Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients

The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1-3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling of >15,000 longitudinal blood and nasal samples from 540 participants of the IMPACC cohort, using 14 distinct assays. These unbiased analyses identify cellular and molecular signatures present within 72 h of hospital admission that distinguish moderate from severe and fatal COVID-19 disease. Importantly, cellular and molecular states also distinguish participants with more severe disease that recover or stabilize within 28 days from those that progress to fatal outcomes (TG4 vs. TG5). Furthermore, our longitudinal design reveals that these biologic states display distinct temporal patterns associated with clinical outcomes. Characterizing host immune responses in relation to heterogeneity in disease course may inform clinical prognosis and opportunities for intervention.

ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data

Human immunoglobulin heavy chain (IGH) locus on chromosome 14 includes more than 40 functional copies of the variable gene (IGHV), which are critical for the structure of antibodies that identify and neutralize pathogenic invaders as a part of the adaptive immune system. Because of its highly repetitive sequence composition, the IGH locus has been particularly difficult to assemble or genotype when using standard short-read sequencing technologies. Here, we introduce ImmunoTyper-SR, an algorithmic tool for the genotyping and CNV analysis of the germline IGHV genes on Illumina whole-genome sequencing (WGS) data using a combinatorial optimization formulation that resolves ambiguous read mappings. We have validated ImmunoTyper-SR on 12 individuals, whose IGHV allele composition had been independently validated, as well as concordance between WGS replicates from nine individuals. We then applied ImmunoTyper-SR on 585 COVID patients to investigate the associations between IGHV alleles and anti-type I IFN autoantibodies, which were previously associated with COVID-19 severity.

ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data

Human immunoglobulin heavy chain (IGH) locus on chromosome 14 includes more than 40 functional copies of the variable gene (IGHV), which, together with the joining genes (IGHJ), diversity genes (IGHD), constant genes (IGHC) and immunoglobulin light chains, code for antibodies that identify and neutralize pathogenic invaders as a part of the adaptive immune system. Because of its highly repetitive sequence composition, the IGH locus has been particularly difficult to assemble or genotype through the use of standard short read sequencing technologies. Here we introduce ImmunoTyper-SR, an algorithmic method for genotype and CNV analysis of the germline IGHV genes using Illumina whole genome sequencing (WGS) data. ImmunoTyper-SR is based on a novel combinatorial optimization formulation that aims to minimize the total edit distance between reads and their assigned IGHV alleles from a given database, with constraints on the number and distribution of reads across each called allele. We have validated ImmunoTyper-SR on 12 individuals with Illumina WGS data from the 1000 Genomes Project, whose IGHV allele composition have been studied extensively through the use of long read and targeted sequencing platforms, as well as nine individuals from the NIAID COVID Consortium who have been subjected to WGS twice. We have then applied ImmunoTyper-SR on 585 samples from the NIAID COVID Consortium to investigate associations between distinct IGHV alleles and anti-type I IFN autoantibodies which have been linked to COVID-19 severity.

The risk of COVID-19 death is much greater and age-dependent with type I IFN autoantibodies

SARS-CoV-2 infection fatality rate (IFR) doubles with every five years of age from childhood onward. Circulating autoantibodies neutralizing IFN-α, IFN-ω, and/or IFN-β are found in ~20% of deceased patients across age groups. In the general population, they are found in ~1% of individuals aged 20-70 years and in >4% of those >70 years old. With a sample of 1,261 deceased patients and 34,159 uninfected individuals, we estimated both IFR and relative risk of death (RRD) across age groups for individuals carrying autoantibodies neutralizing type I IFNs, relative to non-carriers. For autoantibodies neutralizing IFN-α2 or IFN-ω, the RRD was 17.0[95% CI:11.7-24.7] for individuals under 70 years old and 5.8[4.5-7.4] for individuals aged 70 and over, whereas, for autoantibodies neutralizing both molecules, the RRD was 188.3[44.8-774.4] and 7.2[5.0-10.3], respectively. IFRs increased with age, from 0.17%[0.12-0.31] for individuals <40 years old to 26.7%[20.3-35.2] for those ≥80 years old for autoantibodies neutralizing IFN-α2 or IFN-ω, and from 0.84%[0.31-8.28] to 40.5%[27.82-61.20] for the same two age groups, for autoantibodies neutralizing both molecules. Autoantibodies against type I IFNs increase IFRs, and are associated with high RRDs, particularly those neutralizing both IFN-α2 and -ω. Remarkably, IFR increases with age, whereas RRD decreases with age. Autoimmunity to type I IFNs appears to be second only to age among common predictors of COVID-19 death.

