Difference between revisions of "Journal:Comprehensive analyses of SARS-CoV-2 transmission in a public health virology laboratory"

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|title_full  = Comprehensive analyses of SARS-CoV-2 transmission in a public health virology laboratory
|title_full  = Comprehensive analyses of SARS-CoV-2 transmission in a public health virology laboratory
|journal      = ''Viruses''
|journal      = ''Viruses''
|authors      = Zuckerman, Neta S.; Pando, Rakafet; Bucris, Efrat; Drori, Yaron; Lustig, Yaniv; Erster, Oran; Mor, Orna; Mendelson, Ella; Mandelboim, Michael
|authors      = Zuckerman, Neta S.; Pando, Rakafet; Bucris, Efrat; Drori, Yaron; Lustig, Yaniv; Erster, Oran;<br />Mor, Orna; Mendelson, Ella; Mandelboim, Michael
|affiliations = Chaim Sheba Medical Center, Israel Ministry of Health, Tel-Aviv University
|affiliations = Chaim Sheba Medical Center, Israel Ministry of Health, Tel-Aviv University
|contact      = Email: michalman at sheba dot health dot gov dot il
|contact      = Email: michalman at sheba dot health dot gov dot il
Line 27: Line 27:


==Abstract==
==Abstract==
[[SARS-CoV-2]] has become a major global concern as of December 2019, particularly affecting healthcare workers. As person-to-person transmission is airborne, crowded closed spaces have had high potential for rapid virus spread, especially early in the [[pandemic]] when social distancing and mask wearing were not mandatory. This retrospective study thoroughly investigates a small-scale SARS-CoV-2 outbreak in Israel’s central virology laboratory (ICVL) in mid-March 2020, in which six staff members and two related family members were infected. Suspicions regarding infection by contaminated surfaces in ICVL facilities were nullified by the negative results of a SARS-CoV-2 [[Polymerase chain reaction#Variations|real-time polymerase chain reaction]] (qPCR) analysis of swiped work surface samples. Complete SARS-CoV-2 [[Genomics|genomes]] were [[Sequencing|sequenced]], and mutation analyses showed inclusion of all samples to clades 20B and 20C, possessing the spike mutation D614G. Phylogenetic analysis clarified transmission events, confirming S1 as having infected at least three other staff members while refuting the association of a staff member’s infected spouse with the ICVL transmission cluster. Finally, serology tests exhibited IgG and IgA antibodies in all infected individuals and revealed the occurrence of asymptomatic infections in additional staff members. This study demonstrates the advantages of molecular [[epidemiology]] in elucidating transmission events and exemplifies the importance of good [[laboratory]] practice, physical distancing, and mask wearing in preventing SARS-CoV-2 spread, specifically in healthcare facilities.
[[SARS-CoV-2]] has become a major global concern as of December 2019, particularly affecting healthcare workers. As person-to-person transmission is airborne, crowded closed spaces have had high potential for rapid virus spread, especially early in the [[pandemic]] when social distancing and mask wearing were not mandatory. This retrospective study thoroughly investigates a small-scale SARS-CoV-2 outbreak in Israel’s central virology laboratory (ICVL) in mid-March 2020, in which six staff members and two related family members were infected. Suspicions regarding infection by contaminated surfaces in ICVL facilities were nullified by the negative results of a SARS-CoV-2 [[Polymerase chain reaction#Variations|real-time polymerase chain reaction]] (qPCR) analysis of swiped work surface samples. Complete SARS-CoV-2 [[Genomics|genomes]] were [[Sequencing|sequenced]], and mutation analyses showed inclusion of all samples to [[Wikipedia:Clade|clades]] 20B and 20C, possessing the spike mutation D614G. Phylogenetic analysis clarified transmission events, confirming S1 as having infected at least three other staff members while refuting the association of a staff member’s infected spouse with the ICVL transmission cluster. Finally, serology tests exhibited IgG and IgA antibodies in all infected individuals and revealed the occurrence of asymptomatic infections in additional staff members. This study demonstrates the advantages of molecular [[epidemiology]] in elucidating transmission events and exemplifies the importance of good [[laboratory]] practice, physical distancing, and mask wearing in preventing SARS-CoV-2 spread, specifically in healthcare facilities.


