Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance

The COVID-19 pandemic has resulted in extensive surveillance of the genomic diversity of SARS-CoV-2. Sequencing data generated as part of these efforts can also capture the diversity of the SARS-CoV-2 virus populations replicating within infected individuals. To assess this within-host diversity of SARS-CoV-2 we quantified low frequency (minor) variants from deep sequence data of thousands of clinical samples collected by a large urban hospital system over the course of a year. Using a robust analytical pipeline to control for technical artefacts, we observe that at comparable viral loads, specimens from patients hospitalized due to COVID-19 had a greater number of minor variants than samples from outpatients. Since individuals with highly diverse viral populations could be disproportionate drivers of new viral lineages in the patient population, these results suggest that transmission control should pay special attention to patients with severe or protracted disease to prevent the spread of novel variants.

Signals of Significantly Increased Vaccine Breakthrough, Decreased Hospitalization Rates, and Less Severe Disease in Patients with Coronavirus Disease 2019 Caused by the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Houston, Texas

Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to dramatically alter the landscape of the coronavirus disease 2019 (COVID-19) pandemic. The recently described variant of concern designated Omicron (B.1.1.529) has rapidly spread worldwide and is now responsible for the majority of COVID-19 cases in many countries. Because Omicron was recognized recently, many knowledge gaps exist about its epidemiology, clinical severity, and disease course. A genome sequencing study of SARS-CoV-2 in the Houston Methodist health care system identified 4468 symptomatic patients with infections caused by Omicron from late November 2021 through January 5, 2022. Omicron rapidly increased in only 3 weeks to cause 90% of all new COVID-19 cases, and at the end of the study period caused 98% of new cases. Compared with patients infected with either Alpha or Delta variants in our health care system, Omicron patients were significantly younger, had significantly increased vaccine breakthrough rates, and were significantly less likely to be hospitalized. Omicron patients required less intense respiratory support and had a shorter length of hospital stay, consistent with on average decreased disease severity. Two patients with Omicron stealth sublineage BA.2 also were identified. The data document the unusually rapid spread and increased occurrence of COVID-19 caused by the Omicron variant in metropolitan Houston, Texas, and address the lack of information about disease character among US patients.

Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas

Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have repeatedly altered the course of the coronavirus disease 2019 (COVID-19) pandemic. Delta variants are now the focus of intense international attention because they are causing widespread COVID-19 globally and are associated with vaccine breakthrough cases. We sequenced 16,965 SARS-CoV-2 genomes from samples acquired March 15, 2021, through September 20, 2021, in the Houston Methodist hospital system. This sample represents 91% of all Methodist system COVID-19 patients during the study period. Delta variants increased rapidly from late April onward to cause 99.9% of all COVID-19 cases and spread throughout the Houston metroplex. Compared with all other variants combined, Delta caused a significantly higher rate of vaccine breakthrough cases (23.7% for Delta compared with 6.6% for all other variants combined). Importantly, significantly fewer fully vaccinated individuals required hospitalization. Vaccine breakthrough cases caused by Delta had a low median PCR cycle threshold value (a proxy for high virus load). This value was similar to the median cycle threshold value for unvaccinated patients with COVID-19 caused by Delta variants, suggesting that fully vaccinated individuals can transmit SARS-CoV-2 to others. Patients infected with Alpha and Delta variants had several significant differences. The integrated analysis indicates that vaccines used in the United States are highly effective in decreasing severe COVID-19, hospitalizations, and deaths.

Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas

Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have repeatedly altered the course of the coronavirus disease 2019 (COVID-19) pandemic. Delta variants are now the focus of intense international attention because they are causing widespread COVID-19 globally and are associated with vaccine breakthrough cases. We sequenced 16,965 SARS-CoV-2 genomes from samples acquired March 15, 2021, through September 20, 2021, in the Houston Methodist hospital system. This sample represents 91% of all Methodist system COVID-19 patients during the study period. Delta variants increased rapidly from late April onward to cause 99.9% of all COVID-19 cases and spread throughout the Houston metroplex. Compared with all other variants combined, Delta caused a significantly higher rate of vaccine breakthrough cases (23.7% for Delta compared with 6.6% for all other variants combined). Importantly, significantly fewer fully vaccinated individuals required hospitalization. Vaccine breakthrough cases caused by Delta had a low median PCR cycle threshold value (a proxy for high virus load). This value was similar to the median cycle threshold value for unvaccinated patients with COVID-19 caused by Delta variants, suggesting that fully vaccinated individuals can transmit SARS-CoV-2 to others. Patients infected with Alpha and Delta variants had several significant differences. The integrated analysis indicates that vaccines used in the United States are highly effective in decreasing severe COVID-19, hospitalizations, and deaths.

Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein

The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses. IMPORTANCE ARTIC Network primers are commonly used by laboratories worldwide to amplify and sequence SARS-CoV-2 present in clinical samples. As new variants have evolved and spread, it was found that the V3 primer set poorly amplified several key mutations. In this report, we compare the results of sequencing a matched set of samples with the V3 and V4 primer sets. We find that adoption of the ARTIC V4 primer set is critical for accurate sequencing of the SARS-CoV-2 spike region. The absence of metadata describing the primer scheme used will negatively impact the downstream use of publicly available SARS-Cov-2 sequencing reads and assembled genomes.

Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein

The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses. IMPORTANCE ARTIC Network primers are commonly used by laboratories worldwide to amplify and sequence SARS-CoV-2 present in clinical samples. As new variants have evolved and spread, it was found that the V3 primer set poorly amplified several key mutations. In this report, we compare the results of sequencing a matched set of samples with the V3 and V4 primer sets. We find that adoption of the ARTIC V4 primer set is critical for accurate sequencing of the SARS-CoV-2 spike region. The absence of metadata describing the primer scheme used will negatively impact the downstream use of publicly available SARS-Cov-2 sequencing reads and assembled genomes.

Real-world Assessment of 2879 COVID-19 Patients Treated With Monoclonal Antibody Therapy: A Propensity Score-Matched Cohort Study

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread globally and cause significant morbidity and mortality. Antispike protein monoclonal antibody (mAb) therapy has been shown to prevent progression to severe coronavirus disease 2019 (COVID-19). The objective of this study was to report the outcomes of high-risk, SARS-CoV-2-positive patients infused with 1 of the 3 mAb therapies available through Food and Drug Administration Emergency Use Authorization (EUA).

Methods

A total of 4328 SARS-CoV-2-positive patients who satisfied EUA criteria for eligibility for receiving mAb therapy were infused with bamlanivimab or the combination therapies bamlanivimab-etesevimab or casirivimab-imdevimab from November 22, 2020, to May 31, 2021, at 6 infusion clinics and multiple emergency departments within the 8 Houston Methodist Hospitals in Houston, Texas. The primary outcome of hospital admission within 14 and 28 days postinfusion was assessed relative to a propensity score-matched cohort, matched based on age, race/ethnicity, median income by zip code, body mass index, comorbidities, and positive polymerase chain reaction date. Secondary outcomes included intensive care unit admission and mortality.

Results

A total of 2879 infused patients and matched controls were included in the analysis, including 1718 patients infused with bamlanivimab, 346 patients infused with bamlanivimab-etesevimab, and 815 patients infused with casirivimab-imdevimab. Hospital admission and mortality rates were significantly decreased overall in mAb-infused patients relative to matched controls. Among the infused cohort, those who received casirivimab-imdevimab had a significantly decreased rate of admission relative to the other 2 mAb therapy groups (adjusted risk ratio,0.51; P=.001).

Conclusions

Treatment with bamlanivimab, bamlanivimab-etesevimab, or casirivimab-imdevimab significantly decreased the number of patients who progressed to severe COVID-19 disease and required hospitalization.

Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences

Certain genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of substantial concern because they may be more transmissible or detrimentally alter the pandemic course and disease features in individual patients. SARS-CoV-2 genome sequences from 12,476 patients in the Houston Methodist health care system diagnosed from January 1 through May 31, 2021 are reported here. Prevalence of the B.1.1.7 (Alpha) variant increased rapidly and caused 63% to 90% of new cases in the latter half of May. Eleven B.1.1.7 genomes had an E484K replacement in spike protein, a change also identified in other SARS-CoV-2 lineages. Compared with non-B.1.1.7-infected patients, individuals with B.1.1.7 had a significantly lower cycle threshold (a proxy for higher virus load) and significantly higher hospitalization rate. Other variants [eg, B.1.429 and B.1.427 (Epsilon), P.1 (Gamma), P.2 (Zeta), and R.1] also increased rapidly, although the magnitude was less than that in B.1.1.7. Twenty-two patients infected with B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants had a high rate of hospitalization. Breakthrough cases (n = 207) in fully vaccinated patients were caused by a heterogeneous array of virus genotypes, including many not currently designated variants of interest or concern. In the aggregate, this study delineates the trajectory of SARS-CoV-2 variants circulating in a major metropolitan area, documents B.1.1.7 as the major cause of new cases in Houston, TX, and heralds the arrival of B.1.617 variants in the metroplex.

Sequence Analysis of 20,453 Severe Acute Respiratory Syndrome Coronavirus 2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern

Since the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there has been international concern about the emergence of virus variants with mutations that increase transmissibility, enhance escape from the human immune response, or otherwise alter biologically important phenotypes. In late 2020, several variants of concern emerged globally, including the UK variant (B.1.1.7), the South Africa variant (B.1.351), Brazil variants (P.1 and P.2), and two related California variants of interest (B.1.429 and B.1.427). These variants are believed to have enhanced transmissibility. For the South Africa and Brazil variants, there is evidence that mutations in spike protein permit it to escape from some vaccines and therapeutic monoclonal antibodies. On the basis of our extensive genome sequencing program involving 20,453 coronavirus disease 2019 patient samples collected from March 2020 to February 2021, we report identification of all six of these SARS-CoV-2 variants among Houston Methodist Hospital (Houston, TX) patients residing in the greater metropolitan area. Although these variants are currently at relatively low frequency (aggregate of 1.1%) in the population, they are geographically widespread. Houston is the first city in the United States in which active circulation of all six current variants of concern has been documented by genome sequencing. As vaccine deployment accelerates, increased genomic surveillance of SARS-CoV-2 is essential to understanding the presence, frequency, and medical impact of consequential variants and their patterns and trajectory of dissemination.

The role of facial contact in infection control: Renewed import in the age of coronavirus

Background

Decreasing facial contact takes on new urgency as society tries to stem the tide of COVID-19 spread. A better understanding of the pervasiveness of facial contact in social settings is required in order to then take steps to mitigate the action.

Methods

YouTube videos of random individuals were included in a behavioral observation study to document rates of contact to the eyes, nose, and mouth area. Factors including age, sex, the presence of eyewear or facial hair, distraction and fatigue were analyzed as possible contributing factors that increase likelihood of facial contact.

Results

The median rate of facial contact was 22 contacts per hour. Men had a significantly higher rate of facial contact compared to women. Age, glasses, and presence of facial hair were not contributing factors. The mouth was the most frequently observed site of contact. Fatigue and distraction may increase rates of facial contact.

Conclusions

Changing personal behavior is a simple and cost-effective action that can be employed to reduce one's risk of acquiring an infectious disease. This study indicates that there are societal differences that put some individuals at higher risk of contracting infectious disease than others.

Significantly Decreased Mortality in a Large Cohort of Coronavirus Disease 2019 (COVID-19) Patients Transfused Early with Convalescent Plasma Containing High-Titer Anti-Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike Protein IgG

