138 Matching Annotations
  1. Aug 2022
    1. Meng, B., Abdullahi, A., Ferreira, I. A. T. M., Goonawardane, N., Saito, A., Kimura, I., Yamasoba, D., Gerber, P. P., Fatihi, S., Rathore, S., Zepeda, S. K., Papa, G., Kemp, S. A., Ikeda, T., Toyoda, M., Tan, T. S., Kuramochi, J., Mitsunaga, S., Ueno, T., … Gupta, R. K. (2022). Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity. Nature, 1–1. https://doi.org/10.1038/s41586-022-04474-x

    1. 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

  2. May 2022
    1. DICER1 syndrome is a rare genetic condition predisposing to hereditary cancer and caused by variants in the DICER1

      GeneName: DICER1 PMCID: PMC7859642 HGNCID: Unavailable Inheritance Pattern: Autosomal dominant. Disease Entity: Familial pleuropulmonary blastoma (PPB), cervix embryonal rhabdomyosarcoma, multinodular goiter, nasal chondromesenchymal hemartoma, Ciliary body medulloepithelioma, Sertoli-Leydig Cell Tumor (SLCT), differentiated thyroid carcinoma, pituitary blastoma, pineoblastoma, cystic nephroma, Wilm's tumor and sarcomas of different sites including, amongst others, the uterine cervix, kidney and brain. Mutation: Germline Zygosity: Heterozygose Variant: No ClinVarID present. Family Information: No family outline Case: No specified information of patients included. CasePresentingHPO's: n/a CasePrevious Testing: n/a gnomAD: n/a Mutation Type: nonsense, frameshift, or splice affected.

    1. Pathogenic germline variants in DICER1 underlie an autosomal dominant, pleiotropic tumor-predisposition disorder.

      gene name: DICER 1 PMID (PubMed ID): 33570641 HGNCID: n/a Inheritance Pattern: autosomal dominant Disease Entity: benign and malignant tumor mutation Mutation: somatic Zygosity: heterozygous Variant: n/a Family Information: n/a Case: people of all sexes, ages, ethnicities and races participated CasePresentingHPOs: individuals with DICER1-associated tumors or pathogenic germline DICER1 variants were recruited to participate CasePreviousTesting: n/a gnomAD: n/a

    1. DICER1 syndrome is an autosomal-dominant,pleiotropic, tumor-predisposition disorder arisingfrom pathogenic germline variants in DICER1, whichencodes an endoribonuclease integral to processingmicroRNAs

      DICER1 is the gene name. PubMed ID, HGCNCID, and Variant: I can't find Inheritance Pattern: autosomal-dominant The disease entity: DICER1 syndrome The type of mutation: germline. Zygosity: not known. Family Information: a family was used, DICER1 carriers, and non DICER1 variant used, some of the family members had tumors from DICER1 Case Information: mean age is 34, the range of age is 18.6 to 43 years, male, and female used, ethnicity can't find Case Presenting HPO: cancer testing, chemotherapy, radiotherapy gnomeAD: 9.2,8.3.2 Mutation type: Pleiotropic, loss of function, missense

    1. GeneName: DICER1 syndrome (pleuropulmonary blastoma familial tumor susceptibility syndrome), PMID (PubMed ID): 29762508, HGNCID: 17098, Inheritance pattern: autosomal-dominant disease, Disease entity: Plueropulomary Blastoma, Mutation: Somatic, Zygosity: heterozygous, Variant: multiple variants, Family information: NA, Case: young children, CasePresentingHPO: N/A, CasePreviousTesting: N/A, Gnomade #: N/A , Mutation type: deletion

  3. Apr 2022
    1. DICER1 syndrome is a rare genetic condition predisposing to hereditary cancer and caused by variants in the DICER1 gene.

      Gene Name: DICER1 PMID:33552988 HGNCID: Unavailable Inheritance Pattern:Autosomal Dominant Disease Entity: familial pleuropulmonary blastoma (PPB),cystic nephroma, ovarian Sertoli-Leydig cell tumor (SLCT), multinodular goiter, cervix embryonal rhabdomyosarcoma, Wilms’ tumor, nasal chondromesenchymal hamartoma, ciliary body medulloepithelioma, differentiated thyroid carcinoma, pituitary blastoma, pineoblastoma, and sarcomas of different sites. Mutation: Nonsense, Frameshift<br /> Zygosity: Heterosygosity Variant:No ClinVar ID present Family Information:no diseases mentioned in family Case: no specified case in this article gnomAD: n/a Mutation type: Nonsense. frameshift

    1. Ravi K Gupta [@ravgup33_ravi]. (2021, November 24). This one is worrying and I’ve not said that since delta. Please get vaccinated and boosted and mask up in public as the mutations in this virus likely result in high level escape from neutralising antibodies [Tweet]. Twitter. https://twitter.com/ravgup33_ravi/status/1463626745651806208