'''Keywords''': 2019-nCoV, SARS-CoV-2, COVID-19, staff, infection, next generation sequencing (NGS)
'''Keywords''': 2019-nCoV, SARS-CoV-2, COVID-19, staff, infection, next generation sequencing (NGS)


==Introduction==
==Introduction==
 
[[SARS-CoV-2]] (severe acute respiratory syndrome coronavirus 2) is a novel [[coronavirus]] that emerged in Wuhan, China in December 2019<ref name="LuOut20">{{cite journal |title=Outbreak of pneumonia of unknown etiology in Wuhan, China: The mystery and the miracle |journal=Journal of Medical Virology |author=Lu, H.; Stratton, C.W.; Tang, Y.-W. |volume=92 |issue=4 |pages=401–2 |year=2020 |doi=10.1002/jmv.25678 |pmid=31950516 |pmc=PMC7166628}}</ref> and has rapidly spread across China and to many countries worldwide, causing severe respiratory disease leading to substantial morbidity and mortality.<ref name="LiEarly20">{{cite journal |title=Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia |journal=The New England Journal of Medicine |author=Li, Q.; Guan, X.; Wu, P. et al. |year=2020 |doi=10.1056/NEJMoa2001316 |pmid=31995857}}</ref><ref name="WangANovel20">{{cite journal |title=A novel coronavirus outbreak of global health concern |journal=Lancet |author=Wang, C.; Horby, P.W.; Hayden, F.G. et al. |volume=395 |issue=10223 |pages=470–73 |year=2020 |doi=10.1016/S0140-6736(20)30185-9 |pmid=31986257 |pmc=PMC7135038}}</ref><ref name="HolshueFirst20">{{cite journal |title=First Case of 2019 Novel Coronavirus in the United States |journal=New England Journal of Medicine |author=Holshue, M.L.; DeBolt, C.; Lindquist, S. et al. |volume=382 |issue=10 |pages=929–36 |year=2020 |doi=10.1056/NEJMoa2001191 |pmid=32004427 |pmc=PMC7092802}}</ref><ref name="BajemaPersons20">{{cite journal |title=Persons Evaluated for 2019 Novel Coronavirus - United States, January 2020 |journal=Morbidity and Mortality Weekly Report |author=Bajema, K.L.; Oster, A.M.; McGovern, O.L. et al. |volume=69 |issue=6 |pages=166–70 |year=2020 |doi=10.15585/mmwr.mm6906e1 |pmid=32053579 |pmc=PMC7017962}}</ref><ref name="CDCCOVIDView">{{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/covid-data/covidview/index.html |title=COVIDView: A Weekly Surveillance Summary of U.S. COVID-19 Activity |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |accessdate=03 July 2020}}</ref> This novel virus is a potential threat to human health worldwide and a major global health concern due to person-to-person transmission, a current lack of vaccination, and a lack of effective therapeutic options.<ref name="WangANovel20" /><ref name="WHOCorona">{{cite web |url=https://www.euro.who.int/en/health-topics/health-emergencies/coronavirus-covid-19/novel-coronavirus-2019-ncov |title=Coronavirus disease (COVID-19) pandemic |author=World Health Organization |publisher=World Health Organization |accessdate=15 July 2020}}</ref> Major SARS-CoV-2 worldwide [[Wikipedia:Clade|clades]] have been proposed by nomenclature systems, including Nextstrain<ref name="HadfieldNextstrain18">{{cite journal |title=Nextstrain: Real-time tracking of pathogen evolution |journal=Bioinformatics |author=Hadfield, J.; Megill, C.; Bell, S.M. et al. |volume=34 |issue=23 |pages=4121-4123 |year=2018 |doi=10.1093/bioinformatics/bty407 |pmid=29790939 |pmc=PMC6247931}}</ref> and the Global Initiative on Sharing All Influenza Data (GISAID).<ref name="ElbeData17">{{cite journal |title=Data, disease and diplomacy: GISAID's innovative contribution to global health |journal=Global Challenges |author=Elbe, S.; Buckland-Merrett, G. |volume=1 |issue=1 |pages=33–46 |year=2017 |doi=10.1002/gch2.1018 |pmid=31565258 |pmc=PMC6607375}}</ref> These are based on viral genomes from >57,000 sequences submitted in GISAID.<ref name="ElbeData17" /> For example, using Nextstrain’s nomenclature, there are currently five major clades: 19A (the root clade) and 19B, and clades 20A, B, and C. These are widespread in Europe and include a mutation in the spike protein, D614G, that is associated with increased infectivity and higher viral loads.<ref name="KorberTracking20">{{cite journal |title=Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus |journal=Cell |author=Korber, B.; Fischer, W.M.; Gnanakaran, S. et al. |volume=S0092-8674 |issue=20 |pages=30820-5 |year=2020 |doi=10.1016/j.cell.2020.06.043 |pmid=32697968 |pmc=PMC7332439}}</ref>