Coronavirus disease 2019 (COVID-19) convalescent plasma has emerged as a promising therapy and has been granted Emergency Use Authorization by the US Food and Drug Administration for hospitalized COVID-19 patients. We recently reported results from interim analysis of a propensity score-matched study suggesting that early treatment of COVID-19 patients with convalescent plasma containing high-titer anti-spike protein receptor binding domain (RBD) IgG significantly decreases mortality. We herein present results from a 60-day follow-up of a cohort of 351 transfused hospitalized patients. Prospective determination of enzyme-linked immunosorbent assay anti-RBD IgG titer facilitated selection and transfusion of the highest titer units available. Retrospective analysis by the Ortho VITROS IgG assay revealed a median signal/cutoff ratio of 24.0 for transfused units, a value far exceeding the recent US Food and Drug Administration-required cutoff of 12.0 for designation of high-titer convalescent plasma. With respect to altering mortality, our analysis identified an optimal window of 44 hours after hospitalization for transfusing COVID-19 patients with high-titer convalescent plasma. In the aggregate, the analysis confirms and extends our previous preliminary finding that transfusion of COVID-19 patients soon after hospitalization with high-titer anti-spike protein RBD IgG present in convalescent plasma significantly reduces mortality.

Convalescent plasma anti-SARS-CoV-2 spike protein ectodomain and receptor-binding domain IgG correlate with virus neutralization

The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the urgent need for assays that detect protective levels of neutralizing antibodies. We studied the relationship among anti-spike ectodomain (anti-ECD), anti-receptor-binding domain (anti-RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by 2 in vitro assays using convalescent plasma samples from 68 patients with COVID-19. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers and in vitro VN titers. The probability of a VN titer of ≥160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment, was ≥80% when anti-RBD or anti-ECD titers were ≥1:1350. Of all donors, 37% lacked VN titers of ≥160. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease VN or IgG titers. Analysis of 2814 asymptomatic adults found 73 individuals with anti-ECD IgG titers of ≥1:50 and strong positive correlation with anti-RBD and VN titers. Fourteen of these individuals had VN titers of ≥1:160, and all of them had anti-RBD titers of ≥1:1350. We conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titers of ≥1:1350 may provide critical information about protection against COVID-19 disease.

Treatment of Coronavirus Disease 2019 Patients with Convalescent Plasma Reveals a Signal of Significantly Decreased Mortality

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, has spread globally, and proven treatments are limited. Transfusion of convalescent plasma collected from donors who have recovered from COVID-19 is among many approaches being studied as potentially efficacious therapy. We are conducting a prospective, propensity score-matched study assessing the efficacy of COVID-19 convalescent plasma transfusion versus standard of care as treatment for severe and/or critical COVID-19. We present herein the results of an interim analysis of 316 patients enrolled at Houston Methodist hospitals from March 28 to July 6, 2020. Of the 316 transfused patients, 136 met a 28-day outcome and were matched to 251 non-transfused control COVID-19 patients. Matching criteria included age, sex, body mass index, comorbidities, and baseline ventilation requirement 48 hours from admission, and in a second matching analysis, ventilation status at day 0. Variability in the timing of transfusion relative to admission and titer of antibodies of plasma transfused allowed for analysis in specific matched cohorts. The analysis showed a significant reduction (P = 0.047) in mortality within 28 days, specifically in patients transfused within 72 hours of admission with plasma with an anti-spike protein receptor binding domain titer of ≥1:1350. These data suggest that treatment of COVID-19 with high anti-receptor binding domain IgG titer convalescent plasma is efficacious in early-disease patients.

Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area

We sequenced the genomes of 5,085 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains causing two coronavirus disease 2019 (COVID-19) disease waves in metropolitan Houston, TX, an ethnically diverse region with 7 million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston and from viruses recovered in an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotype and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein-the primary target of global vaccine efforts-are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR3022. Our report represents the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.IMPORTANCE There is concern about second and subsequent waves of COVID-19 caused by the SARS-CoV-2 coronavirus occurring in communities globally that had an initial disease wave. Metropolitan Houston, TX, with a population of 7 million, is experiencing a massive second disease wave that began in late May 2020. To understand SARS-CoV-2 molecular population genomic architecture and evolution and the relationship between virus genotypes and patient features, we sequenced the genomes of 5,085 SARS-CoV-2 strains from these two waves. Our report provides the first molecular characterization of SARS-CoV-2 strains causing two distinct COVID-19 disease waves.

Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area

We sequenced the genomes of 5,085 SARS-CoV-2 strains causing two COVID-19 disease waves in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston, and an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotypes and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein - the primary target of global vaccine efforts - are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR30022. Our study is the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves, and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.

