2021 Project: Johns Hopkins University

SARS-CoV-2 genome: viral evolution as a factor of sustained community transmission and prolonged infection

What to know

Johns Hopkins University provided real-time data describing the evolution of the SARS-CoV-2 virus in communities and individuals. Awarded in 2021, this study provided data to help identify whether changes in the SARS-CoV-2 genome meant a variant could spread more easily or make people sicker. Researchers used novel methods to study how the virus evolves.

Decorative image with words "2021" and "SARS-CoV-2"

Findings on SARS-CoV-2 surveillance and investigations

This project:

  • Implemented infection prevention policies to reduce the risk of SARS-CoV-2 transmission between patients and healthcare workers.1
  • Generated genomes that were used for SARS-CoV-2 genomic surveillance and contact tracing and that led to identification of the first cluster of the South African variant in the State of Maryland.2
  • Found that SARS-CoV-2 viruses carrying the spike protein mutation E484K were disproportionately prevalent among persons infected after full vaccination against COVID-19 compared with infected persons who were not fully vaccinated. 3
  • Identified clusters of transmission within Johns Hopkins Hospital (two studies)45

Findings on SARS-CoV-2 variant characteristics

This project found:

  • Compared with the Delta variant, the Omicron variant was more likely to cause breakthrough infections in vaccinated individuals, yet hospital admissions were less likely. 6
  • Certain viral variants or mutations were associated with breakthrough infection after vaccination. 7
  • In both vaccinated and unvaccinated persons, the Delta variant was associated with higher viral loads than the Alpha variant. 8
  • Prolonged infections, prolonged viral shedding, and viral reinfections were revealed by genomic surveillance. 9
  • SARS-CoV-2 genomic diversity was reported over time in the National Capital Region as well as differences in clinical severity among lineages. 10
  • The Delta variant was associated with more severe disease in hospitalized patients. 11
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Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)
  1. Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) exposure investigations using genomic sequencing among healthcare workers and patients in a large academic center. Infect Control Hosp Epidemiol, 2022.
  2. Linked Clusters of SARS-CoV-2 Variant B.1.351 - Maryland, January-February 2021 MMWR Morb Mortal Wkly Rep. 2021 Apr 30;70(17):627-631. doi: 10.15585/mmwr.mm7017a5
  3. Association of E484K Spike Protein Mutation With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Vaccinated Persons: Maryland, January-May 2021. Clin Infect Dis. 2022 Jun 10;74(11):2053-2056. doi: 10.1093/cid/ciab762.
  4. Transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2), delta variant, between two fully vaccinated healthcare personnel. Infect Control Hosp Epidemiol. 2022 Dec;43(12):1983-1985. doi: 10.1017/ice.2021.469. Epub 2021 Nov 8.
  5. Clustering of SARS-CoV-2 Infections in Households of Patients Diagnosed in the Outpatient Setting in Baltimore, Maryland. Open Forum Infect Dis. 2021 Mar 12;8(4):ofab121. doi: 10.1093/ofid/ofab121. eCollection 2021 Apr.
  6. The displacement of the SARS-CoV-2 variant Delta with Omicron: An investigation of hospital admissions and upper respiratory viral loads. eBioMedicine, 2022.
  7. Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels. J Clin Virol, 2022
  8. Infection With the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta Variant Is Associated With Higher Recovery of Infectious Virus Compared to the Alpha Variant in Both Unvaccinated and Vaccinated Individuals. Clin Infect Dis, 2021.
  9. Large Scale SARS-CoV-2 Molecular Testing and Genomic Surveillance Reveal Prolonged Infections, Protracted RNA shedding, and Viral Reinfections. Front Cell Infect Microbiol, 2022.
  10. An Update on SARS-CoV-2 Diversity in the United States National Capital Region: Evolution of Novel and Variants of Concern. Clin Infect Dis, 2022.
  11. Impact of SARS-CoV-2 variants on inpatient clinical outcome. medRxiv, 2022.