    1. Prof. Christina Pagel 🇺🇦 [@chrischirp]. (2021, November 24). As well as Tom’s new one (B.1.1.529), C.1.2 seems to be spreading in S Africa—C.1.2 was the one with lots of worrying mutations first reported in August... Plus cases in S Africa suddenly increasing again in the middle of their summer. Https://t.co/fCqfOMcO83 [Tweet]. Twitter. https://twitter.com/chrischirp/status/1463504890530086917

    1. The DICER1 syndrome is an autosomal dominant tumor‐predisposi-tion disorder associated with pleuropulmonary blastoma, a rare pediatric lung cancer

      GeneName:DICER1 PMID (PubMed ID): PMCID: PMC6418698 PMID: 30672147 HGNCID: NOT LISTED<br /> Inheritance Pattern: Autosomal Dominant Disease Entity: Cancer; benign and malignant tumors including pleuropulmonary blastoma, cystic nephroma, Sertoli-Leydig cell tumors, multinodular goiter, Thryoid cancer, rhabdomyosarcoma, and pineoblastoma. Mutation: Somatic missense variation Mutation type: missense Zygosity: None stated Variant: unregistered…. Family Information: Characterize germline variants in familial early-onset clorectal cancer patients; The observation of germline DICER1 variation with uterine corpus endometrial carcinoma merits additional investigation. CasePresentingHPOs: uterine and rectal cancers in germline mutation

    1. Dr Emma Hodcroft [@firefoxx66]. (2021, November 26). We now have B.1.1.529 sequences (designed at @nextstrain clade 21K) up in our Africa build. You can check them out below. These are from South Africa & Botswana—You can see the high number of mutations. CoVariants focal build & updates will come ASAP. https://t.co/fqBldneF5U [Tweet]. Twitter. https://twitter.com/firefoxx66/status/1464145615571623938

    1. Nathan Grubaugh [@NathanGrubaugh]. (2021, September 24). Hi @Newsweek 👋. I understand that #variant news has been slow recently with the near-complete dominance of Delta, but do you really need to go and make things up? Lineage R.1 is not a concern. Let me briefly explain why. (1/4) https://t.co/OD46PsXZEu [Tweet]. Twitter. https://twitter.com/NathanGrubaugh/status/1441522760832933888

  4. Mar 2022
    1. Mia Malan. (2021, November 25). [Thread] What is the potential impact of the new B.1.1.529 #COVID19 variant? @rjlessells: 1. It’s relatively simple to detect some B.1.1.529 cases, as it’s possible to use PCR tests to do this in some cases 2. B.1.1.529 = has many mutations across different parts of the virus https://t.co/ytktqLzJUi [Tweet]. @miamalan. https://twitter.com/miamalan/status/1463846528578109444

  5. Feb 2022
    1. Meaghan Kall. (2022, February 17). BA.2 risk assessment New this week is upgrading Immune Evasion—Amber 🟨 from low to moderate that BA.2 is antigentically different to BA.1 Unsurprising given the mutation profile, with BA.2 slightly more immune evasive than BA.1 on neuts studies https://t.co/n6DWtiRaNH [Tweet]. @kallmemeg. https://twitter.com/kallmemeg/status/1494100170195312646

    1. Trisha Greenhalgh. (2022, January 8). Apart from (e.g.): 1. Severe disease in clinically vulnerable (they are people too); 2. Long covid in many; 3. Strokes / heart attacks / kidney failure from micro-clots; 4. New-onset diabetes and MIS-C in children; 5. High potential for recombinant mutations. [Tweet]. @trishgreenhalgh. https://twitter.com/trishgreenhalgh/status/1479738523511136258

    1. Ulrich Elling. (2022, January 12). While #Omicron BA.1 leads the race, the little sister BA.2 is catching up in numbers. They are rather different with likely functional implications. BA.2 might be more immune evasive in RBD, less in NTD. And due to reduced mutation load in NTD maybe different fusion properties? Https://t.co/kEACjzQDs3 [Tweet]. @EllingUlrich. https://twitter.com/EllingUlrich/status/1481214901997682692

    1. Jonathan Li on Twitter: “There’s a lineage of Omicron that’s gained the R346K mutation (BA.1.1). This one could spell some trouble for the AZ mAb (tixagevimab/cilgavimab, Evusheld) that’s being used for pre-exposure prophylaxis. If you want to learn about tix/cil vs Omicron, read on 1/7” / Twitter. (n.d.). Retrieved February 6, 2022, from https://twitter.com/DrJLi/status/1487479972293853188