Treatment of Coronavirus Disease 2019 (COVID-19) Patients with Convalescent Plasma

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, has spread globally, and no proven treatments are available. Convalescent plasma therapy has been used with varying degrees of success to treat severe microbial infections for >100 years. Patients (n = 25) with severe and/or life-threatening COVID-19 disease were enrolled at the Houston Methodist hospitals from March 28, 2020, to April 14, 2020. Patients were transfused with convalescent plasma, obtained from donors with confirmed severe acute respiratory syndrome coronavirus 2 infection who had recovered. The primary study outcome was safety, and the secondary outcome was clinical status at day 14 after transfusion. Clinical improvement was assessed on the basis of a modified World Health Organization six-point ordinal scale and laboratory parameters. Viral genome sequencing was performed on donor and recipient strains. At day 7 after transfusion with convalescent plasma, nine patients had at least a one-point improvement in clinical scale, and seven of those were discharged. By day 14 after transfusion, 19 (76%) patients had at least a one-point improvement in clinical status, and 11 were discharged. No adverse events as a result of plasma transfusion were observed. Whole genome sequencing data did not identify a strain genotype-disease severity correlation. The data indicate that administration of convalescent plasma is a safe treatment option for those with severe COVID-19 disease.

Relationship between Anti-Spike Protein Antibody Titers and SARS-CoV-2 In Vitro Virus Neutralization in Convalescent Plasma

Newly emerged pathogens such as SARS-CoV-2 highlight the urgent need for assays that detect levels of neutralizing antibodies that may be protective. We studied the relationship between anti-spike ectodomain (ECD) and anti-receptor binding domain (RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by two different in vitro assays using convalescent plasma samples obtained from 68 COVID-19 patients, including 13 who donated plasma multiple times. Only 23% (16/68) of donors had been hospitalized. We also studied 16 samples from subjects found to have anti-spike protein IgG during surveillance screening of asymptomatic individuals. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers, and in vitro VN titer. Anti-RBD plasma IgG correlated slightly better than anti-ECD IgG titer with VN titer. The probability of a VN titer ≥160 was 80% or greater with anti-RBD or anti-ECD titers of ≥1:1350. Thirty-seven percent (25/68) of convalescent plasma donors lacked VN titers ≥160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease either VN or IgG titers. Analysis of 2,814 asymptomatic adults found 27 individuals with anti-RBD or anti-ECD IgG titers of ≥1:1350, and evidence of VN ≥1:160. Taken together, we conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titer of ≥1:1350 may provide critical information about protection against COVID-19 disease.

Treatment of COVID-19 Patients with Convalescent Plasma in Houston, Texas

BACKGROUND

COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread globally, and no proven treatments are available. Convalescent plasma therapy has been used with varying degrees of success to treat severe microbial infections for more than 100 years.

METHODS

Patients (n=25) with severe and/or life-threatening COVID-19 disease were enrolled at the Houston Methodist hospitals from March 28 to April 14, 2020. Patients were transfused with convalescent plasma obtained from donors with confirmed SARS-CoV-2 infection and had been symptom free for 14 days. The primary study outcome was safety, and the secondary outcome was clinical status at day 14 post-transfusion. Clinical improvement was assessed based on a modified World Health Organization 6-point ordinal scale and laboratory parameters. Viral genome sequencing was performed on donor and recipient strains.

RESULTS

At baseline, all patients were receiving supportive care, including anti-inflammatory and anti-viral treatments, and all patients were on oxygen support. At day 7 post-transfusion with convalescent plasma, nine patients had at least a 1-point improvement in clinical scale, and seven of those were discharged. By day 14 post-transfusion, 19 (76%) patients had at least a 1-point improvement in clinical status and 11 were discharged. No adverse events as a result of plasma transfusion were observed. The whole genome sequencing data did not identify a strain genotype-disease severity correlation.

CONCLUSIONS

The data indicate that administration of convalescent plasma is a safe treatment option for those with severe COVID-19 disease. Randomized, controlled trials are needed to determine its efficacy.

