Covid Sepsis Gene Expression Subphenotypes Manifest Differential Plasma Protein Signatures

INTRODUCTION: Transcriptome-derived sepsis subphenotypes, termed 'adaptive', 'inflammopathic' and 'coagulopathic', have been reliably identified in sepsis cohorts, however plasma proteomics in these groups have not been well characterized. We hypothesized that inflammatory and vascular injury markers would be elevated in the inflammopathic and coagulopathic groups compared to the adaptive group. METHOD(S): We prospectively enrolled and obtained blood from 130 inpatients with COVID19-related sepsis. Severity was classified by NIH ordinal scale. Gene expression analysis was performed by Nanostring nCounter (Inflammatix). Inflammatory proteins interleukin (IL)-6, IL8, IL10, IL1RA, IL1RL1, and IFNg and vascular markers ANGPT2, sICAM, vWF, ADAMTS13, and protein C were measured with OLINK proximity extension assay. Clinical variables were compared by chi-square and protein levels were compared using ANOVA with Bonferroni adjustment. RESULT(S): The transcriptomic classifier identified 32% (41) inflammopathic, 50% (65) adaptive and 18% (24) coagulopathic subjects. The inflammopathic group had more patients requiring mechanical ventilation (39% vs 9% vs 21%;p < 0.001) and higher 90-day mortality (32% vs 8% vs 13%, p = 0.016). Inflammatory cytokines IL8 and IL10 were significantly higher in inflammopathic compared to adaptive (p=0.038 and p=0.017 respectively), but not compared to coagulopathic (p>0.99 and p=0.24, respectively). Both the inflammopathic and coagulopathic groups expressed higher IL1RL1 and interferon-gamma compared to adaptive (IL1RL1;p< 0.001, p=0.002, IFNg;p=0.007, p=0.001). Plasma IL6 and IL1RA did not differ between groups, nor did many vascular proteins. The inflammopathic group expressed higher sICAM (p=0.049 vs adaptive) and lower ADAMTS13 compared to the adaptive group, and the coagulopathic group did not differ in its vascular protein expression. CONCLUSION(S): Transcriptomic subphenotypes are present in COVID-19 sepsis at similar proportions to non-COVID-19 sepsis. Inflammopathic subjects manifested higher severity of illness at admission, higher expression of inflammatory proteins and higher mortality. Markers of vascular injury did not distinguish the coagulopathic group. Integrating RNA and protein expression may offer new insights to host immune dysregulation during COVID sepsis.

Examining retirees perceptions of the effects of COVID-19 mitigation strategies on leisure participation and social relationships. (Leisure and aging in difficult times.)

In response the designation of COVID-19 as a global pandemic in March of 2020, people across the world have been tasked with adopting extreme social distancing protocols and lockdowns resulting in substantial interruptions to their daily lives. Specific to leisure, COVID-19-related changes have presented unanticipated disruptions to activities in areas where opportunities were once abundant, especially for retirees. The purpose of the current study is to examine adult retirees' perceptions of COVID-19 related change to their recreation and leisure activities and social relationships. Findings revealed that a majority of participants reported experiencing varying levels of modification to recreation and leisure participation and changes to relationships with friends. A qualitative comparison revealed a general trend among participants where a majority of those who reported modifications to recreation and leisure activities also reported negative impacts to relationships with friends.

