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Bulletin references July 2020

A full list of references for each article is available below.

  • Page 117 – COVID-19: a new plague year
  • Page 118 – The role of viral genomics in shaping the response to the COVID-19 pandemic
  • Page 121 – Nightingale tales
  • Page 125 – Cytology and the COVID-19 pandemic
  • Page 126 – Establishing convalescent plasma as an effective therapy
  • Page 128 – Healthcare scientists in pathology: the challenges of responding to the virus
  • Page 130 – Death certification: lessons learned within the hospital setting
  • Page 133 – A chaplaincy view from a multi-faith university hospital community
  • Page 141 – The journey to pathology 3.0: more on ‘bricks’ and ‘clicks’
  • Page 159 – Creating e-learning modules for undergraduate medical students
  • Page 160 – Digital pathology validation for trainees: the good, the bad and the ugly
  • Page 163 – Antibiotic prescribing following a positive Clostridioides difficile result
  • Page 179 – LETTER: Reporting of race in autopsy reports – time to review?

You can download a copy of the July 2020 Bulletin from our Bulletin pages.  

Page 117 – COVID-19: a new plague year

  1. World Health Organization. Novel coronavirus (2019-nCov). Situation Report − 1. Published 21 January 2020. Available at: www.who.int/docs/default-source/coronaviruse/situation-reports/20200121-sitrep-1-2019-ncov.pdf?sfvrsn=20a99c10_4
  2. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med 2020;382:727–733.
  3. BBC News. Coronavirus: Latest patient was first to be infected in UK. Available at: www.bbc.co.uk/news/uk-51683428
  4. World Health Organisation. Coronavirus disease 2019 (COVID-19). Situation Report – 51. Available at: www.who.int/docs/default-source/coronaviruse/situation-reports/20200311-sitrep-51-covid-19.pdf?sfvrsn=1ba62e57_10
  5. BBC News. Coronavirus: Two cases confirmed in UK. Available at: www.bbc.co.uk/news/health-51325192
  6. Gov.uk. Coronavirus (COVID-19) in the UK. Available at: https://coronavirus.data.gov.uk/
  7. Dong N, Yang X, Ye L, Chen K, Chan EW-C, Yang M et al. Genomic and protein structure modelling analysis depicts the origin and infectivity of 2019-nCoV, a new coronavirus which caused a pneumonia outbreak in Wuhan, China. bioRxiv 2020;doi:10.1101/2020.01.20.913368. Available at: http://biorxiv.org/lookup/doi/10.1101/2020.01.20.913368
  8. BBC News. Coronavirus: Scientists brand 5G claims ‘complete rubbish’. Available at: www.bbc.co.uk/news/52168096
  9. Kirkcaldy RD, King BA, Brooks JT. COVID-19 and Postinfection Immunity: Limited Evidence, Many Remaining Questions. JAMA 2020;doi:10.1001/jama.2020.7869. Available at: https://jamanetwork.com/journals/jama/fullarticle/2766097
  10. The Guardian. What was Exercise Cygnus and what did it find? Available at: www.theguardian.com/world/2020/may/07/what-was-exercise-cygnus-and-what-did-it-find  

Page 118 – The role of viral genomics in shaping the response to the COVID-19 pandemic

