Nida Patel Journal Week 10

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Assignment

The goal for this assignment is to create a class shared annotated bibliography of references for the next phase of the HIV research project where we will investigate the structure-function implications of mutations in the gp120 protein.

  1. Warm up exercise (announced in class).
  2. Perform a search in Google Scholar .
    1. Record the number of “hits” you found:63,600 results
    2. Record the top 10 papers, this time using APA format:
      • Ibarrondo, F. J., Fulcher, J. A., Goodman-Meza, D., Elliott, J., Hofmann, C., Hausner, M. A., ... & Yang, O. O. (2020). Rapid decay of anti–SARS-CoV-2 antibodies in persons with mild Covid-19. New England Journal of Medicine, 383(11), 1085-1087.
      • Ju, B., Zhang, Q., Ge, J., Wang, R., Sun, J., Ge, X., ... & Tang, X. (2020). Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature, 584(7819), 115-119.
      • Pinto, D., Park, Y. J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., ... & Peter, A. (2020). Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature, 1-6.
      • paper 4 Gudbjartsson, D. F., Norddahl, G. L., Melsted, P., Gunnarsdottir, K., Holm, H., Eythorsson, E., ... & Thorsteinsdottir, B. (2020). Humoral immune response to SARS-CoV-2 in Iceland. New England Journal of Medicine.
      • Li, Z., Yi, Y., Luo, X., Xiong, N., Liu, Y., Li, S., ... & Zhang, Y. (2020). Development and clinical application of a rapid IgM‐IgG combined antibody test for SARS‐CoV‐2 infection diagnosis. Journal of medical virology.
      • Van Bavel, J. J., Baicker, K., Boggio, P. S., Capraro, V., Cichocka, A., Cikara, M., ... & Drury, J. (2020). Using social and behavioural science to support COVID-19 pandemic response. Nature Human Behaviour, 1-12.
      • Grzelak, L., Temmam, S., Planchais, C., Demeret, C., Tondeur, L., Huon, C., ... & Planas, D. (2020). A comparison of four serological assays for detecting anti–SARS-CoV-2 antibodies in human serum samples from different populations. Science translational medicine, 12(559).
      • Wang, C., Li, W., Drabek, D., Okba, N. M., van Haperen, R., Osterhaus, A. D., ... & Bosch, B. J. (2020). A human monoclonal antibody blocking SARS-CoV-2 infection. Nature communications, 11(1), 1-6.
      • Liu, L., Wang, P., Nair, M. S., Yu, J., Rapp, M., Wang, Q., ... & Guo, X. V. (2020). Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature, 584(7821), 450-456.
      • Long, Q. X., Tang, X. J., Shi, Q. L., Li, Q., Deng, H. J., Yuan, J., ... & Su, K. (2020). Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections. Nature medicine, 26(8), 1200-1204.
  3. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    • Alberca, G. G. F., & Alberca, R. W. What is the long‐term clinical significance of anti‐SARS‐CoV‐2‐specific IgG?. Influenza and Other Respiratory Viruses.
    • Pirsalehi, A., Salari, S., Baghestani, A., Vahidi, M., Khave, L. J., Akbari, M. E., & Bashash, D. (2020). Neutrophil-to-lymphocyte ratio (NLR) greater than 6.5 may reflect the progression of COVID-19 towards an unfavorable clinical outcome. Iranian Journal of Microbiology, 12(5), 466-474.
    • Hantz, S. (2020). Diagnostic biologique de l’infection à Sars-CoV-2: stratégies et interprétation des résultats. Revue Francophone des Laboratoires, 2020(526), 48-56.
    • Weisshoff, H., Krylova, O., Nikolenko, H., Düngen, H. D., Dallmann, A., Becker, S., ... & Haberland, A. (2020). Aptamer BC 007-Efficient binder of spreading-crucial SARS-CoV-2 proteins. Heliyon, e05421.