Development and validation of Houston Methodist Variant Viewer version 3: updates to our application for interpretation of next-generation sequencing data

Objectives

Informatics tools that support next-generation sequencing workflows are essential to deliver timely interpretation of somatic variants in cancer. Here, we describe significant updates to our laboratory developed bioinformatics pipelines and data management application termed Houston Methodist Variant Viewer (HMVV).

Materials and Methods

We collected feature requests and workflow improvement suggestions from the end-users of HMVV version 1. Over 1.5 years, we iteratively implemented these features in five sequential updates to HMVV version 3.

Results

We improved the performance and data throughput of the application while reducing the opportunity for manual data entry errors. We enabled end-user workflows for pipeline monitoring, variant interpretation and annotation, and integration with our laboratory information system. System maintenance was improved through enhanced defect reporting, heightened data security, and improved modularity in the code and system environments.

Discussion and Conclusion

Validation of each HMVV update was performed according to expert guidelines. We enabled an 8× reduction in the bioinformatics pipeline computation time for our longest running assay. Our molecular pathologists can interpret the assay results at least 2 days sooner than was previously possible. The application and pipeline code are publicly available at https://github.com/hmvv.

Real-time Communication With Health Care Providers Through an Online Respiratory Pathogen Laboratory Report

We implemented a real-time report to distribute respiratory pathogen data for our 8-hospital system to anyone with an Internet connection and a web browser. Real-time access to accurate regional laboratory observation data during an epidemic influenza season can guide diagnostic and therapeutic strategies.

In situ FTIR studies on the oxidation of isopropyl alcohol over SnO2 as a function of temperature up to 600 °C and a comparison to the analogous plasma-driven process

This paper reports the application of in situ reflectance Fourier Transform InfraRed spectroscopy to the study of the thermal and plasma driven reaction of IsoPropyl Alcohol (IPA) at SnO2-coated Macor, the latter a ceramic material comprised of the oxides of Al, Mg and Si. The data so obtained were compared to those obtained using uncoated Macor. When uncoated Macor was employed, no reaction of the IPA was observed up to 600 °C in the thermal experiments, whereas a number of products were observed in the plasma-driven experiments. The results obtained using coated Macor were somewhat different, with no reaction taking place in the plasma-driven experiments, whilst significant reaction took place in the thermally-driven process. In the latter experiments, the chemistry was observed to show four distinct temperature regions, with electron injection into the conduction band of the SnO2 playing a significant role, culminating in the production of CO2. The data were interpreted in terms of a model in which physisorbed IPA was converted to two forms of isopropoxide: this was converted to acetone and acetaldehyde via adsorbed enolate. The data clearly support the catalytic activity of Macor in the plasma-driven conversion of IPA.

Houston Methodist Variant Viewer: An Application to Support Clinical Laboratory Interpretation of Next-generation Sequencing Data for Cancer

Introduction

Next-generation-sequencing (NGS) is increasingly used in clinical and research protocols for patients with cancer. NGS assays are routinely used in clinical laboratories to detect mutations bearing on cancer diagnosis, prognosis and personalized therapy. A typical assay may interrogate 50 or more gene targets that encompass many thousands of possible gene variants. Analysis of NGS data in cancer is a labor-intensive process that can become overwhelming to the molecular pathologist or research scientist. Although commercial tools for NGS data analysis and interpretation are available, they are often costly, lack key functionality or cannot be customized by the end user.

Methods

To facilitate NGS data analysis in our clinical molecular diagnostics laboratory, we created a custom bioinformatics tool termed Houston Methodist Variant Viewer (HMVV). HMVV is a Java-based solution that integrates sequencing instrument output, bioinformatics analysis, storage resources and end user interface.

Results

Compared to the predicate method used in our clinical laboratory, HMVV markedly simplifies the bioinformatics workflow for the molecular technologist and facilitates the variant review by the molecular pathologist. Importantly, HMVV reduces time spent researching the biological significance of the variants detected, standardizes the online resources used to perform the variant investigation and assists generation of the annotated report for the electronic medical record. HMVV also maintains a searchable variant database, including the variant annotations generated by the pathologist, which is useful for downstream quality improvement and research projects.