  1. Wu F, Zhao S, Yu B, Chen Y-M, Wang W, Song Z-G et al. A new coronavirus associated with human respiratory disease in China. Nature2020;579:265–269. Available at: www.nature.com/articles/s41586-020-2008-3
  2. Shu Y, McCauley J. GISAID: Global initiative on sharing all influenza data – from vision to reality. Eurosurveillance 2017;22:30494. Available at: www.eurosurveillance.org/ViewArticle.aspx?ArticleId=22750
  3. Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance 2020;25:3. Available at: www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.3.2000045
  4. Next Strain. Novel coronavirus. Accessed 13 May 2020. Available at: www.nextstrain.org
  5. Rambaut A, Holmes EC, Hill V, O’Toole Á, McCrone JT, Ruis C et al. A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology. bioRxiv 2020;2020.04.17.046086. Available at: http://biorxiv.org/content/early/2020/04/19/2020.04.17.046086.abstract
  6. Lau SKP, Woo PCY, Li KSM, Huang Y, Tsoi H-W, Wong BHL et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci USA 2005;102:14040–14045. Available at: www.pnas.org/cgi/doi/10.1073/pnas.0506735102
  7. Menachery VD, Yount BL, Debbink K, Agnihothram S, Gralinski LE, Plante JA et al. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat Med 2015;21:1508–1513. Available at: www.nature.com/articles/nm.3985
  8. Wang N, Li S-Y, Yang X-L, Huang H-M, Zhang Y-J, Guo H et al. Serological Evidence of Bat SARS-Related Coronavirus Infection in Humans, China. Virol Sin 2018;33:104–107. Available at: http://link.springer.com/10.1007/s12250-018-0012-7
  9. Hoffmann M, Kleine-Weber H, Schroeder S, Kruger N, Herrler T, Erichsen S et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell 2020;181:271−280.e8. 
  10. Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L, Zhang W et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020;579: 270–273. Available at: www.nature.com/articles/s41586-020-2012-7
  11. Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med 2020;26:450–452. Available at: www.nature.com/articles/s41591-020-0820-9
  12. Zhou H, Chen X, Hu T, Li J, Song H, Liu Y et al. A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19. Curr Biol 2020;30:2196–2203. Available at: https://doi.org/10.1016/j.cub.2020.05.023
  13. Sun X, Belser JA, Tumpey TM. A novel eight amino acid insertion contributes to the hemagglutinin cleavability and the virulence of a highly pathogenic avian influenza A (H7N3) virus in mice. Virology 2016;488:120–128. Available at: https://linkinghub.elsevier.com/retrieve/pii/S0042682215004602
  14. Zhang Y-Z, Holmes EC. A Genomic Perspective on the Origin and Emergence of SARS-CoV-2. Cell 2020;181:223–227. Available at: https://linkinghub.elsevier.com/retrieve/pii/S0092867420303287
  15. Liu P, Jiang J-Z, Wan X-F, Hua Y, Li L, Zhou J et al. Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)?PLOS Pathog 2020;16:e1008421. Available at: https://dx.plos.org/10.1371/journal.ppat.1008421
  16. Shi J, Wen Z, Zhong G, Yang H, Wang C, Huang B et al. Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS–coronavirus 2. Science 2020;eabb7015. Available at: www.sciencemag.org/lookup/doi/10.1126/science.abb7015
  17. Oreshkova N, Molenaar RJ, Vreman S, Harders F, Munnink BBO , Hakze-van der Honing RW et al. SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020. Eurosurveillance 2020;25:pii=2001005. Available at: www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.23.2001005
  18. Bedford Lab. Cryptic transmission of novel coronavirus revealed by genomic epidemiology. Accessed 13 May. Available at:https://bedford.io/blog/ncov-cryptic-transmission
  19. Hodcroft EB. Preliminary case report on the SARS-CoV-2 cluster in the UK, France, and Spain. Swiss Med Wkly 2020;150:w20212. Available at: https://doi.emh.ch/smw.2020.20212
  20. Pung R, Chiew CJ, Young BE, Chin S, Chen MI-C, Clapham HE et al. Investigation of three clusters of COVID-19 in Singapore: implications for surveillance and response measures. The Lancet 2020;395:1039–1046. Available at: https://linkinghub.elsevier.com/retrieve/pii/S0140673620305286
  21. Arons MM, Hatfield KM, Reddy SC, Kimball A, James A, Jacobs JR et al. Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility. N Engl J Med 2020;382:2081−2090. Available at: www.nejm.org/doi/10.1056/NEJMoa2008457
  22. COVID-19 Genomics UK (COG-UK). Consortium Report #8 – 11 June 2020. Available at: www.cogconsortium.uk/wp-content/uploads/2020/06/11th-June-2020-Report-COVID-19-Genomics-UK-COG-UK-Consortium.pdf
  23. Artesi M, Bontems S, Gobbels P, Franckh M, Boreux R, Meex C et al. Failure of the cobas® SARS-CoV-2 (Roche) E-gene assay is associated with a C-to-T transition at position 26340 of the SARS-CoV-2 genome. medRxiv 2020; doi:10.1101/2020.04.28.20083337. Available at: http://medrxiv.org/content/early/2020/05/03/2020.04.28.20083337.abstract
  24. Davidson AD, Williamson MK, Lewis S, Shoemark D, Carroll MW, Heesom K et al. Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site. bioRxiv 2020; doi:10.1101/2020.03.22.002204 Available at: http://biorxiv.org/content/early/2020/03/24/2020.03.22.002204.abstract
  25. Vogels CBF, Brito AF, Wyllie AL, Fauver JR, Ott IM, Kalinich CC et al. Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR primer-probe sets. medRxiv 2020; doi:10.1101/2020.03.30.20048108. Available at: http://medrxiv.org/content/early/2020/04/26/2020.03.30.20048108.abstract
  26. Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W et al. Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2. bioRxiv 2020; doi:10.1101/2020.04.29.069054. Available at: http://biorxiv.org/content/early/2020/04/30/2020.04.29.069054.abstract  

