COVID-19ScientificRapid Detection of Asymptomatic SARS-CoV-2 in the Workforce Using the CosmosID-HUB COVID-19 Pipeline

6 June 2022by Dana Walsh0

As the COVID-19 pandemic continues, new and various SARS-CoV-2 variants have emerged, affecting morbidity, mortality and effectiveness of the initial COVID-19 vaccines. Despite the effectiveness of vaccines, cases have increased due to a combination of pandemic fatigue and  a sense of security in a growing number of vaccinated people. This puts unvaccinated health care workers at high risk of infection, which could in turn put them out of work. This in turn may contribute to the global shortage of health care workers. Under these circumstances, it is important to rapidly detect otherwise undocumented, asymptomatic COVID-19 cases, which accounts for 79% of transmission events. Testing both symptomatic and asymptomatic people has been useful during the course of the current pandemic. Additionally, SARS-CoV-2 infection has been described in fully vaccinated individuals, but not in asymptomatic vaccinated individuals. To fill the gap in the literature and find a rapid, effective screening program to identify asymptomatic cases in healthcare settings, Hijano et al. (2022) collected nasal swab samples from St. Jude Hospital employees. SARS-CoV-2 infection status in each sample was determined through PCR and 16 positive samples were sent for paired-end sequencing. Variants in samples were identified through the consensus analysis of sequences via the St. Jude Hospital’s internal computational COVID-19 pipeline and CosmosID’s commercial SARS-CoV-2 pipeline (for more information, please click here). Results are as follows:

  • A 14 month program detected 414 out of 820 (50.55%) COVID-19 cases
  • 152 of 414 healthcare workers tested positive for COVID-19 but remained asymptomatic
  • 16 of 152 employees tested positive for asymptomatic COVID-19
  • SARS-CoV-2 sequencing was attempted in 16 asymptomatic, vaccinated cases but achieved only in 4
  • Sequencing showed 3 of 16 asymptomatic & vaccinated workers were infected with B.1.1.7 lineage and 1 worker was infected with B.1.526
  • Distribution by age or race remained similar to those found by SARS-CoV-2 symptomatic PCR screening

Key Findings:

A routine SARS CoV-2 PCR-based, multicomponent COVID-19 screening and risk mitigation program is feasible, sustainable and can be adapted through the phases of the pandemic. It could be combined with sequencing methods and computational analysis for effective typing of the disease. Such a program may help curb the disease incidence, as well as granting institutions greater COVID-related decision-making power.

Hijano et al. 2022. An adaptive, asymptomatic SARS-CoV-2 workforce screening program providing real-time, actionable monitoring of the COVID-19 pandemic.

Dana Walsh

Dana Walsh is a microbiome scientist whose career has consisted of a blend of wet bench and computational research. Currently, she is a Microbiome Scientist for CosmosID where she helps clients with custom microbiome analysis and interpretation as well as exploring new tools and methods for microbiome studies. She applies cutting-edge tools to integrate multi-omics data, including taxonomic, functional, meta-transcriptomics and metabolomics data, in order to help clients derive meaning from their results. Her previous work has spanned a range of human microbiome areas and experimental models, from airway to vaginal to gut using cell, mouse, and human models. In her last role at Rebiotix she focused on the analysis and evaluation of complex microbiome data supporting the development of formulations for microbiome-based live biotherapeutic drugs. She completed a postdoctoral fellowship at Mayo Clinic in Rochester, Minnesota (USA), where she investigated the role of the microbiome in cancers of the reproductive tract, including ovarian and endometrial cancer. She received her PhD from the University of North Carolina in Chapel Hill, where she studied the impact of inhaled toxins on the airway microbiome in victims of burn and inhalation injury. In her free time she enjoys teaching Zumba classes and hanging out with her three dogs, 7 month old daughter, and husband on the beach! Fun fact: Dana has been to the top of Mount Kilimanjaro in Tanzania, Africa!

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