Conclusions

HMVV is a clinical grade, low-cost, feature-rich, highly customizable platform that we have made available for continued development by the pathology informatics community.

RecutClub.com: An Open Source, Whole Slide Image-based Pathology Education System

BACKGROUND

Our institution's pathology unknown conferences provide educational cases for our residents. However, the cases have not been previously available digitally, have not been collated for postconference review, and were not accessible to a wider audience. Our objective was to create an inexpensive whole slide image (WSI) education suite to address these limitations and improve the education of pathology trainees.

MATERIALS AND METHODS

We surveyed residents regarding their preference between four unique WSI systems. We then scanned weekly unknown conference cases and study set cases and uploaded them to our custom built WSI viewer located at RecutClub.com. We measured site utilization and conference participation.

RESULTS

Residents preferred our OpenLayers WSI implementation to Ventana Virtuoso, Google Maps API, and OpenSlide. Over 16 months, we uploaded 1366 cases from 77 conferences and ten study sets, occupying 793.5 GB of cloud storage. Based on resident evaluations, the interface was easy to use and demonstrated minimal latency. Residents are able to review cases from home and from their mobile devices. Worldwide, 955 unique IP addresses from 52 countries have viewed cases in our site.

CONCLUSIONS

We implemented a low-cost, publicly available repository of WSI slides for resident education. Our trainees are very satisfied with the freedom to preview either the glass slides or WSI and review the WSI postconference. Both local users and worldwide users actively and repeatedly view cases in our study set.

An in situ FTIR spectroscopic and thermogravimetric analysis study of the dehydration and dihydroxylation of SnO2: the contribution of the (100), (110) and (111) facets

Nanoparticulate SnO2 produced by a hydrothermal method was characterised by BET, XRD, TGA-MS and in situ variable temperature diffuse reflectance infra red spectroscopy (DRIFTS) to determine the surface behaviour of water. For the (100) facets, hydrogen bonding does not occur, and water adsorption is less strong than for the (111) and (110) facets where hydrogen bonding does occur. Reversible uptake of oxygen was observed. These findings have implications for other surface-gas reactions in which Ni and Sb co-doped SnO2 (NATO) anodes are used for ozone generation. BET showed the relatively high surface area and nanometer scale of the SnO2 particles, whilst XRD confirmed the nano dimension of the crystallites and showed only the cassiterite phase. TGA analysis indicated four temperature regions over which mass loss was observed. These and the in situ DRIFTS studies revealed the existence of various forms of water associated with specific crystal facets of the SnO2, as well as the existence of isolated O-H groups and adsorbed oxygen species. Electronic absorptions were also observed and the data rationalised in terms of the existence of both free electron absorptions, and absorptions from oxygen vacancy states. The role of adsorbed molecular oxygen in electrochemical ozone generation at Ni and Sb co-doped SnO2 (NATO) anodes was strongly suggested by this work.

Alterations in molecular muscle mass regulators after 8 days immobilizing Special Forces mission

In military operations, declined physical capacity can endanger the life of soldiers. During special support and reconnaissance (SSR) missions, Special Forces soldiers sustain 1-2 weeks full-body horizontal immobilization, which impairs muscle strength and performance. Adequate muscle mass and strength are necessary in combat or evacuation situations, which prompt for improved understanding of muscle mass modulation during SSR missions. To explore the molecular regulation of myofiber size during a simulated SSR operation, nine male Special Forces soldiers were biopsied in m. vastus lateralis pre and post 8 days immobilizing restricted prone position. After immobilization, total mammalian target of rapamycin protein was reduced by 42% (P < 0.05), whereas total and phosphorylated protein levels of Akt, ribosomal protein S6k, 4E-BP1, and glycogen synthase kinase3β were unchanged. Messenger RNA (mRNA) levels of the atrogenes forkhead box O3 (FoxO3), atrogin1, and muscle ring finger protein1 (MuRF1) increased by 36%, 53%, and 71% (P < 0.01), MuRF1 protein by 51% (P = 0.05), whereas FoxO1 and peroxisome proliferator-activated receptor γ coactivator-1 β mRNAs decreased by 29% and 40% (P < 0.01). In conclusion, occupational immobilization in Special Forces soldiers led to modulations in molecular muscle mass regulators during 8 days prone SSR mission, which likely contribute to muscle loss observed in such operations. The present data expand our knowledge of human muscle mass regulation during short-term immobilization.

