Preserved C-reactive protein responses to blood stream infections following tocilizumab treatment for COVID-19 (preprint)

C-reactive protein (CRP) levels are elevated following bacterial infections but may be attenuated by the IL-6-receptor antagonist tocilizumab. In hospitalised COVID-19 patients, tocilizumab induced a transient (<21 day) fall in CRP but retained CRP responses to nosocomial blood stream infections, and therefore its utility in guiding antibiotic prescribing.

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. (preprint)

The correlates of natural protective immunity to SARS-CoV-2 in the majority who experience asymptomatic infection or non-severe disease are not fully characterised, and remain important as new variants emerge. We addressed this question using blood transcriptomics, multiparameter flow cytometry and T cell receptor (TCR) sequencing spanning the time of incident infection. We identified a type 1 interferon (IFN) response common to other acute respiratory viruses, and a cell proliferation response that discriminated SARS-CoV-2 from other viruses. These responses peaked by the time the virus was first detected, and in some preceded virus detection. Cell proliferation was most evident in CD8 T cells and associated with rapid expansion of SARS-CoV-2 reactive TCRs. We found an equally rapid increase in immunoglobulin transcripts, but circulating virus-specific antibodies lagged by 1-2 weeks. Our data support a protective role for rapid induction of type 1 IFN and CD8 T cell responses to SARS-CoV-2.

C-reactive protein guided use of procalcitonin in COVID-19 (preprint)

Low procalcitonin (PCT) concentrations (<0.5ng/mL) can facilitate exclusion of bacterial co-infection in viral infections, including COVID-19. However, costs associated with PCT measurement preclude universal adoption, indicating a need to identify settings where PCT provides clinical information beyond that offered by other inflammatory markers, such as C-reactive protein (CRP) and white cell count (WCC). In an unselected cohort of 299 COVID-19 patients, we tested the hypothesis that PCT<0.5ng/mL was associated with lower levels of CRP and WCC. We demonstrated that CRP values below the geometric mean of the entire patient population had a negative predictive value for PCT<0.5ng/mL of 97.6% and 100% at baseline and 48 hours into admission respectively, and that this relationship was not confounded by intensive care admission or microbiological findings. CRP-guided PCT testing algorithms can reduce costs and support antimicrobial stewardship strategies in COVID-19.

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

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.

Exclusion of bacterial co-infection in COVID-19 using baseline inflammatory markers and their response to antibiotics (preprint)

BackgroundCOVID-19 is infrequently complicated by secondary bacterial infection, but nevertheless antibiotic prescriptions are common. We used community-acquired pneumonia (CAP) as a benchmark to define the processes that occur in a bacterial pulmonary infection, and tested the hypothesis that baseline inflammatory markers and their response to antibiotic therapy could distinguish CAP from COVID-19. MethodsIn patients admitted to Royal Free Hospital (RFH) and Barnet Hospital (BH) we defined CAP by lobar consolidation on chest radiograph, and COVID-19 by SARS-CoV-2 detection by PCR. Data were derived from routine laboratory investigations. ResultsOn admission all CAP and >90% COVID-19 patients received antibiotics. We identified 106 CAP and 619 COVID-19 patients at RFH. CAP was characterised by elevated white cell count (WCC) and C-reactive protein (CRP) compared to COVID-19 (median WCC 12.48 (IQR 8.2-15.3) vs 6.78 (IQR 5.2-9.5) x106 cells/ml and median CRP CRP 133.5 (IQR 65-221) vs 86 (IQR 42-160) mg/L). Blood samples collected 48-72 hours into admission revealed decreasing CRP in CAP but not COVID-19 (CRP difference -33 (IQR -112 to +3.5) vs +15 (IQR -15 to +70) mg/L respectively). In the independent validation cohort (BH) consisting of 169 CAP and 181 COVID-19 patients, admission WCC >8.2x106 cells/ml or falling CRP during admission identified 95% of CAP cases, and predicted the absence of bacterial co-infection in 45% of COVID-19 patients. ConclusionsWe propose that in COVID-19 the absence of both elevated baseline WCC and antibiotic-related decrease in CRP can exclude bacterial co-infection and facilitate antibiotic stewardship efforts.

Transcriptional response modules characterise IL-1 and IL-6 activity in COVID-19 (preprint)

Dysregulated IL-1{beta} and IL-6 responses have been implicated in the pathogenesis of severe Coronavirus Disease 2019 (COVID-19). Innovative approaches for evaluating the biological activity of these cytokines in vivo are urgently needed to complement clinical trials of therapeutic targeting of IL-1{beta} and IL-6 in COVID-19. We show that the expression of IL-1{beta} or IL-6 inducible transcriptional signatures (modules) reflects the bioactivity of these cytokines in immunopathology modelled by juvenile idiopathic arthritis (JIA) and rheumatoid arthritis. In COVID-19, elevated expression of IL-1{beta} and IL-6 response modules, but not the cytokine transcripts themselves, is a feature of infection in the nasopharynx and blood, but is not associated with severity of COVID-19 disease, length of stay or mortality. We propose that IL-1{beta} and IL-6 transcriptional response modules provide a dynamic readout of functional cytokine activity in vivo, aiding quantification of the biological effects of immunomodulatory therapies in COVID-19.