Online Resources in Blindness and Disability: An International Overview

For professionals conducting research in the fields of blindness and disability, searching the literature by computer offers speedy access to existing data and facilitates the efficient exchange of information. As computer use becomes more prevalent on an international scale, it is useful for researchers to have knowledge of online searching procedures and resources. This overview outlines important databases produced in the United States and elsewhere, where relevant articles and information may be found.

Historic tobacco legislation in Israel: a moment to celebrate

BACKGROUND

Israel was once a leader in tobacco control, but fell behind other countries, particularly during the past decade, as smoking rates stagnated. TEXT: Landmark tobacco control legislation, which banned advertising (with the exception of the print press) and limited marketing, was passed in Israel on Dec. 31^rst, 2018. The changes occurred following years of attempts which culminated in successful last-minute efforts to promote the legislation just before the early disbanding of the 20th Knesset (Israeli Parliament). Regulations concerning marketing and advertising were substantially strengthened to address all tobacco, nicotine and smoking products. Digital media was included for the first time. Electronic cigarettes, which were previously largely unregulated, now fall under existing tobacco legislation. The changes overcame intense opposition from the tobacco lobby, and occurred despite the fact that the basic elements for prevention policy postulated by the Richmond model were not in place.

CONCLUSIONS

This legislation represents an important and long-awaited change in Israeli tobacco control policy. Many deficiencies in existing tobacco control regulation were overcome, and some measures went beyond current international regulations. The cohesive partnership between legislators, public health organizations and professionals, advocacy groups, academia, and leading journalists was critical to this success. The progress was lauded by the World Health Organization with its highest award for tobacco control, which was presented to Smoke Free Israel. This case study provides important lessons for up-to-date tobacco control policy, in the age of rapid global changes in the tobacco, vaping and nicotine landscape.

Varicella-zoster virus Neurovasculitis (VZV-NV) in the Setting of Autoantibodies to Interferon alpha (anti-IFNα)

Background

VZV-NV resulting in CNS damage is rare in immunocompetent hosts. Humoral immunity protects against acquiring VZV, and T-cell mediated immunity shields against reactivation of the latent virus. Individuals who are immunocompromised due to T-cell mediated defects can present with systemic VZV.

Methods

Case report of a previously healthy man who developed VZV-NV associated with autoantibodies to IFNα.

Results

A previously healthy 64 year-old man developed an acute T3 Brown-Sequard syndrome. Symptoms progressed to include bilateral lower extremity weakness, ptosis, ophthalmoplegia, and encephalopathy. Magnetic resonance imaging (MRI) showed diffuse T2 hyperintensities with enhancement throughout the spine and brain, including enhancement of his meninges, roots, and cranial nerves. Successive cerebrospinal fluid (CSF) studies revealed increasing B-cell lymphocytosis, (maximum 661 cells/mcl), and CSF protein (maximum 242 mg/dL). CSF PCR was positive for VZV and IgM antibodies. Further testing showed anti-IFNα autoantibodies in the plasma and CSF. Serum anti-IFNα fluorescence intensity was 30 times normal, and his plasma blocked IFNα-induced STAT-1 phosphorylation in normal monocytes. Treatment with acyclovir and methylprednisolone resulted in improvement. Repeat LP following treatment revealed 32 WBC/mcl with normal protein. Follow-up MRI did not show any new lesions. Three years after initial presentation, he continues to be stable without clinical relapses, or subclinical changes on MRI. Serum studies were positive for VZV IgG and negative for IgM. CSF PCR was positive for VZV. Lastly, serum anti-IFNα fluorescence intensity remained 25 times normal, and his plasma continued to block IFNα-induced STAT-1 phosphorylation in normal monocytes.