Page 121 – Nightingale tales

Table 1: 

Test
Samples required per patient per day
Samples required per patient per week
Tests per request 
Tests per 1000 patients per week
Arterial Blood Gas (ABG)
6
42
POCT on site
42,000
Full Blood Count (FBC)
1
7
1
7000
Urea and electrolytes 
1
7
4
28000
Magnesium
1
7
1
7000
Clotting
1
7
3
21000
CRP
 
3
1
3000
Liver function tests
 
3
4
12000
Troponin
 
3
1
3000
d-dimer
 
3
1
3000
ferritin
 
3
1
3000
Bone profile
 
3
3
9000
Cross match
 
 
1
3000
Blood Culture
 
2
2 bottles
2000 (4000 bottles)* 
Urine
 
2
1
2000
Sputum/BAL
 
2
1
2000
Misc
 
1
1
1000
HIV
Required preadmission. 

* Blood culture standard for adults is 2 bottles incubated for 5 days. Incubator capacity required for 1000 patients approx. 15000. It was agreed due to the nature of the patient group and likely organisms only an aerobic bottle would be used and cultured for 3 days. Reducing blood culture incubator capacity to approx. 1000.  

Page 125 – Cytology and the COVID-19 pandemic

  1. Pambuccian S. The COVID-19 pandemic: implications for the cytology laboratory. J Am Soc Cytopathol2020;9:202−211.
  2. Royal College of Pathologists. Coronavirus: COVID-19 resources hub. Available at: www.rcpath.org/profession/coronavirus-resource-hub.html
  3. Rossi ED, Fadda G, Mule A, Zannoni GF, Rindi G. Cytologic and histologic samples from patients infected by the novel coronavirus 2019 SARS-CoV-2: An Italian institutional experience focusing on biosafety procedures. Cancer Cytopathol 2020;128:317−320.
  4. Madrigal E. Going remote: Maintaining normalcy in our pathology laboratory during the COVD-19 pandemic. Cancer Cytopathol 2020;128:321−322. 

Page 126 – Establishing convalescent plasma as an effective therapy

  1. Guan WJ, Ni ZY, Hu Y, Liang WH, Ou CQ, He JX et al. for the China Medical Treatment Expert Group for Covid-19. Clinical Characteristics of Coronavirus Disease 2019 in China. N Engl J Med 2020;382:1708−1720. 
  2. Berlin DA, Gulick RM, Martinez FJ. Severe Covid-19. N Engl J Med 15 May 2020; DOI:10.1056/NEJMcp2009575.
  3. Luke TC, Kilbane EM, Jackson JL, Hoffman SL . Meta-Analysis: Convalescent Blood Products for Spanish Influenza Pneumonia: A Future H5N1 Treatment? Ann Intern Med 2006;145:599−609.
  4. Mair-Jenkins J, Saavedra-Campos M, Baillie JK, Cleary P, Khaw F-M, Lim WS et al. The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis. J Infect Dis 2015;211:80−90.
  5. Valk S, Piechotta V, Chai K et al. Convalescent plasma or hyperimmune immunoglobulin for people with COVID-19: a rapid review. Cochrane Database Syst Rev 2020;5:CD013600.
  6. Joyner M, Scott Wright R, Fairweather D, Senefeld J, Bruno K, Klassen S et al. Early Indicators of Safety of Convaescent Plasma in COVID-19 in 5,000 patients. medRxiv 2020:DOI:10.1101/2020.05.12.20099879.
  7. Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell2020;181:271−280. 

Page 128 – Healthcare scientists in pathology: the challenges of responding to the virus

  1. Crook D, Adams E, Ainsworth M, Anand R, Andersson MI, Auckland M et al. Evaluation of antibody testing for SARS-CoV-2 using ELISA and lateral flow immunoassays. Available at: www.medrxiv.org/content/10.1101/2020.04.15.20066407v1.full.pdf 

