Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory.

Neta Zuckerman,Rakefet Pando,Ella Mendelson,Yaron Drori,Michal Mandelboim,Orna Mor,Oran Erster,Efrat Bucris,Yaniv Lustig

doi:10.3390/v12080854

Neta Zuckerman, Rakefet Pando + Show 7 more

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https://doi.org/10.3390/v12080854

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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 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 SARS-CoV-2 negative real time polymerase chain reaction (PCR) of work surfaces swipe tests. 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 and 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, distancing and mask wearing in preventing SARS-CoV-2 spread, specifically in healthcare facilities.

Highlights

This study demonstrates the added value of molecular epidemiology based on complete viral genomes in elucidating person-to-person transmission, reveals silent infections in non-symptomatic Israel’s central virology laboratory (ICVL) staff members via serology testing and confirms that the strict safety regulations observed in ICVL most likely prevented further spread of the virus
Following confirmed SARS-CoV-2 in ICVL staff member S1, SARS-CoV-2 specific qRT-polymerase chain reaction (PCR) assays were conducted for all ICVL staff and relevant family members on March 15, 2020 and on the day
Two additional staff members tested positive for SARS-CoV-2 (Table 2)—S2, with a relatively high cycle threshold (Ct) (Ct = 33.07) and S3 with a much lower Ct (Ct = 18.77)

Summary

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 and current lack of vaccination and effective therapeutic options [3,7].Major SARS-CoV-2 worldwide clades have been proposed by nomenclature systems includingNextstrain [8] and the global initiative on sharing all influenza data (GISAID, https://www.gisaid.org) [9].These are based on viral genomes from >57,000 sequences submitted in GISAID [9]. 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 and current lack of vaccination and effective therapeutic options [3,7]. Viruses 2020, 12, 854 using Nextstrain’s nomenclature, there are currently five major clades: 19A (the root clade) and 19B, and clades 20A, B and C that are widespread in Europe and include a mutation in the spike protein, D614G, that is associated with increased infectivity and higher viral loads [10].

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