Conclusion

This is the first identified case of CNS VZV-NV in the setting of binding and blocking autoantibodies to IFNα in the serum and CSF. Elevated serum and CSF levels of anti-INFα may impair natural killer, T-cell and neuronal antiviral activity. Disruption of T-cell mediated immunity due to anti-IFNα could cause an adult-onset immunocompromised state with severe VZV reactivation. The association of high-titer neutralizing autoantibodies to INFα in an adult with CNS VZV is novel and may be clinically relevant.

Disclosures

All authors: No reported disclosures.

Survival following salvage abdominoperineal resection for persistent and recurrent squamous cell carcinoma of the anus: do these disease categories affect survival?

AIM

This study aimed to investigate the results of salvage abdominoperineal excision (APR) in patients with persistent or recurrent squamous cell carcinoma of the anus (SCCA).

METHOD

Patients with anal neoplasia were identified from a prospective database. Patients with invasive SCCA with demonstrated failure of chemoradiation therapy (CRT) who underwent salvage APR for one of three disease categories (persistent, < 6 months post-CRT; early recurrent, 6-24 months post-CRT; late recurrent, > 24 months post-CRT) were included. The primary outcome was overall survival after salvage APR. Tumour size, metastatic lymph nodes (LN), circumferential resection margin positivity (CRM) and neurolymphovascular invasion (NLVI) were correlated with the outcome.

RESULTS

Thirty-six patients with a median 3-year overall survival of 46% (median follow-up 24 months) underwent salvage APR due to persistent or recurrent SCCA (14 men, mean age 59 years). Eleven (31%) patients were diagnosed with persistent disease, 17 (47%) with early and 8 (22%) with late recurrence. Two-year overall survival of Stage 0/I/II and III/IV disease was 81.5% and 33.74%, respectively (P = 0.022). Overall disease stage was associated with disease categorization (P = 0.009): patients with persistent disease or early recurrence had a significantly higher disease stage than patients with late recurrence (OR = 20.9 and 17.2). Despite apparently improved survival in patients with late disease recurrence on live table analysis, no significant difference was identified in overall survival when stratified by disease category on log-rank test analysis.

CONCLUSION

Persistent and recurrent disease does not show any significant difference in survival, but patients with late recurrence may have a better prognosis.

Identification of patients with RAG mutations previously diagnosed with common variable immunodeficiency disorders

PURPOSE

Combined immunodeficiency (CID) presents a unique challenge to clinicians. Two patients presented with the prior clinical diagnosis of common variable immunodeficiency (CVID) disorder marked by an early age of presentation, opportunistic infections, and persistent lymphopenia. Due to the presence of atypical clinical features, next generation sequencing was applied documenting RAG deficiency in both patients.

METHODS

Two different genetic analysis techniques were applied in these patients including whole exome sequencing in one patient and the use of a gene panel designed to target genes known to cause primary immunodeficiency disorders (PIDD) in a second patient. Sanger dideoxy sequencing was used to confirm RAG1 mutations in both patients.

RESULTS

Two young adults with a history of recurrent bacterial sinopulmonary infections, viral infections, and autoimmune disease as well as progressive hypogammaglobulinemia, abnormal antibody responses, lymphopenia and a prior diagnosis of CVID disorder were evaluated. Compound heterozygous mutations in RAG1 (1) c256_257delAA, p86VfsX32 and (2) c1835A>G, pH612R were documented in one patient. Compound heterozygous mutations in RAG1 (1) c.1566G>T, p.W522C and (2) c.2689C>T, p. R897X) were documented in a second patient post-mortem following a fatal opportunistic infection.