    • Azzi, L., Maurino, V., Baj, A., Dani, M., d’Aiuto, A., Fasano, M., ... & Alberio, T. (2020). <? covid19?> Diagnostic Salivary Tests for SARS-CoV-2. Journal of Dental Research, 0022034520969670.
  4. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • Ibarrondo, F. J., Fulcher, J. A., Goodman-Meza, D., Elliott, J., Hofmann, C., Hausner, M. A., ... & Yang, O. O. (2020). Rapid decay of anti–SARS-CoV-2 antibodies in persons with mild Covid-19. New England Journal of Medicine, 383(11), 1085-1087.
    • Biggs, H. M., Harris, J. B., Breakwell, L., Dahlgren, F. S., Abedi, G. R., Szablewski, C. M., ... & Gilani, Z. (2020). Estimated community seroprevalence of SARS-CoV-2 antibodies—two Georgia counties, April 28–May 3, 2020. Morbidity and Mortality Weekly Report, 69(29), 965.
    • Weidner, L., Gänsdorfer, S., Unterweger, S., Weseslindtner, L., Drexler, C., Farcet, M., ... & Jungbauer, C. (2020). Quantification of SARS-CoV-2 antibodies with eight commercially available immunoassays. Journal of Clinical Virology, 129, 104540.
    • Ju, B., Zhang, Q., Ge, J., Wang, R., Sun, J., Ge, X., ... & Tang, X. (2020). Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature, 584(7819), 115-119.
    • Pinto, D., Park, Y. J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., ... & Peter, A. (2020). Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature, 1-6.
  5. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    • Ibarrondo, F. J., Fulcher, J. A., Goodman-Meza, D., Elliott, J., Hofmann, C., Hausner, M. A., ... & Yang, O. O. (2020). Rapid decay of anti–SARS-CoV-2 antibodies in persons with mild Covid-19. New England Journal of Medicine, 383(11), 1085-1087.
    • pGrzelak, L., Temmam, S., Planchais, C., Demeret, C., Tondeur, L., Huon, C., ... & Planas, D. (2020). A comparison of four serological assays for detecting anti–SARS-CoV-2 antibodies in human serum samples from different populations. Science translational medicine, 12(559).
    • Biggs, H. M., Harris, J. B., Breakwell, L., Dahlgren, F. S., Abedi, G. R., Szablewski, C. M., ... & Gilani, Z. (2020). Estimated community seroprevalence of SARS-CoV-2 antibodies—two Georgia counties, April 28–May 3, 2020. Morbidity and Mortality Weekly Report, 69(29), 965.
    • Weidner, L., Gänsdorfer, S., Unterweger, S., Weseslindtner, L., Drexler, C., Farcet, M., ... & Jungbauer, C. (2020). Quantification of SARS-CoV-2 antibodies with eight commercially available immunoassays. Journal of Clinical Virology, 129, 104540.
    • Lee, W. S., Wheatley, A. K., Kent, S. J., & DeKosky, B. J. (2020). Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies. Nature microbiology, 5(10), 1185-1191.
  6. We will now make a list of the search terms that were used by each student in the class. Record the list written on the board here:
    • COVID-19 deaths
    • COVID-19 transmission
    • SARS-CoV-2 dying, getting better/worse
    • COVID-19 transmission
    • D614G
    • civet
    • long-term respiratory effects of COVID
    • SARS-CoV-2 antibodies
    • D614G mutation
    • SARS-CoV-2 immune response
    • 2019-nCoV transmission
    • SARS-CoV-2 antibodies
    • Record the search terms that have now been assigned specifically to you:
      • SARS-CoV-2 antibodies
  7. Now access the PubMed database by using the LMU-specific link. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits: 2,901
    • Record the top 10 papers (you don't need to do APA format for this):
      1. Zhou G, Zhao Q. Perspectives on therapeutic neutralizing antibodies against the Novel Coronavirus SARS-CoV-2. Int J Biol Sci. 2020 Mar 15;16(10):1718-1723. doi: 10.7150/ijbs.45123. PMID: 32226289; PMCID: PMC7098029.
