Good section to skim

for - follow up - 2001 human genome Nature paper - proteins synthesized by higher level processes, not just genes - 2001 Nature paper on human genome project

to - 2001 human genome project Nature paper - https://hyp.is/KMjUJBYFEe-U9JdKN9-cVw/www.nature.com/articles/35057062

for - adjacency - progress trap - Crispr - gene therapy - Denis Noble - human genome project

adjacency - between - human genome project - gene therapy - Crispr - progress trap - adjacency relationship - The idea that we can find specific causal relationships between genes and disease and use gene therapy to cure disease, - an envisioned goal of the human genome project - can be very dangerous because - usually one gene collaborates with many other genes to bring about an effect - If we don't know all the relationships, we can bring about a progress trap

for - comparison - genome coding to computer program

for - metaphor - refuting genome as - book of life

for - size comparison - genome to cell

for - book - Biology Beyond the Genome - author - scientist - biologist - Denis Noble - book - Understanding Living Systems

• for: progress trap, cumulative cultural evolution, gene-culture co-evolution, speed of cultural evolution, human genome project
• paraphrase
  • the human genome project took 10 years and cost 3 billion dollars
  • with NGS technology, 10 years later, the same job takes 1 day and costs $15,000 dollars

Varmus, H. (2021, August 31). Covid has revealed the need for genomic sequencing around the world. Financial Times. https://www.ft.com/content/342fd3c3-5a22-49a0-9cef-135f2ccd8700

ReconfigBehSci. (2021, December 12). RT @ryan_landay: > A new diverse genome has appeared within the B.1.1.529 lineage that has all of the shared mutations of B.1.1.529, some o… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1470066521615605766

Purpose of WGS in population epidemiology

1. Surveillance
2. Outbreak Investigation
3. Source attribution
4. Microbial population

Omicron BA2 infects more in vaccinated

Shelton, J. F., Shastri, A. J., Fletez-Brant, K., Stella Aslibekyan, & Auton, A. (2022). The UGT2A1/UGT2A2 locus is associated with COVID-19-related loss of smell or taste. Nature Genetics, 54(2), 121–124. https://doi.org/10.1038/s41588-021-00986-w

Mallapaty, Smriti. ‘Where Did Omicron Come from? Three Key Theories’. Nature 602, no. 7895 (28 January 2022): 26–28. https://doi.org/10.1038/d41586-022-00215-2.

Viral Genome sequencing facility in India

• 38 labs

Maxmen, A. (2021). Omicron blindspots: Why it’s hard to track coronavirus variants. Nature. https://doi.org/10.1038/d41586-021-03698-7

Sridhar, D. (2021, November 28). How bad will the Omicron Covid variant be in Britain? Three things will tell us. The Guardian. https://www.theguardian.com/commentisfree/2021/nov/28/omicron-covid-variant-britain-southern-africa

Mallapaty, S. (2021). The search for people who never get COVID. Nature. https://doi.org/10.1038/d41586-021-02978-6

Rono, E. K. (2021). Covid-19 genomic analysis reveals clusters of emerging sublineages within the delta variant [Preprint]. Genomics. https://doi.org/10.1101/2021.10.08.463334

This is what the research is studying.

Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., Baele, G., Parag, K. V., Battle, A. L., Gutierrez, B., Jackson, B., Colquhoun, R., O’Toole, Á., Klein, B., Vespignani, A., COVID-19 Genomics UK (COG-UK) Consortium‡, Volz, E., Faria, N. R., Aanensen, D. M., … Pybus, O. G. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science, 373(6557), 889–895. https://doi.org/10.1126/science.abj0113

O’Toole, Á., Scher, E., Underwood, A., Jackson, B., Hill, V., McCrone, J. T., Colquhoun, R., Ruis, C., Abu-Dahab, K., Taylor, B., Yeats, C., du Plessis, L., Maloney, D., Medd, N., Attwood, S. W., Aanensen, D. M., Holmes, E. C., Pybus, O. G., & Rambaut, A. (2021). Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution, veab064. https://doi.org/10.1093/ve/veab064

Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., Baele, G., Parag, K. V., Battle, A. L., Gutierrez, B., Jackson, B., Colquhoun, R., O’Toole, Á., Klein, B., Vespignani, A., Consortium‡, T. C.-19 G. U. (CoG-U., Volz, E., Faria, N. R., Aanensen, D., … Pybus, O. G. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science. https://doi.org/10.1126/science.abj0113