Revision as of 18:37, 17 August 2020

Full article title Comprehensive analyses of SARS-CoV-2 transmission in a public health virology laboratory
Journal Viruses
Author(s) Zuckerman, Neta S.; Pando, Rakafet; Bucris, Efrat; Drori, Yaron; Lustig, Yaniv; Erster, Oran;
Mor, Orna; Mendelson, Ella; Mandelboim, Michael
Author affiliation(s) Chaim Sheba Medical Center, Israel Ministry of Health, Tel-Aviv University
Primary contact Email: michalman at sheba dot health dot gov dot il
Year published 2020
Volume and issue 12(8)
Article # 854
DOI 10.3390/v12080854
ISSN 1999-4915
Distribution license Creative Commons Attribution 4.0 International
Website https://www.mdpi.com/1999-4915/12/8/854/htm
Download https://www.mdpi.com/1999-4915/12/8/854/pdf (PDF)
Emblem-important-yellow.svg This article should be considered a work in progress and incomplete. Consider this article incomplete until this notice is removed.

Abstract

SARS-CoV-2 has become a major global concern as of December 2019, particularly affecting healthcare workers. As person-to-person transmission is airborne, crowded closed spaces have had high potential for rapid virus spread, especially early in the pandemic when social distancing and mask wearing were not mandatory. This retrospective study thoroughly investigates a small-scale SARS-CoV-2 outbreak in Israel’s central virology laboratory (ICVL) in mid-March 2020, in which six staff members and two related family members were infected. Suspicions regarding infection by contaminated surfaces in ICVL facilities were nullified by the negative results of a SARS-CoV-2 real-time polymerase chain reaction (qPCR) analysis of swiped work surface samples. Complete SARS-CoV-2 genomes were sequenced, and mutation analyses showed inclusion of all samples to clades 20B and 20C, possessing the spike mutation D614G. Phylogenetic analysis clarified transmission events, confirming S1 as having infected at least three other staff members while refuting the association of a staff member’s infected spouse with the ICVL transmission cluster. Finally, serology tests exhibited IgG and IgA antibodies in all infected individuals and revealed the occurrence of asymptomatic infections in additional staff members. This study demonstrates the advantages of molecular epidemiology in elucidating transmission events and exemplifies the importance of good laboratory practice, physical distancing, and mask wearing in preventing SARS-CoV-2 spread, specifically in healthcare facilities.