      2. Ju, B., Zhang, Q., Ge, J., Wang, R., Sun, J., Ge, X., Yu, J., Shan, S., Zhou, B., Song, S., Tang, X., Yu, J., Lan, J., Yuan, J., Wang, H., Zhao, J., Zhang, S., Wang, Y., Shi, X., Liu, L., … Zhang, L. (2020). Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature, 584(7819), 115–119. https://doi.org/10.1038/s41586-020-2380-z
      3. Jiang S, Hillyer C, Du L. Neutralizing Antibodies against SARS-CoV-2 and Other Human Coronaviruses. Trends Immunol. 2020 May;41(5):355-359. doi: 10.1016/j.it.2020.03.007. Epub 2020 Apr 2. Erratum in: Trends Immunol. 2020 Apr 24;: PMID: 32249063; PMCID: PMC7129017.
      4. Cao Y, Su B, Guo X, Sun W, Deng Y, Bao L, Zhu Q, Zhang X, Zheng Y, Geng C, Chai X, He R, Li X, Lv Q, Zhu H, Deng W, Xu Y, Wang Y, Qiao L, Tan Y, Song L, Wang G, Du X, Gao N, Liu J, Xiao J, Su XD, Du Z, Feng Y, Qin C, Qin C, Jin R, Xie XS. Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients' B Cells. Cell. 2020 Jul 9;182(1):73-84.e16. doi: 10.1016/j.cell.2020.05.025. Epub 2020 May 18. PMID: 32425270; PMCID: PMC7231725. Review.
      5. Klasse PJ, Moore JP. Antibodies to SARS-CoV-2 and their potential for therapeutic passive immunization. Elife. 2020 Jun 23;9:e57877. doi: 10.7554/eLife.57877. PMID: 32573433; PMCID: PMC7311167.
      6. Gao Q, Bao L, Mao H, Wang L, Xu K, Yang M, Li Y, Zhu L, Wang N, Lv Z, Gao H, Ge X, Kan B, Hu Y, Liu J, Cai F, Jiang D, Yin Y, Qin C, Li J, Gong X, Lou X, Shi W, Wu D, Zhang H, Zhu L, Deng W, Li Y, Lu J, Li C, Wang X, Yin W, Zhang Y, Qin C. Development of an inactivated vaccine candidate for SARS-CoV-2. Science. 2020 Jul 3;369(6499):77-81. doi: 10.1126/science.abc1932. Epub 2020 May 6. PMID: 32376603; PMCID: PMC7202686.
      7. Liu L, Wang P, Nair MS, Yu J, Rapp M, Wang Q, Luo Y, Chan JF, Sahi V, Figueroa A, Guo XV, Cerutti G, Bimela J, Gorman J, Zhou T, Chen Z, Yuen KY, Kwong PD, Sodroski JG, Yin MT, Sheng Z, Huang Y, Shapiro L, Ho DD. Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature. 2020 Aug;584(7821):450-456. doi: 10.1038/s41586-020-2571-7. Epub 2020 Jul 22. PMID: 32698192.
      8. Yuan M, Wu NC, Zhu X, Lee CD, So RTY, Lv H, Mok CKP, Wilson IA. A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. Science. 2020 May 8;368(6491):630-633. doi: 10.1126/science.abb7269. Epub 2020 Apr 3. PMID: 32245784; PMCID: PMC7164391.
      9. Nie J, Li Q, Wu J, Zhao C, Hao H, Liu H, Zhang L, Nie L, Qin H, Wang M, Lu Q, Li X, Sun Q, Liu J, Fan C, Huang W, Xu M, Wang Y. Establishment and validation of a pseudovirus neutralization assay for SARS-CoV-2. Emerg Microbes Infect. 2020 Dec;9(1):680-686. doi: 10.1080/22221751.2020.1743767. PMID: 32207377; PMCID: PMC7144318.
