COVID-19 Pandemic
Genomic Epidemiology Reveals Multiple SARS-CoV-2 Introductions in a Long-Term Care Facility Outbreak Magdalena Dorvil-Joanem* Magdalena Dorvil-Joanem Jyoti Narayana Pamela Obodoechina Shoana M Anderson Emily J Gateley Jane Yackley
The COVID-19 pandemic significantly advanced whole genome sequencing (WGS) technologies and expanded the application of genomic epidemiology. Analyzing SARS-CoV-2 genomic data offers valuable insights into outbreaks, including viral introductions and transmission patterns. Combined with traditional epidemiological methods, this data enhances disease prevention and control strategies. This study examines SARS-CoV-2 genetic sequences from a COVID-19 outbreak in a long-term care facility (LTCF) in Tennessee.
Between December 2023 and January 2024, an LTCF experienced a COVID-19 outbreak involving 46 cases. Collaboration between outbreak response and genomic epidemiology teams facilitated timely specimen retrieval, sequencing, and analysis. Nine remnant SARS-CoV-2-positive specimens were sent to the state laboratory for WGS; seven were successfully sequenced. Lineage assignment using Pangolin and GISAID databases, followed by NextStrain phylogenetic analysis, revealed two distinct SARS-CoV-2 lineages circulating during the outbreak.
Four cases belonged to the HV.1 parent lineage, including three from sublineage EG.5.1.6, while three cases were associated with the JN.1 parent lineage, all from sublineage JN.1.8.1. The presence of two lineages indicates multiple virus introductions rather than a single-source transmission event. These findings align with the lineages circulating in the surrounding community, underscoring the role of community transmission in seeding LTCF outbreaks.
This study emphasizes the critical role of integrating genomic surveillance with public health measures to manage outbreaks in high-risk settings like LTCFs. Combining genomic and epidemiological data clarified transmission dynamics and informed interventions such as testing, patient cohorting, and infection control measures. Limited sample availability remains a challenge, highlighting the need for active surveillance and robust support systems to enhance data collection. Continuous genomic monitoring is essential for providing insights into outbreak responses and enabling LTCFs to adapt effectively as SARS-CoV-2 reporting guidelines evolve.