    1. Trevor Bedford. (2022, January 28). Omicron viruses can be divided into two major groups, referred to as PANGO lineages BA.1 and BA.2 or @nextstrain clades 21K and 21L. The vast majority of globally sequenced Omicron have been 21K (~630k) compared a small minority of 21L (~18k), but 21L is gaining ground. 1/15 [Tweet]. @trvrb. https://twitter.com/trvrb/status/1487105396879679488

  6. Jan 2022
    1. Pajon, R., Doria-Rose, N. A., Shen, X., Schmidt, S. D., O’Dell, S., McDanal, C., Feng, W., Tong, J., Eaton, A., Maglinao, M., Tang, H., Manning, K. E., Edara, V.-V., Lai, L., Ellis, M., Moore, K. M., Floyd, K., Foster, S. L., Posavad, C. M., … Montefiori, D. C. (2022). SARS-CoV-2 Omicron Variant Neutralization after mRNA-1273 Booster Vaccination. New England Journal of Medicine, 0(0), null. https://doi.org/10.1056/NEJMc2119912

    1. Cornelius Roemer. (2021, December 22). @mccarthy_kr I took a look at all these NY sequences. I don’t think these point mutations S:681H are real. Why? Because they appear all over the Omicron diversity. Some sequences have S:346K, some S:701V, most miss S679K, a few have it. That’s the signature of contamination/co-infection. Https://t.co/DcJD4q44EM [Tweet]. @CorneliusRoemer. https://twitter.com/CorneliusRoemer/status/1473507369455923203

  7. Dec 2021
    1. Garcia-Beltran, W. F., Denis, K. J. S., Hoelzemer, A., Lam, E. C., Nitido, A. D., Sheehan, M. L., Berrios, C., Ofoman, O., Chang, C. C., Hauser, B. M., Feldman, J., Gregory, D. J., Poznansky, M. C., Schmidt, A. G., Iafrate, A. J., Naranbhai, V., & Balazs, A. B. (2021). MRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant (p. 2021.12.14.21267755). https://doi.org/10.1101/2021.12.14.21267755

    1. nference. (2021, November 27). Here is how B.1.1.529 (#Omicron #B11529) compares to Alpha, Beta, Gamma, Delta variants. Omicron has highest novel Spike mutations including striking cluster on the “crown” suggesting significant selection pressure & antigenic distinction from prior strains (Credits: Nference) https://t.co/4oZQbjhbG8 [Tweet]. @_nference. https://twitter.com/_nference/status/1464404770098229250

  8. Nov 2021
  9. Oct 2021
    1. Mlcochova, P., Kemp, S. A., Dhar, M. S., Papa, G., Meng, B., Ferreira, I. A. T. M., Datir, R., Collier, D. A., Albecka, A., Singh, S., Pandey, R., Brown, J., Zhou, J., Goonawardane, N., Mishra, S., Whittaker, C., Mellan, T., Marwal, R., Datta, M., … Gupta, R. K. (2021). SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature, 1–6. https://doi.org/10.1038/s41586-021-03944-y

  10. Sep 2021
  11. Aug 2021
    1. Liu, Y., Arase, N., Kishikawa, J., Hirose, M., Li, S., Tada, A., Matsuoka, S., Arakawa, A., Akamatsu, K., Ono, C., Jin, H., Kishida, K., Nakai, W., Kohyama, M., Nakagawa, A., Yamagishi, Y., Nakagami, H., Kumanogoh, A., Matsuura, Y., … Arase, H. (2021). The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines (p. 2021.08.22.457114). https://doi.org/10.1101/2021.08.22.457114

  12. Jun 2021
    1. In general, top-level errors should only be used for exceptional circumstances when a developer should be made aware that the system had some kind of problem. For example, the GraphQL specification says that when a non-null field returns nil, an error should be added to the "errors" key. This kind of error is not recoverable by the client. Instead, something on the server should be fixed to handle this case. When you want to notify a client some kind of recoverable issue, consider making error messages part of the schema, for example, as in mutation errors.
  13. May 2021
    1. Eric Topol. (2021, May 1). Downgrading the concern on B.1.617, the poorly named ‘double mutant’—98% effectiveness of mRNA vaccine in an Israeli outbreak @CT_Bergstrom https://t.co/tGbuwPUmAL —Lab studies: Minimal immune evasion, expected full protection from vaccine @GuptaR_lab https://t.co/AIp24G0ROK https://t.co/AK20UWlDBD [Tweet]. @EricTopol. https://twitter.com/EricTopol/status/1388539223230140422

    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

  14. 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

  15. 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

  16. 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

  17. Dec 2020
  18. Aug 2020
  19. 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

  20. 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

  21. May 2020
  22. May 2018
  23. 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
  24. Sep 2017