A quality improvement evaluation of the speech at home intervention approach through teletherapy

Background/Purpose: Speech@Home (S@H), an evidenced-based, integrated online intervention package designed specifically for children with cleft palate type speech disorders, provides the speech and language therapist (SLT) with a therapy program builder and linked resources which can be used to deliver therapy at home via telehealth, ideally following parent training. COVID-19 has driven the need for SLTs to move rapidly from a face-to-face delivery model to telehealth service delivery. The aim of this presentation is to describe how S@H addressed this problem, evaluated using a quality improvement (QI) methodology framework of plan, do, study, act cycle. Methods/Description: Six speech pathologists from 4 cleft centers in the United Kingdom/Ireland volunteered to participate in the project and completed a S@H training webinar. Following assessment and consent to participate, 16 naive parents in the S@H approach and their child received 10 teletherapy sessions. Each session was followed up with an emailed link to the parent, with that week's program, and all the resources required to complete the activities. Data collection of therapists' and parents' views of the website's usability/functionality, content (therapy activities and resources), together with their emotional responses using the virtual platform, were collected at weeks 1, 5, and 10, on a 1 to 5 point Likert scale. The nature of the children's speech disorders and speech changes was documented. The S@H team provided feedback to the SLTs at week 5 to inform the second cycle of intervention. Results: In cycle 1, therapists and parents rated usability, activities, and resources with almost all high positive scores of 4 or 5 (mean 4.4, mode, 4, median 4). Minor functionality errors identified by the therapists were corrected, including the parent/therapist ongoing notation system. The speech sound videos and cleft speech-specific resources were especially highly praised. The need for downloading resources on an iPhone and iPad was identified, and this functionality added. Therapists also suggested improvements to the Program Builder, such as reducing the need to enter the same consonants across activities and the imbalance in activities at different levels. Conclusions: Following one training webinar, Speech@Home was found to be very suitable for use in teletherapy, with therapists and parents reporting positive experiences, especially encouraging given these were untrained parents. Furthermore, the QI methodology has provided excellent insights into the S@H platform by 6 novel therapists, building the evidence for its effectiveness. This project has already improved the virtual platform but also informed the S@H team as to other areas for improvement, suggestions for ways to address some of these, and identified further training items for therapists.

Speech at home: An innovative approach to intervention in children with cleft palate

Background/Purpose: The Parent Led Articulation Therapy study has shown that parent-led intervention for cleft palate articulation therapy could be an alternative model of service delivery. An integral aspect of this intervention was parent training and the development of speech therapy programs with their resources, all labor-intensive activities for busy therapists. Based on this, Speech@Home has been developed an online integrated, innovative speech intervention package for children with cleft palate and related conditions. This approach shifts the onus of speech therapy delivery to parents at home under the supervision of a speech and language therapist (SLT) using telehealth. Parents are an untapped resource where services are very stretched. With the Covid crisis, teletherapy has become a safe way to deliver speech and language therapy services. The aim of this presentation is to provide an overview of the Speech@Home approach. Methods/Description: Speech@Home provides (1) in depth parent training courses and (2) a novel online Therapy Programme Builder and linked resources which can be used in conjunction with therapist led teletherapy. Parent training is available in 2 formats: (1) A 2-day course for parents undertaking regular therapy activities, working in partnership with a therapist. Everything an SLT requires to run a training course for a group of parents is available including videoed lectures, lecture handouts, sound videos, parent quizzes and answers, and course evaluation forms, (2) A stand-alone 1-day course to support parents who are able to access therapy, whose child is on the waiting list or is too young to receive direct therapy but therapy is highly likely to be required. The Speech@Home Therapy Programme Builder enables the SLT to produce a child-specific program in a short space of time. It provides the SLT with a drop-down menu software package containing over 150 therapy activities each linked to the appropriate picture and video resources. The parent is emailed the link to their child's therapy program with all the picture resources required for each activity. This presentation will provide an overview, with illustrations, of the parent training courses, a demonstration of the Therapy Programme Builder with resources and the professionally presented parent programme.

