Longitudinal home self-collection of capillary blood usinghomeRNA correlates interferon and innate viral defense pathways with SARS-CoV-2 viral clearance

Abstract

Blood transcriptional profiling is a powerful tool to evaluate immune responses to infection; however, blood collection via traditional phlebotomy remains a barrier to precise characterization of the immune response in dynamic infections (e.g., respiratory viruses). Here we present an at-home self-collection methodology, homeRNA, to study the host transcriptional response during acute SARS-CoV-2 infections. This method uniquely enables high frequency measurement of the host immune kinetics in non-hospitalized adults during the acute and most dynamic stage of their infection. COVID-19+ and healthy participants self-collected blood every other day for two weeks with daily nasal swabs and symptom surveys to track viral load kinetics and symptom burden, respectively. While healthy uninfected participants showed remarkably stable immune kinetics with no significant dynamic genes, COVID-19+ participants, on the contrary, depicted a robust response with over 418 dynamic genes associated with interferon and innate viral defense pathways. When stratified by vaccination status, we detected distinct response signatures between unvaccinated and breakthrough (vaccinated) infection subgroups; unvaccinated individuals portrayed a response repertoire characterized by higher innate antiviral responses, interferon signaling, and cytotoxic lymphocyte responses while breakthrough infections portrayed lower levels of interferon signaling and enhanced early cell-mediated response. Leveraging cross-platform longitudinal sampling (nasal swabs and blood), we observed that IFI27, a key viral response gene, tracked closely with SARS-CoV-2 viral clearance in individual participants. Taken together, these results demonstrate that at-home sampling can capture key host antiviral responses and facilitate frequent longitudinal sampling to detect transient host immune kinetics during dynamic immune states.

homeRNA self-blood collection enables high-frequency temporal profiling of presymptomatic host immune kinetics to respiratory viral infection: a prospective cohort study

“…Relative to the first sample collection, the median days PVS was 0 (range: -4 – 2) and the median days PSO was -1 (range: -5 – 3) ( Table 1 ). When longitudinal samples from COVID-19+ participants (n samples =92; n participants =8) were compared to those of unexposed uninfected (healthy) participants (n samples =32; n participants =5) derived from a similar dataset (16), a total of 206 genes were differentially expressed ( Fig. 3A ).…”

“…Nucleic acid extraction and pathogen quantification using the Multi-pathogen OpenArray platform for non-clinical testing of respiratory pathogens was performed as previously described (28). For each participant, 3-4 nasal swabs were tested for SARS-CoV-2 and 18 common respiratory pathogens as previously described (28). For participants with positive SARS-CoV-2 results, one representative swab with the lowest Crt value (highest viral load) was selected for SARS-CoV-2 sequencing as previously described (28).…”

“…For each participant, 3-4 nasal swabs were tested for SARS-CoV-2 and 18 common respiratory pathogens as previously described (28). For participants with positive SARS-CoV-2 results, one representative swab with the lowest Crt value (highest viral load) was selected for SARS-CoV-2 sequencing as previously described (28).…”

“…R scripts developed to perform analyses and visualizations are available upon request. (16). Statistical significance between groups were determined using the Wilcoxon signed rank test with Benjamini-Hochberg multiple testing correction procedure and significance between groups were labeled as follows: p>0.05 (ns), p £0.05 (*), p £0.01 (**), p £0.001 (***), p £0.0001 (****).…”

“…1 ). Our team developed a home blood collection kit ( home RNA) that enables self-sampling and stabilization of liquid capillary blood (14, 15) and demonstrated its capability of capturing host response to SARS-CoV-2 in non-hospitalized adults in addition to distinguishing differential infection response between previously vaccinated and unvaccinated adults (16). Here, we leveraged home RNA to profile, at high temporal resolution, the pre-symptomatic host immunity to natural ARVIs in exposed close contacts (CCs) ( Fig.…”