Page 130 – Death certification: lessons learned within the hospital setting

  1. Coronavirus Act. Excess death provisions: information and guidance for medical practitioners. 31 March 2020.
  2. Public Health England. PHE data series on deaths in people with COVID-19: technical summary. Summary of the PHE data series on deaths in people with COVID-19, outlining what the changes mean and how the data compare to other COVID-19 death data series. Published 29 April 2020. Available at: www.gov.uk/government/publications/phe-data-series-on-deaths-in-people-with-covid-19-technical-summary
  3. Office for National Statistics. Guidance for doctors completing Medical Certificates of Cause of Death in England and Wales. F66 Guidance. 2020. Available at: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/877302/guidance-for-doctors-completing-medical-certificates-of-cause-of-death-covid-19.pdf
  4. Ministry of Justice. Revised guidance for registered medical practitioners on the Notification of Deaths Regulations. March 2020. Available at: www.gov.uk/government/publications/notification-of-deaths-regulations-2019-guidance
  5. Chief Coroner. Chief Coroner’s Guidance on COVID-19. Published 26 March 2020. Available at: www.judiciary.uk/wp-content/uploads/2020/03/Chief-Coroner-Guidance-No.-34-COVID-19_26_March_2020-.pdf
  6. Chief Coroner. Chief Coroner’s Guidance No. 37. COVID-19 deaths and possible exposure in the workplace.Published 28 April 2020. Available at: judiciary.uk/wp-content/uploads/2020/04/Chief-Coroners-Guidance-No-37-28.04.20.pdf
  7. Ministry of Justice. The Cremation (England and Wales) Regulations 2008. Revised guidance for medical practitioners completing form cremation 4. Updated 3 April 2020. Available at: www.gov.uk/government/publications/medical-practitioners-guidance-on-completing-cremation-forms 

Page 133 – A chaplaincy view from a multi-faith university hospital community

  1. Davie K. Blinking Red: 25 Missed pandemic Warning Signs. 17 April 2020. Available at: www.genengnews.com/a-lists/blinking-red-25-missed-pandemic-warning-signs 

Page 141 – The journey to pathology 3.0: more on ‘bricks’ and ‘clicks’

  1. Cancer Research UK. Testing Times to Come. London, UK: CRC UK; 2016.
  2. The Royal College of Pathologists. Meeting pathology demand: Histopathology workforce census 17/18. London, UK: RCPath, 2018. Available at: www.rcpath.org/profession/workforce-planning/our-workforce-research/histopathology-workforce-survey-2018.html
  3. Metter DM, Colgan TJ, Leung ST, Timmons CF, Park JY. Trends in the US and Canadian Pathologist Workforces From 2007 to 2017. JAMA Netw Open 2019;2:e194337.
  4. Wilson ML, Fleming KA, Kuti MA, Looi LM, Lago N, Ru K. Access to pathology and laboratory medicine services: a crucial gap. The Lancet 2018;391:1927−1938.
  5. Jones JL, Oien KA, Lee JL, Salto-Tellez M. Morphomolecular pathology: setting the framework for a new generation of pathologists. Br J Cancer 2017;117:1581.
  6. Perunovic B, Hughes D. Moving cellular pathology from 'bricks' to 'clicks'. Bulletin of Royal College of Pathologists 2017;179:160−162.
  7. Zarella MD, Bowman D, Aeffner F, Farahani N, Xthona A, Absar SF et al. A Practical Guide to Whole Slide Imaging: A White Paper From the Digital Pathology Association. Arch Pathol Lab Med 2019;143:222−234.
  8. The Royal College of Pathologists. Best practice recommendations for implementing digital pathology. London, UK: Royal College of Pathologists, 2018. Available at: www.rcpath.org/profession/guidelines/specialty-specific-publications.html
  9. Williams BJ, Lee J, Oien KA, Treanor D. Digital pathology access and usage in the UK: results from a national survey on behalf of the National Cancer Research Institute's CM-Path initiative. J Clin Pathol2018;71:463−466.
  10. The Royal College of Pathologists. Guidance for remote reporting of digital pathology slides during periods of exceptional service pressure. RCPath, 2020. Available at: www.rcpath.org/profession/coronavirus-resource-hub.html
  11. NHS Improvement. Consolidated pathology network: Commercial structure and operational guide. 2018. Available at: https://improvement.nhs.uk/documents/2383/Operational_Governance_Guide_RE05.pdf
  12. Keeling L, Bury J, Perunovic B. Best of both worlds. Bulletin of the Royal College of Pathologists2018;184:257.
  13. The Royal College of Pathologists. Guidelines on staffing and workload for histopathology and cytopathology departments (5th edition) [Draft for consultation]. London, UK: RCPath, 2019.
  14. Royal College of Pathologists. Guidelines on staffing and workload for histopathology and cytopathology departments (4th edition). London, UK: RCPath, 2015.
  15. Retamero JA, Aneiros-Fernandez J, Del Moral RG. Complete Digital Pathology for Routine Histopathology Diagnosis in a Multicenter Hospital Network. Arch Pathol Lab Med 2020;144:221−228.
  16. Baidoshvili A, Bucur A, van Leeuwen J, van der Laak J, Kluin P, van Diest PJ. Evaluating the benefits of digital pathology implementation: time savings in laboratory logistics. Histopathology 2018;73:784−794.
  17. Nguyen BN, Dion N, Pomerol JF, Trudel D. Implementation of Digital Pathology for Primary Diagnosis at the CHUM. DPA 2019. Orlando, USA: Centre hospitalier de l'Universite de Montreal, 2019.
  18. Hanna MG, Reuter VE, Samboy J, England C, Corsale L, Fine SW et al. Implementation of Digital Pathology Offers Clinical and Operational Increase in Efficiency and Cost Savings. Arch Pathol Lab Med 2019;143:1545−1555.
  19. Stathonikos N, Nguyen TQ, Spoto CP, Verdaasdonk MAM, van Diest PJ. Being fully digital: perspective of a Dutch academic pathology laboratory. Histopathology 2019;75:621−635. 