      10. Nie J, Li Q, Wu J, Zhao C, Hao H, Liu H, Zhang L, Nie L, Qin H, Wang M, Lu Q, Li X, Sun Q, Liu J, Fan C, Huang W, Xu M, Wang Y. Establishment and validation of a pseudovirus neutralization assay for SARS-CoV-2. Emerg Microbes Infect. 2020 Dec;9(1):680-686. doi: 10.1080/22221751.2020.1743767. PMID: 32207377; PMCID: PMC7144318.
  8. Perform a title/abstract search on your assigned keywords.
    • Record the total number of hits: 248
    • Record the top 10 papers (you don't need to do APA format for this):
      1. Ju B, Zhang Q, Ge J, Wang R, Sun J, Ge X, Yu J, Shan S, Zhou B, Song S, Tang X, Yu J, Lan J, Yuan J, Wang H, Zhao J, Zhang S, Wang Y, Shi X, Liu L, Zhao J, Wang X, Zhang Z, Zhang L. Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature. 2020 Aug;584(7819):115-119. doi: 10.1038/s41586-020-2380-z. Epub 2020 May 26. PMID: 32454513.
      2. Zhao R, Li M, Song H, Chen J, Ren W, Feng Y, Gao GF, Song J, Peng Y, Su B, Guo X, Wang Y, Chen J, Li J, Sun H, Bai Z, Cao W, Zhu J, Zhang Q, Sun Y, Sun S, Mao X, Su J, Chen X, He A, Gao W, Jin R, Jiang Y, Sun L. Early detection of SARS-CoV-2 antibodies in COVID-19 patients as a serologic marker of infection. Clin Infect Dis. 2020 May 1:ciaa523. doi: 10.1093/cid/ciaa523. Epub ahead of print. PMID: 32357209; PMCID: PMC7197602.
      3. Wu Y, Li C, Xia S, Tian X, Kong Y, Wang Z, Gu C, Zhang R, Tu C, Xie Y, Yang Z, Lu L, Jiang S, Ying T. Identification of Human Single-Domain Antibodies against SARS-CoV-2. Cell Host Microbe. 2020 Jun 10;27(6):891-898.e5. doi: 10.1016/j.chom.2020.04.023. Epub 2020 May 14. PMID: 32413276; PMCID: PMC7224157.
      4. Lee WS, Wheatley AK, Kent SJ, DeKosky BJ. Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies. Nat Microbiol. 2020 Oct;5(10):1185-1191. doi: 10.1038/s41564-020-00789-5. Epub 2020 Sep 9. PMID: 32908214. Review.
      5. Zhang L, Pang R, Xue X, Bao J, Ye S, Dai Y, Zheng Y, Fu Q, Hu Z, Yi Y. Anti-SARS-CoV-2 virus antibody levels in convalescent plasma of six donors who have recovered from COVID-19. Aging (Albany NY). 2020 Apr 22;12(8):6536-6542. doi: 10.18632/aging.103102. Epub 2020 Apr 22. PMID: 32320384; PMCID: PMC7202482.
      6. Stringhini S, Wisniak A, Piumatti G, Azman AS, Lauer SA, Baysson H, De Ridder D, Petrovic D, Schrempft S, Marcus K, Yerly S, Arm Vernez I, Keiser O, Hurst S, Posfay-Barbe KM, Trono D, Pittet D, Gétaz L, Chappuis F, Eckerle I, Vuilleumier N, Meyer B, Flahault A, Kaiser L, Guessous I. Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Geneva, Switzerland (SEROCoV-POP): a population-based study. Lancet. 2020 Aug 1;396(10247):313-319. doi: 10.1016/S0140-6736(20)31304-0. Epub 2020 Jun 11. PMID: 32534626; PMCID: PMC7289564.
      7. Caturegli G, Materi J, Howard BM, Caturegli P. Clinical Validity of Serum Antibodies to SARS-CoV-2 : A Case-Control Study. Ann Intern Med. 2020 Oct 20;173(8):614-622. doi: 10.7326/M20-2889. Epub 2020 Jul 6. PMID: 32628534; PMCID: PMC7370852.