Keywords: 2019-nCoV, SARS-CoV-2, COVID-19, staff, infection, next generation sequencing (NGS)

Introduction

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel coronavirus that emerged in Wuhan, China in December 2019[1] and has rapidly spread across China and to many countries worldwide, causing severe respiratory disease leading to substantial morbidity and mortality.[2][3][4][5][6] This novel virus is a potential threat to human health worldwide and a major global health concern due to person-to-person transmission, a current lack of vaccination, and a lack of effective therapeutic options.[3][7] Major SARS-CoV-2 worldwide clades have been proposed by nomenclature systems, including Nextstrain[8] and the Global Initiative on Sharing All Influenza Data (GISAID).[9] These are based on viral genomes from >57,000 sequences submitted in GISAID.[9] For example, using Nextstrain’s nomenclature, there are currently five major clades: 19A (the root clade) and 19B, and clades 20A, B, and C. These are widespread in Europe and include a mutation in the spike protein, D614G, that is associated with increased infectivity and higher viral loads.[10]


References

  1. ↑ Lu, H.; Stratton, C.W.; Tang, Y.-W. (2020). "Outbreak of pneumonia of unknown etiology in Wuhan, China: The mystery and the miracle". Journal of Medical Virology 92 (4): 401–2. doi:10.1002/jmv.25678. PMC PMC7166628. PMID 31950516. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166628. 
  2. ↑ Li, Q.; Guan, X.; Wu, P. et al. (2020). "Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia". The New England Journal of Medicine. doi:10.1056/NEJMoa2001316. PMID 31995857. 
  3. ↑ 3.0 3.1 Wang, C.; Horby, P.W.; Hayden, F.G. et al. (2020). "A novel coronavirus outbreak of global health concern". Lancet 395 (10223): 470–73. doi:10.1016/S0140-6736(20)30185-9. PMC PMC7135038. PMID 31986257. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7135038. 
  4. ↑ Holshue, M.L.; DeBolt, C.; Lindquist, S. et al. (2020). "First Case of 2019 Novel Coronavirus in the United States". New England Journal of Medicine 382 (10): 929–36. doi:10.1056/NEJMoa2001191. PMC PMC7092802. PMID 32004427. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092802. 
  5. ↑ Bajema, K.L.; Oster, A.M.; McGovern, O.L. et al. (2020). "Persons Evaluated for 2019 Novel Coronavirus - United States, January 2020". Morbidity and Mortality Weekly Report 69 (6): 166–70. doi:10.15585/mmwr.mm6906e1. PMC PMC7017962. PMID 32053579. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017962. 
  6. ↑ Centers for Disease Control and Prevention. "COVIDView: A Weekly Surveillance Summary of U.S. COVID-19 Activity". Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-ncov/covid-data/covidview/index.html. Retrieved 03 July 2020. 
  7. ↑ World Health Organization. "Coronavirus disease (COVID-19) pandemic". World Health Organization. https://www.euro.who.int/en/health-topics/health-emergencies/coronavirus-covid-19/novel-coronavirus-2019-ncov. Retrieved 15 July 2020. 
  8. ↑ Hadfield, J.; Megill, C.; Bell, S.M. et al. (2018). "Nextstrain: Real-time tracking of pathogen evolution". Bioinformatics 34 (23): 4121-4123. doi:10.1093/bioinformatics/bty407. PMC PMC6247931. PMID 29790939. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247931. 
  9. ↑ 9.0 9.1 Elbe, S.; Buckland-Merrett, G. (2017). "Data, disease and diplomacy: GISAID's innovative contribution to global health". Global Challenges 1 (1): 33–46. doi:10.1002/gch2.1018. PMC PMC6607375. PMID 31565258. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6607375. 
  10. ↑ Korber, B.; Fischer, W.M.; Gnanakaran, S. et al. (2020). "Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus". Cell S0092-8674 (20): 30820-5. doi:10.1016/j.cell.2020.06.043. PMC PMC7332439. PMID 32697968. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7332439. 

Notes

This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added.

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