Mallapaty, S. (2021). India’s neighbours race to sequence genomes as COVID surges. Nature, 593(7860), 485–486. https://doi.org/10.1038/d41586-021-01287-2

Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: Preliminary findings - SARS-CoV-2 coronavirus / nCoV-2019 Genomic Epidemiology. (2021, January 25). Virological. https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586/2

Merrick, J. (2021, April 20). Covid-19 variants: South African strain is causing the most concern for UK scientists. iNews. https://inews.co.uk/news/politics/covid-19-variants-south-african-strain-is-causing-the-most-concern-for-uk-scientists-965679?utm_term=Autofeed&ito=social_itw_theipaper&utm_medium=Social&utm_source=Twitter#Echobox=1618951521

Nabavi, N., & Dobson, J. (2021, April 21). Covid-19 new variants—known unknowns. The BMJ Opinion. https://blogs.bmj.com/bmj/2021/04/21/covid-19-new-variants-known-unknowns/?utm_campaign=shareaholic&utm_medium=twitter&utm_source=socialnetwork

More transmissible and evasive SARS-CoV-2 variant growing rapidly in Brazil | Imperial News | Imperial College London. (n.d.). Imperial News. Retrieved 18 April 2021, from https://www.imperial.ac.uk/news/216053/more-transmissible-evasive-sarscov2-variant-growing/

de Oliveira T, Lutucuta S, Nkengasong J, Morais J, Paixao JP, Neto Z, Afonso P, Miranda J, David K, Ingles L, Amilton P A P R R C, Freitas H R, Mufinda F, Tessema K S , Tegally H, San E J, Wilkinson E, Giandhari J, Pillay S, Giovanetti M, Naidoo Y, Katzourakis A, Ghafari M, Singh L, Tshiabuila D, Martin D, Lessells R. (2021) A Novel Variant of Interest of SARS-CoV-2 with Multiple Spike Mutations Detected through Travel Surveillance in Africa. medRxiv. https://www.krisp.org.za/publications.php?pubid=330. Accessed 26 March 2021.

Volz, E., Mishra, S., Chand, M. et al. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature (2021). https://doi.org/10.1038/s41586-021-03470-x

Virological. ‘Recombinant SARS-CoV-2 Genomes Involving Lineage B.1.1.7 in the UK - SARS-CoV-2 Coronavirus / SARS-CoV-2 Molecular Evolution’, 17 March 2021. https://virological.org/t/recombinant-sars-cov-2-genomes-involving-lineage-b-1-1-7-in-the-uk/658.

Miro Weinberger. (2020, December 3). Our 1st Covid-19 wastewater tests since Thanksgiving just came in—Virus levels are up significantly citywide. I hope that all of #BTV will look at this graph and see what I see: A call to action, to stop gathering with other households, and to get tested ASAP if you have https://t.co/8nxTwOOcFA [Tweet]. @MiroBTV. https://twitter.com/MiroBTV/status/1334613511692017664

Here’s what we know about the new variant of coronavirus | Sharon Peacock. (2020, December 22). The Guardian. http://www.theguardian.com/commentisfree/2020/dec/22/new-variant-coronavirus-genomic-sars-cov-2-pandemic

Efficiency sounds too exciting to not try!

Ferretti, A. P., Kula, T., Wang, Y., Nguyen, D. M., Weinheimer, A., Dunlap, G. S., Xu, Q., Nabilsi, N., Perullo, C. R., Cristofaro, A. W., Whitton, H. J., Virbasius, A., Olivier, K. J., Baiamonte, L. B., Alistar, A. T., Whitman, E. D., Bertino, S. A., Chattopadhyay, S., & MacBeath, G. (2020). COVID-19 Patients Form Memory CD8+ T Cells that Recognize a Small Set of Shared Immunodominant Epitopes in SARS-CoV-2. MedRxiv, 2020.07.24.20161653. https://doi.org/10.1101/2020.07.24.20161653