      8. Padoan A, Sciacovelli L, Basso D, Negrini D, Zuin S, Cosma C, Faggian D, Matricardi P, Plebani M. IgA-Ab response to spike glycoprotein of SARS-CoV-2 in patients with COVID-19: A longitudinal study. Clin Chim Acta. 2020 Aug;507:164-166. doi: 10.1016/j.cca.2020.04.026. Epub 2020 Apr 25. PMID: 32343948; PMCID: PMC7194886.
      9. Montesinos I, Gruson D, Kabamba B, Dahma H, Van den Wijngaert S, Reza S, Carbone V, Vandenberg O, Gulbis B, Wolff F, Rodriguez-Villalobos H. Evaluation of two automated and three rapid lateral flow immunoassays for the detection of anti-SARS-CoV-2 antibodies. J Clin Virol. 2020 Jul;128:104413. doi: 10.1016/j.jcv.2020.104413. Epub 2020 May 5. PMID: 32403010; PMCID: PMC7198434.
      10. Havers FP, Reed C, Lim T, Montgomery JM, Klena JD, Hall AJ, Fry AM, Cannon DL, Chiang CF, Gibbons A, Krapiunaya I, Morales-Betoulle M, Roguski K, Rasheed MAU, Freeman B, Lester S, Mills L, Carroll DS, Owen SM, Johnson JA, Semenova V, Blackmore C, Blog D, Chai SJ, Dunn A, Hand J, Jain S, Lindquist S, Lynfield R, Pritchard S, Sokol T, Sosa L, Turabelidze G, Watkins SM, Wiesman J, Williams RW, Yendell S, Schiffer J, Thornburg NJ. Seroprevalence of Antibodies to SARS-CoV-2 in 10 Sites in the United States, March 23-May 12, 2020. JAMA Intern Med. 2020 Jul 21. doi: 10.1001/jamainternmed.2020.4130. Epub ahead of print. PMID: 32692365.
  9. Add the word “Review” to any articles that are review articles that you listed in question 8.
  10. Pick an author that shows up in multiple citations (if there isn’t one, just pick a last author from one of the papers) and perform an author search on the name.
    • Do you find any new articles that you did not find before on PubMed?
    • List up to 5 new articles that were found on the author name search:
      1. Ju B, Zhang Q, Ge J, Wang R, Sun J, Ge X, Yu J, Shan S, Zhou B, Song S, Tang X, Yu J, Lan J, Yuan J, Wang H, Zhao J, Zhang S, Wang Y, Shi X, Liu L, Zhao J, Wang X, Zhang Z, Zhang L. Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature. 2020 Aug;584(7819):115-119. doi: 10.1038/s41586-020-2380-z. Epub 2020 May 26. PMID: 32454513.
      2. Kumar S, Ju B, Shapero B, Lin X, Ren L, Zhang L, Li D, Zhou Z, Feng Y, Sou C, Mann CJ, Hao Y, Sarkar A, Hou J, Nunnally C, Hong K, Wang S, Ge X, Su B, Landais E, Sok D, Zwick MB, He L, Zhu J, Wilson IA, Shao Y. A VH1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite. Sci Adv. 2020 Sep 16;6(38):eabb1328. doi: 10.1126/sciadv.abb1328. PMID: 32938661; PMCID: PMC7494343.
      3. Han YJ, Kim DY, An K, Kang KT, Ju BK, Cho KH. Sequential Improvement from Cosolvents Ink Formulation to Vacuum Annealing for Ink-Jet Printed Quantum-Dot Light-Emitting Diodes. Materials (Basel). 2020 Oct 24;13(21):E4754. doi: 10.3390/ma13214754. PMID: 33114302.
