Blood transcriptional biomarkers of acute viral infection for detection of pre-symptomatic SARS-CoV-2 infection

Abstract

We hypothesised that host-response biomarkers of viral infections may contribute to early identification of SARS-CoV-2 infected individuals, critical to breaking chains of transmission. We identified 20 candidate blood transcriptomic signatures of viral infection by systematic review and evaluated their ability to detect SARS-CoV-2 infection, compared to the gold-standard of virus PCR tests, among a prospective cohort of 400 hospital staff subjected to weekly testing when fit to attend work. The transcriptional signatures had limited overlap, but were mostly co-correlated as components of type 1 interferon responses. We reconstructed each signature score in blood RNA sequencing data from 41 individuals over sequential weeks spanning a first positive SARS-CoV-2 PCR, and after 6-month convalescence. A single blood transcript for IFI27 provided the highest accuracy for discriminating individuals at the time of their first positive viral PCR result from uninfected controls, with area under the receiver operating characteristic curve (AUROC) of 0.95 (95% confidence interval 0.91–0.99), sensitivity 0.84 (0.7–0.93) and specificity 0.95 (0.85–0.98) at a predefined test threshold. The test performed equally well in individuals with and without symptoms, correlated with viral load, and identified incident infections one week before the first positive viral PCR with sensitivity 0.4 (0.17–0.69) and specificity 0.95 (0.85–0.98). Our findings strongly support further urgent evaluation and development of blood IFI27 transcripts as a biomarker for early phase SARS-CoV-2 infection, for screening individuals such as contacts of index cases, in order to facilitate early case isolation and early antiviral treatments as they emerge.

Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2 infection

“…Therefore, a low-level systemic interferon response indicative of virus exposure was detectable in individuals who had the strongest SARS-CoV-2-specific T cell response post-exposure, despite them lacking PCR or antibody confirmation of SARS-CoV-2 infection. Extrapolating from our previous data showing that IFI27 is induced at the time of incident infection and correlates with viral load 16 , this supports the ES with stronger RTCspecific T cell responses representing HCW who have experienced a low-level/transient infection. Thus, ES with SARS-CoV-2 T cell reactivity could be distinguished by both their innate IFI27 signature and the propensity of their T cells to target RTC.…”

“…Our T cell data raised the possibility that SARS-CoV-2 infection in HCW represents a spectrum, with some ES expanding T cell responses having had a sub-clinical abortive infection not detectable by PCR or antibody seroconversion. To test this postulate, we applied blood transcript measurements of the interferon-inducible gene IFI27 as a biomarker, which we recently showed discriminates early SARS-CoV-2 infection at, or one week before, PCR positivity (specificity 0.95 and sensitivity 0.84 16 ). ES with the highest post-exposure RTCspecific responses had significantly raised peak IFI27 levels when compared to baseline controls (Fig.…”

“…We then reverted to the ES HCW cohort, where small volume PBMC collections were available from the time of recruitment, allowing targeted analysis of baseline responses in those with the strongest RTC responses at wk16. 1b) 16,43 , with seroconversion within the first 3 weeks of follow-up for most 36 . Focusing on the most common specificity of pre-existing responses, NSP12-specific T cells were already detectable at baseline in 74% of those ES with the strongest NSP12 responses post-exposure (Fig.…”

“…16-weeks postrecruitment, ES had memory T cells that were stronger and more multispecific than an unexposed pre-pandemic cohort, and more frequently directed against the RTC than the structural protein-dominated responses seen post-detectable infection (matched concurrent cohort). The postulate that HCW with the strongest RTC-specific T cells had an abortive infection was supported by a low-level increase in IFI27 transcript, a robust early innate signature of SARS-CoV-2 infection 16 . We showed that the RNA-polymerase within RTC was the largest region of high sequence conservation across human seasonal coronaviruses (HCoV) and was preferentially targeted by T cells from UK and Singapore pre-pandemic cohorts and from ES.…”

Non-severe SARS-CoV-2 infection is characterised by very early T cell proliferation independent of type 1 interferon responses and distinct from other acute respiratory viruses

“…We propose that such early detection of IFN-inducible genes in the blood transcriptome may arise from localised immune responses as a result of leukocyte trafficking through lymphoid tissues or the site of infection, and may provide greater sensitivity than detection of circulating IFNs. As we have previously reported, an additional translational application of this finding is the detection of IFN-inducible transcripts in blood, as a diagnostic biomarker of early viral infection that may precede PCR detection of the virus and symptoms 11 .…”