To better understand the extent of protection of elderly individuals from COVID-19 after receiving the first dose of BNT162b vaccine, we investigated a unique cohort of hospitalized patients from an old people’s home that experienced an outbreak of the SARS-CoV-2 variant B.1.351 in January of 2021 with similar kinetics of vaccination, infection and disease development. Six elderly individuals (average age 82 yr.) developed COVID-19 symptoms whole viral genome sequencing confirmed the B.1.351 strain (Supplementary Table 1). Four patients had received the first dose of the BNT162b (Pfizer-BioNTech) vaccine 11 days before the onset of COVID-19 symptoms and one patient eight days prior (Fig. 1a). All patients had underlying health conditions, they were hospitalized and cared for by the same physician and received dexamethasone treatment. Three additional hospitalized B.1.351-positive unvaccinated patients (average age 56) from other communities in Tyrol and South Tyrol (Italy) were included in the broader study (Fig. 1a; Supplementary Table 1). Having this well-controlled cohort of individuals with equivalent ages from the same nursing home, provided the opportunity to explore the impact of the first vaccination on the immune transcriptome in hospitalized COVID-19 patients.
Blood was drawn at ~10 and 30 days after the development of COVID-19 symptoms, RNA was prepared from buffy coats followed by RNA-seq analyses. The principal component analysis (PCA) showed a separation between RNA-seq samples from non-COVID controls8 and the first and second time points from COVID-19 patients on the first principal component (PC1) (Fig. 1b). In total, 3410 genes were significantly differentially expressed between non-COVID controls and the nine COVID-19 patients infected with the B.1.351 variant. The expression of 2026 genes was elevated in COVID-19 patients compared to non-COVID controls (Fig. 1c; Supplementary Table 2). As shown previously9,10, the significantly up-regulated genes are enriched in immune response pathways, including IL-JAK/STAT signaling and interferon alpha/gamma responses (Fig. 1d). Expression of the angiotensin-converting enzyme 2 (ACE2) receptor11,12 was elevated in the patients (Fig. 1e) suggesting that that the classical or novel dACE2 promoter responded to immune activation13,14. Of note, the immune response was linked to viral defense mechanisms (Fig. 1f).
Elevated immune response in patients infected after the first vaccination
Next, we focused on the immune transcriptome response in six hospitalized elderly patients (average age 82 yr.) from the same old people’s home (Supplementary Table 1), four of which had received the first dose of the BNT162b vaccine 11 days prior to developing COVID-19 symptoms. All six patients developed COVID-19 within two days of each other, were admitted to the same hospital, treated with Fortecortin (Dexamethasone) and were cared for by the same physician. First, we generated the transcriptomes from PBMCs isolated between 9 and 12 days after developing COVID-19 (Fig. 1a; Supplementary Table 1). The PCA plot shows a separation between the vaccinated and unvaccinated groups on PC1 (Fig. 2a), which is further strengthened by hierarchical clustering of the 181 significantly differentially expressed genes between the six patients (Fig. 2b; Supplementary Table 3). Of the 85 genes significantly upregulated in vaccinated patients, 72% (61 genes) are enriched in anti-viral immune responses and influenza vaccination15, such as IFN a/g responses, complement and IL6-JAK/STAT3 signaling pathways (Fig. 2c-d; Supplementary Table 3). Interferon stimulated genes (ISGs), and genes associated with innate antiviral immunity and COVID-19-SARS-CoV-2 infection are highly enriched in vaccinated patients (red dots) (Fig. 2e; Supplementary Fig. 1; Supplementary Table 3). Specifically, the highly ranked ETV7, STAT1 and STAT2 (Fig. 2f) are key transcription factors executing interferon responses and are top predictors for ACE2 expression in human airway epithelium14,16-20. Notably, expression of IFITM3, a gene with a polymorphism that has been linked to the severity of COVID-1921, is highly induced in vaccinated patients (Supplementary Fig. 1a). While three out of the four vaccinated patients had a highly activated immune transcriptome, patient ID-02 had a blunted immune response, more similar to that seen in the non-vaccinated patients (Supplementary Fig. 1b). One explanation is the shorter time period between vaccination and the onset of symptoms.
Temporal progression of the immune response
From our cohort of the four vaccinated patients, one died of COVID-19 and three were discharged from the hospital after a single stay of 10-14 days (Fig. 1a). From the two non-vaccinated patients, one was discharged after a single ten day stay and one was re-admitted. To dig deeper into the temporal immune response after discharge from the hospital we analyzed the immune transcriptome of the three vaccinated patients approximately three weeks after the first transcriptome analysis (Figs. 1a and 3; Supplementary Table 4). Gene enrichment analyses of differentially expressed transcripts illustrate a greatly diminished immune response, including INFa/g signaling, in the recovered patients (Fig. 3a; Supplementary Table 4). Expression of specific ISGs (e.g., IFI35, IFIT5, IFITM3, STAT1, STAT2, OAS2) was sharply reduced (Fig. 3b), approaching levels seen in non-COVID samples.
Immune responses at different ages
Having analyzed the immune transcriptome from the elderly hospitalized population (average age 82 yr.) we addressed potential age differences and included RNA-seq transcriptomes from three hospitalized patients all below 62 years of age (average age 56 yr.) (Fig. 1a). The two groups were separated in the PCA plot (Fig. 4a; Supplementary Table 5). The immune response in the three younger patients exceeded that of the elderly population and of the 417 significant differentially activated genes, most are related to immune responses and virus infection pathways (Fig. 4b-c; Supplementary Table 5). These results support the concept that age might be a defining factor in the immune response in COVID-19 patients.