Guo, L., Boocock, J., Tome, J. M., Chandrasekaran, S., Hilt, E. E., Zhang, Y., Sathe, L., Li, X., Luo, C., Kosuri, S., Shendure, J. A., Arboleda, V. A., Flint, J., Eskin, E., Garner, O. B., Yang, S., Bloom, J. S., Kruglyak, L., & Yin, Y. (2020). Rapid cost-effective viral genome sequencing by V-seq. BioRxiv, 2020.08.15.252510. https://doi.org/10.1101/2020.08.15.252510

Science Facebook Live: Understanding SARS-CoV-2 structure informs vaccine design, clinical trials. (2020, March 20). https://www.youtube.com/watch?v=nOzEx3OpKe8

Qu, J., Cai, Z., Liu, Y., Duan, X., Han, S., Zhu, Y., Jiang, Z., Zhang, Y., Zhuo, C., Liu, Y., Liu, Y., Liu, L., & Yang, L. (2020). Persistent bacterial coinfection of a COVID-19 patient caused by a genetically adapted Pseudomonas aeruginosa chronic colonizer. BioRxiv, 2020.08.05.238998. https://doi.org/10.1101/2020.08.05.238998

Lednicky, J. A., Lauzardo, M., Fan, Z. H., Jutla, A. S., Tilly, T. B., Gangwar, M., Usmani, M., Shankar, S. N., Mohamed, K., Eiguren-Fernandez, A., Stephenson, C. J., Alam, M. M., Elbadry, M. A., Loeb, J. C., Subramaniam, K., Waltzek, T. B., Cherabuddi, K., Morris, J. G., & Wu, C.-Y. (2020). Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients. MedRxiv, 2020.08.03.20167395. https://doi.org/10.1101/2020.08.03.20167395

LucyinLockdown: Viruses, Pandemics and Lessons Learnt with Dr Jane Greatorex—YouTube. (2020, June 18). https://youtu.be/5U1go5hyen8

How coronavirus mutations can track its spread—And disprove conspiracies. (2020, March 26). Science. https://www.nationalgeographic.com/science/2020/03/how-coronavirus-mutations-can-track-its-spread-and-disprove-conspiracies/

How scientists know COVID-19 is way deadlier than the flu. (2020, July 2). Science. https://www.nationalgeographic.com/science/2020/07/coronavirus-deadlier-than-many-believed-infection-fatality-rate-cvd/

Behrmann, Ole, and Martin Spiegel. ‘COVID-19: From Rapid Genome Sequencing to Fast Decisions’. The Lancet Infectious Diseases 0, no. 0 (14 July 2020). https://doi.org/10.1016/S1473-3099(20)30580-6.

Balloux, F. (2020, May 22) A thread written by @BallouxFrancois. Threader. https://threader.app/thread/1263745877702737920

Andersen, K.G., Rambaut, A., Lipkin, W.I. et al. The proximal origin of SARS-CoV-2. Nat Med 26, 450–452 (2020). https://doi.org/10.1038/s41591-020-0820-9

More on Nala in the Vet Candy blog https://www.myvetcandy.com/clinicalupdblog/2020/4/2/first-complete-german-shepherd-dna-offers-new-tool-to-fight-disease

Coverage in GenomeWeb https://www.genomeweb.com/scan/german-shepherds-own-sequence#.XoeoXG4o-qA

discussion of tools; recently revived

re Venter study in PNAS, claiming to be able to identify people based on whole genome data

mentioned tools are focused on (capture) Hi-C data

Napoleon oak genome sequencing project web site: example of public engagement in tree genomics

data (not yet live) associated with https://hyp.is/4DerrmIaEeehDPNBqsRcxQ/www.biorxiv.org/content/biorxiv/early/2017/06/13/149203.full.pdf

NIG Mouse Genome Database: JF1 and MSM SNPs; effective genome browser

restart may be insufficient; had to modify prefs.properties in ~/igv (removing old cached genome values) before i could see my genomes

This paper was studied in a case study that lead to some corrections. See the paper here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127612

Poorly studied in some part to its very high degree of heterozygosity. You can get some more insight here, where it was nominated as a "top ten genome" http://www.homolog.us/blogs/blog/2015/05/08/top-ten-genomes-ix-pacific-oyster/

See Nature doi:10.1038/nature11236 for more on how LFR works: http://www.nature.com/nature/journal/v487/n7406/full/nature11236.html