Comprehensive nationwide mapping of high-mortality SARS-CoV-2 outbreaks in nursing homes

In a recent study published in the Nature Aging Journal, researchers analyzed data from three SARS-CoV-2 outbreaks in nursing homes in Belgium with high case fatality rates (CFR, 209 to 35%) to identify the risk factors and determine the genetic signature of fatal disease post-coronavirus 2019 (COVID-19) following vaccination.

Study: Immunovirological and environmental screening reveals actionable risk factors for deadly COVID-19 in post-vaccination nursing home outbreaks. Image Credit: Ground Image/


The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak is associated with high mortality rates among nursing home residents, resulting from the effects of advanced age, frailty, comorbidities , polypharmacy and impaired immune function.

COVID-19 vaccines have conferred immunity to all individuals, including the elderly, against the consequences of the severity of COVID-19. However, factors that increase the risk of mortality from SARS-CoV-2 infections in COVID-19 vaccinees have not been widely studied and warrant further research.

About the study

In the current national surveillance study, researchers investigated risk factors and genetic alterations for deadly COVID-19 after vaccination.

Quantitative polymerase chain reaction (PCR) was used to detect SARS-CoV-2 in nasopharyngeal swabs obtained from participants, and whole genome sequencing (WGS) was performed to identify the causative variant of SARS-CoV -2.

Additionally, phylogenetic analysis was performed to determine the genetic clade. The primary outcome was death associated with COVID-19, assessed according to World Health Organization (WHO) criteria.

Multivariable logistic regression modeling was performed for the demographic and clinical profiling of COVID-19. Mortality predictors were checked using Kaplan-Meier statistics and the Cox proportional hazards regression model.

Additionally, immunovirological profiles of nasal mucosal cells were assessed using nCounter digital transcriptomics to identify potential biomarkers of life-threatening post-vaccination COVID-19 that can be targeted for developing therapies.

In addition, environmental aerosol sampling was performed. The results were compared to publicly available RNA sequencing (RNA-seq) datasets. Nursing homes provided participants’ medical records to analyze demographic and clinical data.

All participants had received doses of the BNT162b2 vaccine from Pfizer. Additionally, sensitivity analyzes included only PCR-positive and two-dose BNT162b2 vaccinates.


The most predictive model of COVID-19-associated mortality included age, being male, interferon beta 1 (IFNB1), host angiotensin-converting enzyme 2 (ACE2), open reading frame 7a (ORF7a) transcripts of SARS-CoV-2, SARS-CoV-2 Gamma and Mu variants, and late onset of infection (SARS-CoV-2 positivity by PCR after one week of d SARS-CoV-2 epidemic).

The results indicated that IFNB1-targeted therapies could be developed and should be initiated within the first days of infection for best results.

Each SARS-CoV-2 outbreak originated from the same introductory event, but with different causative variants of SARS-CoV-2 concern (VOC), i.e. Gamma and Delta, and variants of interest (VOI), i.e. Mu. SARS-CoV-2 was identified among aerosol samples from spaces used by residents and staff up to 52 days after initial infection. Similar results were observed in the sensitivity analysis.

Apart from interferon-λ2 (IFNL2) and IFNB1, genes expressed primarily by cells of the innate immune system were elevated, including those expressed by (i) macrophages and monocytes [C-X3-C motif chemokine receptor 1 (CX3CR1); tumor necrosis factor superfamily number 15 (TNFSF15); C-type lectin domain containing 6A (CLEC6A); intelectin 1; and leukocyte immunoglobulin-like receptor b5 (LILRB5)](ii) dendritic cells [X-C motif chemokine receptor 1 (XCR1)]and (iii) natural killer cells [Thy-1 cell surface antigen (THY1); cadherin 5; the cluster of differentiation 160 (CD160); beta-1,3-glucuronyltransferase 1 (B3GAT1); the neural cell adhesion molecule 1 (NCAM1); and C-C motif chemokine ligand 3 (CCL3)].

In addition, B cell genes [complement receptor type 2 (CR2), CD19, CD70, CD79A, CD79B, and paired box 5 (PAX5)]regulatory T cells [prostaglandin E receptor 4 (PTGER4) and forkhead box P3 (FOXP3)]and cytotoxic T cells (PTGER4 and eomesodermin) were significantly elevated in fatal COVID-19.

The results indicated that, in older vaccinees, deadly COVID-19 is characterized by heightened innate and cell-mediated immunological responses. In contrast, major histocompatibility complex (MHC) class I activity was reduced at functional, epigenomic, and transcriptomic levels in fatal COVID-19.

The most down-regulated genes represented mucosal epithelial cells (CD9, polymeric immunoglobulin receptor (PIGR) and mucin-1 (MUC1), indicating SARS-CoV-2-associated damage to the mucosal epithelial.

Additionally, SARS-CoV-2 antisense was selectively increased in fatal cases, indicating increased intracellular viral replication. Increased expression of interferon regulatory factor 7 (IRF7) and leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) and decreased expression of IRF3 were also observed with significant enrichment of regulatory T cell (Treg) and helper T cell 17 (Th17) differentiation pathways.

The finding also indicated that interleukin-6 signaling could be a “downstream” therapeutic target in IFNB1-overexpressing COVID-19 patients.


Overall, the study results highlighted the risk factors and genetic alterations underlying deadly COVID-19. The results could inform drug development, contribute to risk estimation of fatal COVID-19, help design tailored strategies, and reduce the health burden of COVID-19.

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