      4. Zhao XC, Ju B, Wei N, Ding J, Meng FJ, Zhao HG. Severe hyperlipemia-induced pseudoerythrocytosis - Implication for misdiagnosis and blood transfusion: A case report and literature review. World J Clin Cases. 2020 Oct 6;8(19):4595-4602. doi: 10.12998/wjcc.v8.i19.4595. PMID: 33083423; PMCID: PMC7559684.
      5. Liu C, Mendonça L, Yang Y, Gao Y, Shen C, Liu J, Ni T, Ju B, Liu C, Tang X, Wei J, Ma X, Zhu Y, Liu W, Xu S, Liu Y, Yuan J, Wu J, Liu Z, Zhang Z, Liu L, Wang P, Zhang P. The Architecture of Inactivated SARS-CoV-2 with Postfusion Spikes Revealed by Cryo-EM and Cryo-ET. Structure. 2020 Nov 3;28(11):1218-1224.e4. doi: 10.1016/j.str.2020.10.001. Epub 2020 Oct 15. PMID: 33058760; PMCID: PMC7557167.
  11. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits:
    • Record the top 10 papers (you don't need to use APA format for this):
      1. Therapeutic Strategies of COVID-19: From Natural Compounds to Vaccine Trials
      2. Survey of the current status of subclinical coronavirus disease 2019 (COVID-19)
      3. First report of manic-like symptoms in a COVID-19 patient with no previous history of a psychiatric disorder
      4. Corona-Like Illness: Did we get it before WHO Announcement of the Disease? A Cross-sectional Survey
      5. Analysis of COVID-19 convalescent plasma for SARS-CoV-2 IgG using two commercial immunoassays
      6. Retrospective clinical evaluation of 4 lateral flow assays for the detection of SARS-CoV-2 IgG
      7. ARS-CoV-2 IgG antibody responses in New York City
      8. alse-positive SARS-CoV-2 serology in 3 children with Kawasaki disease
      9. Monitoring antibody response following SARS-CoV-2 infection: diagnostic efficiency of 4 automated immunoassays
      10. Optimized Pseudotyping Conditions for the SARS-COV-2 Spike Glycoprotein
  12. We will now create a shared bibliography for the entire class. Go through the search results that you have found and add articles to the class shared bibliography page.
    • Only add articles that are unique (everyone will be adding to the page and we do not want redundant articles)
    • Put review articles and primary research articles in their respective sections. If the article does not fit either of those two categories, place it in the other articles section.
    • Add the articles in APA format (re-find them in Google Scholar to easily obtain APA format, if necessary). Add your wiki signature to the end of the citation.
    • Ideally, each student will contribute 2-3 unique articles.
  13. Now that we have our shared bibliography, each student will be assigned one article. Record the citation for your article in APA format:
    • Liu, L., Wang, P., Nair, M. S., Yu, J., Rapp, M., Wang, Q., ... & Guo, X. V. (2020). Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature, 584(7821), 450-456.
    • In Web of Science, search for the specific article that you have been assigned.
      • How many cited references does that article have? (46)
      • How many articles have cited the article you have been assigned? (16)
  14. What are the relative merits of searching with Google Scholar, PubMed, and Web of Science? Name two advantages and disadvantages for each.
    • Google Scholar: vast information, clean organization of information
    • Google Scholar: broadness, lack of access to articles
    • PubMed: specific information available, accessible
    • Pubmed: difficult navigation of website and articles, difficult search words
    • Web of Science: Easy interface, specific sources
    • Web of Science: narrow and limited results, needs specific search word format
  15. What impact does choice of keywords have on your results?
    • Based on the type of information one is looking for, using and knowing the specific diction in the type of article you need helps filter relevant sources.
  16. For your Conclusion section, write a short reflection about what you learned by doing this exercise. Include in your answer what you knew previously about searching the biological literature, and what you learned that was new today.
    • In this assignment we learned and familiarized ourselves with multiple search engines and refined our abilities to source and look for relevant information. The outcome of this assignment is familiarity with article banks as well as comfort in learning and finding resources on any subject whenever it is deemed necessary in our academic or professional fields.

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