have "basic blocks" = "Secondary Structure"
  • 80% accuracy in prediction: https://en.wikipedia.org/wiki/Protein_structure_prediction#Secondary_structure
• "Tertiary Structure" forms a function
  • This seems like the hard one to predict: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205819
• "Quaternary Structure" is like compiled function with inlining
  • https://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction_prediction
• Gene ~ library (bacteria are static linked, viruses are dynamically linked)
• Transcription = loading off disk

Analysis

• There is no equivalent to execution, we are reverse engineering a CAD format
• Static analysis, looking at the DNA, protein structure prediction, FLIRT signatures, etc...
• Simulation doesn't seem to work yet
• Tons of in system dynamic analysis, but the tools are crap
• Runs more like FPGA code, all at once, no serial execution (what are the FPGA re tools?)

Tests (how they 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?

Treatments

• 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/
• Novel RdRp inhibitors
  • Favipiravir (prodrug for favipiravir-RTP)
• Adenosine Analog
  • Remdesivir (prodrug for GS-441524)
  • Galidesivir

Resources

• corona
  • 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
• textbooks
  • Molecular Biology of the Cell
• classes
  • better tests - https://ocw.mit.edu/courses/biology/7-012-introduction-to-biology-fall-2004/index.htm
  • suspected better lectures - https://ocw.mit.edu/courses/biology/7-014-introductory-biology-spring-2005/index.htm