52 Matching Annotations
  1. Last 7 days
  2. May 2021
    1. Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. da S., Mishra, S., Crispim, M. A. E., Sales, F. C. S., Hawryluk, I., McCrone, J. T., Hulswit, R. J. G., Franco, L. A. M., Ramundo, M. S., Jesus, J. G. de, Andrade, P. S., Coletti, T. M., Ferreira, G. M., Silva, C. A. M., Manuli, E. R., … Sabino, E. C. (2021). Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. https://doi.org/10.1126/science.abh2644

  3. Apr 2021
    1. Trevor Bedford. (2021, January 14). After ~10 months of relative quiescence we’ve started to see some striking evolution of SARS-CoV-2 with a repeated evolutionary pattern in the SARS-CoV-2 variants of concern emerging from the UK, South Africa and Brazil. 1/19 [Tweet]. @trvrb. https://twitter.com/trvrb/status/1349774271095062528

  4. Mar 2021
    1. 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.

    1. The dominant mutant D614G

      D614G mutation not associated with higher mortality, but is associated with a higher viral load and affecting younger patients https://doi.org/10.1016/j.cell.2020.11.020 . D614G mutation proposed to allow increased epitope exposure and greater neutralisation, thus should not affect vaccine efficacy https://doi.org/10.1016/j.chom.2020.11.012

      Additionally a N501Y mutation in the S1 has been reported. This mutation is already present in the UK SARS-CoV-2 variant (20B/501Y.V1, B1.1.7 lineage), and is associated with high higher rates of transmission through increased receptor binding https://doi.org/10.1101/2021.01.04.425316 and potentially higher viral loads https://doi.org/10.1101/2021.01.12.20249080 . However, post vaccination sera can neutralise this variant and thus current vaccines in circulation should protect against this strain https://doi.org/10.1101/2021.01.19.21249592 .

      Interestingly, examination of the global effects of the N501Y mutation revealed that MHCII presentation was poorer than wild type controls. This implicates the N501Y mutation in hindering immune cell cooperation, resulting in immune escape https://doi.org/10.1101/2021.02.02.429431

    2. possibly via reduced shedding of the S1 domain

      and also possibly by enhancing the lysosomal trafficking of the SARS-CoV-2 spike protein https://doi.org/10.1101/2020.12.08.417022

    3. S1 mediates receptor binding

      Another mutation in the receptor binding domain of the S protein, E484K, has been found in the South African and Brazilian variants of the virus. The glutamate to lysine substitution switches the charge on the flexible loop region of the RBD resulting in the formation of novel favourable contacts https://doi.org/10.1101/2021.01.13.426558 . Early studies indicate that higher antibody titres will be required post vaccination to neutralise the variant https://doi.org/10.1101/2021.01.26.21250543

    4. ACE2 expression varies by age and ethnicity and has been associated with comorbidities and severe COVID-19

      Indeed, a recent study indicates that diversity of ACE2 expression amongst those of different ethnicities impacts selection pressures for mutations in SARS-CoV-2, for example, the D614G mutation has become dominant in North America, Europe and Africa where ACE2 expression amongst the population is low in comparison with those from China, where D614G is not the dominant form https://doi.org/10.3390/genes12010016

  5. Feb 2021
    1. Eric Feigl-Ding. (2020, December 6). HUMAN➡️MINKS➡️HUMAN transmission on mink farms in NL. 68% of the tested farm workers and/or contacts had evidence of #SARSCoV2 infection. The coronavirus mutated & even evolved within minks before transmitted back to humans—& keeps #COVID19 perpetuating. Https://t.co/5ARZ6Pq5mO https://t.co/fhrQC9ZVDo [Tweet]. @DrEricDing. https://twitter.com/DrEricDing/status/1335419078446551041

    1. Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Lambson, B. E., Vermeulen, M., Berg, K. van den, Rossouw, T., Boswell, M., Ueckermann, V., Meiring, S., Gottberg, A. von, Cohen, C., Morris, L., Bhiman, J. N., & Moore, P. L. (2021). SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma. BioRxiv, 2021.01.18.427166. https://doi.org/10.1101/2021.01.18.427166

    1. Shen, X., Tang, H., McDanal, C., Wagh, K., Fischer, W. M., Theiler, J., Yoon, H., Li, D., Haynes, B. F., Saunders, K. O., Gnanakaran, S., Hengartner, N. W., Pajon, R., Smith, G., Dubovsky, F., Glenn, G. M., Korber, B. T., & Montefiori, D. C. (2021). SARS-CoV-2 Variant B.1.1.7 is Susceptible to Neutralizing Antibodies Elicited by Ancestral Spike Vaccines (SSRN Scholarly Paper ID 3777473). Social Science Research Network. https://papers.ssrn.com/abstract=3777473

  6. Dec 2020
  7. Aug 2020
  8. Jul 2020
    1. Yurkovetskiy, L., Wang, X., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T., Wang, Y., Baum, A., Diehl, W. E., Dauphin, A., Carbone, C., Veinotte, K., Egri, S. B., Schaffner, S. F., Lemieux, J. E., Munro, J., Rafique, A., Barve, A., Sabeti, P. C., Kyratsous, C. A., … Luban, J. (2020). Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. BioRxiv, 2020.07.04.187757. https://doi.org/10.1101/2020.07.04.187757

    1. Corbett, K. S., Edwards, D., Leist, S. R., Abiona, O. M., Boyoglu-Barnum, S., Gillespie, R. A., Himansu, S., Schäfer, A., Ziwawo, C. T., DiPiazza, A. T., Dinnon, K. H., Elbashir, S. M., Shaw, C. A., Woods, A., Fritch, E. J., Martinez, D. R., Bock, K. W., Minai, M., Nagata, B. M., … Graham, B. S. (2020). SARS-CoV-2 mRNA Vaccine Development Enabled by Prototype Pathogen Preparedness. BioRxiv, 2020.06.11.145920. https://doi.org/10.1101/2020.06.11.145920

    1. Sapoval, N., Mahmoud, M., Jochum, M. D., Liu, Y., Elworth, R. A. L., Wang, Q., Albin, D., Ogilvie, H., Lee, M. D., Villapol, S., Hernandez, K., Berry, I. M., Foox, J., Beheshti, A., Ternus, K., Aagaard, K. M., Posada, D., Mason, C., Sedlazeck, F. J., & Treangen, T. J. (2020). Hidden genomic diversity of SARS-CoV-2: Implications for qRT-PCR diagnostics and transmission. BioRxiv, 2020.07.02.184481. https://doi.org/10.1101/2020.07.02.184481

  9. Jun 2020
    1. Starr, T. N., Greaney, A. J., Hilton, S. K., Crawford, K. H., Navarro, M. J., Bowen, J. E., Tortorici, M. A., Walls, A. C., Veesler, D., & Bloom, J. D. (2020). Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding [Preprint]. Microbiology. https://doi.org/10.1101/2020.06.17.157982

  10. May 2020
  11. May 2018
  12. Nov 2017
    1. tier 1 contains all changes in the amino acid coding regions of annotated exons, consensus splice-site regions, and RNA genes (including microRNA genes). Tier 2 contains changes in highly conserved regions of the genome or regions that have regulatory potential. Tier 3 contains mutations in the nonrepetitive part of the genome that does not meet tier 2 criteria, and tier 4 contains mutations in the remainder of the genome
  13. Sep 2017