CONCLUSION

Astute clinical judgment in the evaluation of patients with PIDD is necessary. Atypical clinical findings such as early onset, granulomatous disease, or opportunistic infections should support the consideration of atypical forms of late onset CID secondary to RAG deficiency. Next generation sequencing approaches provide powerful tools in the investigation of these patients and may expedite definitive treatments.

Phantom rectum following abdominoperineal excision for rectal neoplasm: appearance and disappearance

AIM

The sensation that the rectum remains or is functioning after abdominoperineal excision (APE) is called phantom rectum (PR). Its postoperative and long-term morbidity are not well documented. Informed consent may not include the risk and consequences of this condition. We assessed the incidence and morbidity of PR after APE and compared those with vs those without vertical rectus abdominis myocutaneous flaps.

METHOD

Patients who underwent APE between 1 January 2004 and 31 December 2008 were identified. Preoperative radiation and operative reconstruction by vertical rectus abdominis myocutaneous (VRAM) flaps were noted. Patients were interviewed by telephone to assess the presence and timing of PR symptoms and their effect on quality of life.

RESULTS

Thirty-six of 80 patients who underwent APE were available for follow-up. Twenty-three (64%) described PR symptoms including urgency to evacuate [22 (61%)], sensation of faeces in the rectum [19 (52%)] and sensation of passing flatus [17 (48%)]. Eleven (47%) who had VRAM vs 25 who did not, reported having symptoms of PR at < 3 months after APE. Patients described their symptoms as 'unchanged over time' [20 (56%)], 'gradually decreasing and ultimately disappearing' [13 (35%)] or 'worsening' [3 (9%)]. Preoperative radiation and laparoscopic approach were not associated with PR symptoms. Significantly more patients having a VRAM flap reported early PR symptoms [7/11 (64%) vs 4/25 (16%)] (P = 0.008).

CONCLUSION

PR sensations were experienced by 23 (64%) patients who underwent APE for rectal cancer. VRAM reconstruction was associated with early PR presentation. The possibility of PR should be discussed preoperatively in patients undergoing APE for anorectal neoplasm.

Measures of user experience in a streptococcal pharyngitis and pneumonia clinical decision support tools

OBJECTIVE

To understand clinician adoption of CDS tools as this may provide important insights for the implementation and dissemination of future CDS tools.

MATERIALS AND METHODS

Clinicians (n=168) at a large academic center were randomized into intervention and control arms to assess the impact of strep and pneumonia CDS tools. Intervention arm data were analyzed to examine provider adoption and clinical workflow. Electronic health record data were collected on trigger location, the use of each component and whether an antibiotic, other medication or test was ordered. Frequencies were tabulated and regression analyses were used to determine the association of tool component use and physician orders.

RESULTS

The CDS tool was triggered 586 times over the study period. Diagnosis was the most frequent workflow trigger of the CDS tool (57%) as compared to chief complaint (30%) and diagnosis/antibiotic combinations (13%). Conversely, chief complaint was associated with the highest rate (83%) of triggers leading to an initiation of the CDS tool (opening the risk prediction calculator). Similar patterns were noted for initiation of the CDS bundled ordered set and completion of the entire CDS tool pathway. Completion of risk prediction and bundled order set components were associated with lower rates of antibiotic prescribing (OR 0.5; CI 0.2-1.2 and OR 0.5; CI 0.3-0.9, respectively).

DISCUSSION

Different CDS trigger points in the clinician user workflow lead to substantial variation in downstream use of the CDS tool components. These variations were important as they were associated with significant differences in antibiotic ordering.

CONCLUSIONS

These results highlight the importance of workflow integration and flexibility for CDS success.