Validation of inflammopathic, adaptive, and coagulopathic sepsis endotypes in COVID-19

INTRODUCTION: Complex critical syndromes like sepsis and COVID-19 may be composed of underlying subclasses, or 'endotypes,' which may respond differently to treatment. We previously reported the discovery and validation of a 33-mRNA host response classifier which defined three sepsis endotypes across 1,300 patients with bacterial sepsis at hospital or ICU admission. Here, we aimed to test whether our 33-mRNA bacterial sepsis endotypes classifier recapitulates the same clinical and immunological endotypes in COVID-19. METHODS: In this prospective, single-center observational cohort study, we recruited adult patients with RT-PCRconfirmed COVID-19 within 24 hours of admission to an Athens, Greece hospital. RNA was extracted from whole blood collected in PAXgene RNA tubes, and then profiled on the NanoString nCounter® platform to quantify the 33 mRNAs. The endotypes classifier then assigned one of three endotypes (Inflammopathic, Adaptive, or Coagulopathic) to each patient. We tested endotype status against other clinical parameters including lab values, severity scores, and outcomes. RESULTS: We enrolled 71 patients with COVID-19, of which 33 went on to severe respiratory failure (SRF), of which 6 (8%) died. Patients were assigned as Inflammopathic (34%), Adaptive (39%), or Coagulopathic (27%);Adaptive patients had lower rates of SRF and no mortalities. Coagulopathic and Inflammopathic endotypes had 12% and 16% mortality rates. The Coagulopathic group was significantly associated with D-dimers, and the Inflammopathic group showed high clinical severity and highest C-reactive protein and IL-6 levels. CONCLUSIONS: Our predefined 33-mRNA endotypes classifier recapitulated immune phenotypes in viral sepsis (COVID-19) despite its prior training and validation only in bacterial sepsis. Further work should focus on continued validation of the endotypes and their interaction with immunomodulatory therapy. If confirmed with future studies, the 33-mRNA classifer could be used as a companiondiagnostic test to guide a precision-medicine-based intervention.

Similarities and differences in transcriptomic host response between SARS-CoV-2 and other viral infections

Background: COVID-19 is a pandemic caused by the SARS-CoV-2 virus that shares and differs in clinical characteristics of known viral infections. Methods: We obtained RNAseq profiles of 62 prospectively enrolled COVID-19 patients and 24 healthy controls (HC). We collected 23 independent studies profiling 1,855 blood samples from patients covering six viruses (influenza, RSV, HRV, Ebola, Dengue and SARS-CoV-1). We studied host whole-blood transcriptomic responses in COVID-19 compared to non-COVID-19 viral infections to understand similarities and differences in host response. Gene signature threshold was absolute effect size ≥1, FDR ≤ 0.05%. Results: Differential gene expression of COVID-19 vs HC are highly correlated with non-COVID-19 vs HC (r=0.74, p< 0.001). We discovered two gene signatures: COVID-19 vs HC (2002 genes) (COVIDsig) and non-COVID-19 vs HC (635 genes) (nonCOVIDsig). Pathway analysis of over-expressed signature genes in COVIDsig or nonCOVIDsig identified similar pathways including neutrophil activation, innate immune response, immune response to viral infection and cytokine production. Conversely, for under-expressed genes, pathways indicated repression of lymphocyte differentiation and activation (Fig1). Intersecting the two gene signatures found two genes significantly oppositely regulated (ACO1, ATL3). We derived a third gene signature using COCONUT to compare COVID-19 to non-COVID-19 viral infections (416 genes) (Fig2). Pathway analysis did not result in significant enrichment, suggesting identification of novel biology (Fig1). Statistical deconvolution of bulk transcriptomic data found M1 macrophages, plasmacytoid dendritic cells, CD14+ monocytes, CD4+ T cells and total B cells changed in the same direction across COVID-19 and non-COVID-19 infections. Cell types that increased in COVID-19 relative to non-COVID-19 were CD56bright NK cells, M2 macrophages and total NK cells. Those that decreased in non- COVID-19 relative to COVID-19 were CD56dim NK cells & memory B cells and eosinophils (Fig3). Conclusion: The concordant and discordant responses mapped here provide a window to explore the pathophysiology of COVID-19 vs other viral infections and show clear differences in signaling pathways and cellularity as part of the host response to SARS-CoV-2.