Page 159 – Creating e-learning modules for undergraduate medical students

  1. Ruiz JG, Mintzer MJ, Leipzig RM. The impact of E-learning in medical education. Acad Med 2006;81:207−212. 

Page 160 – Digital pathology validation for trainees: the good, the bad and the ugly

  1. Williams BJ, Bottoms D, Treanor, D. Future-proofing pathology: the case for clinical adoption of digital pathology. J Clin Pathol 2017;70:1010−1018.
  2. Hirst A. Journey to the Center of the Digitization Dilemma: Can two guys in a garage really shake-up current thinking on the transition to digital pathology? The Pathologists, 2018. Accessed 15 July 2019. Available at: https://thepathologist.com/outside-the-lab/journey-to-the-center-of-the-digitization-dilemma
  3. Randell R, Ruddle RA, Treanor D. Barriers and facilitators to the introduction of digital pathology for diagnostic work. Stud Health Technol Inform 2015;216:443−447.
  4. Pantanowitz L, Sinard JH, Henricks WH, Fatheree LA, Carter AB., Contis L et al. Validating whole slide imaging for diagnostic purposes in pathology: guideline from the College of American Pathologists Pathology and Laboratory Quality Center. Arch Pathol Lab Med 2013;137:1710−1722.
  5. Cross S, Furness P, Igali L, Snead D, Treanor D. Best practice recommendations for implementing digital pathology. London, UK: The Royal College of Pathologists, 2018. Available at: www.rcpath.org/profession/guidelines/specialty-specific-publications.html
  6. Williams BJ, DaCosta P, Goacher E, Treanor D. A systematic analysis of discordant diagnoses in digital pathology compared with light microscopy. Arch Pathol Lab Med 2017;141:1712−1718. 

Page 163 – Antibiotic prescribing following a positive Clostridioides difficile result

  1. Department of Health and Health Protection Agency. Clostridium difficile infection: How to deal with the problem. Accessed January 2020. Available at: www.gov.uk/government/publications/clostridium-difficile-infection-how-to-deal-with-the-problem
  2. National Clostridium difficile Standards Group: Report to the Department of Health. J Hosp Infect 2004;56:1-38
  3. Davey P, Marwick CA, Scott CL, Charani E, McNeil K, Brown E et al. Interventions to improve antibiotic prescribing practices for hospital inpatients. Cochrane Database Syst Rev 2017;2.
  4. Pakyz AL, Moczygemba LR, VanderWielen LM, Edmond MB, Stevens MP, Kuzel AJ. Facilities and barriers to implementing antimicrobial stewardship strategies: Results from a qualitative study. Am J Infect Control 2014;42:257−263.
  5. Cruz-Rodriguez NC, Hernandez-Garcia R, Salinas-Caballero AG, Perez-Rodriguez E, Garza-Gonzalez E, Camacho-Ortiz A. The effect of pharmacy restriction on clindamycin on Clostridium difficile infection rates in an orthopedics ward. Am J Infect Control 2014;42:e71−73
  6. Hood K, Nuttall J, Gillespie D, Shepherd V, Wood F, Duncan D et al. Probiotics for Antibiotic-Associated Diarrhoea (PAAD): a prospective observational study of antibiotic-associated diarrhoea (including Clostridium difficile-associated diarrhoea) in care homes. Health Technol Assess 2014;18:1−63.
  7. Thomas C, Stevenson M, Riley TV. Antibiotics and hospital-acquired Clostridium difficile- associated diarrhoea: a systematic review. J Antimicrob Chemother 2003;51:1339−1350. 

Page 179 – LETTER: Reporting of race in autopsy reports – time to review?

  1. Rutherford A. How to argue with a racist. London, UK: Weidenfeld & Nicolson, 2020.