Al2O3 Disk Supported Si3N4 Hydrogen Purification Membrane for Low Temperature Polymer Electrolyte Membrane Fuel Cells

Reformate gas, a commonly employed fuel for polymer electrolyte membrane fuel cells (PEMFCs), contains carbon monoxide, which poisons Pt-containing anodes in such devices. A novel, low-cost mesoporous Si3N4 selective gas separation material was tested as a hydrogen clean-up membrane to remove CO from simulated feed gas to single-cell PEMFC, employing Nafion as the polymer electrolyte membrane. Polarization and power density measurements and gas chromatography showed a clear effect of separating the CO from the gas mixture; the performance and durability of the fuel cell was thereby significantly improved.

A Monoclonal Antibody to Lewis Y/Lewis b Revealing Mimicry of the Histone H1 to Carbohydrate Structures

Antibodies to either peptide or carbohydrate tumour antigens are established tools for diagnostics and therapy. We here describe an antibody (A70-A/A9) recognizing a carbohydrate epitope common to the tumour-associated Lewis Y and Lewis b antigens (Fucalpha1-2Galbeta1-4/3[Fucalpha1-3/4]GlcNAcbeta-). Its specificity was established without doubt with a panel of 86 synthetic mono- and oligosaccharidic structures. This antibody was found to cross-react with the nuclear protein histone H1. Binding to H1 was specific, periodate-insensitive (non-carbohydrate) and saturable. Histone H1 was able to inhibit Lewis Y binding very effectively in a concentration-dependent manner. We conclude that it represents an example of natural peptide mimicry of a carbohydrate epitope. It may explain the observed occurrence of 'anti-histone autoantibodies' in cancer patients.

PtRu/Ti anodes with varying Pt ? Ru ratio prepared by electrodeposition for the direct methanol fuel cell

PtRu/Ti anodes with varying Pt ratio Ru ratio were prepared by electrodeposition of a thin PtRu catalyst layer onto Ti mesh for a direct methanol fuel cell (DMFC). The morphology and structure of the catalyst layers were analyzed by SEM, EDX and XRD. The catalyst coating layer shows an alloy character. The relative activities of the PtRu/Ti electrodes were assessed and compared in half cell and single DMFC experiments. The results show that these electrodes are very active for the methanol oxidation and that the optimum Ru surface coverage was ca. 9 at.% for DMFC operating at 20 degrees C and 11 at.% at 60 degrees C. The PtRu/Ti anode shows a performance comparable to that of the conventional carbon-based anode in a DMFC operating with 0.25 M or 0.5 M methanol solution and atmosphere oxygen gas at 90 degrees C.

Photoelectrocatalytic disinfection of E. coli suspensions by iron doped TiO2

Photoelectrocatalytic disinfection of E. coli by an iron doped TiO(2) sol-gel electrode is shown to be more efficient than disinfection by the corresponding undoped electrode. Thus, the improvements in photocatalytic efficiency associated with selective doping have been combined with the electric field enhancement associated with the application of a small positive potential to a UV irradiated titanium dioxide electrode. The optimum disinfection rate corresponds to the replacement of approximately 0.1% of the Ti atoms by Fe. The enhanced disinfection associated with iron doping is surprising because iron doping decreases the photocurrent, and photocurrent is generally taken to be a good indicator of photoelectrocatalytic efficiency. As the level of iron is increased, the character of the current-voltage curve changes and the enhancement of photocurrent associated with methanol addition decreases. This suggests that iron reduces the surface recombination which in the absence of iron is reduced by methanol. Therefore the enhanced photocatalysis is interpreted as due to iron reducing surface recombination, by trapping electrons. It is proposed that at low iron levels the photo-generated electrons are trapped at surface Fe(III) centres and that consequently, because the electron-hole recombination rate is reduced, the number of holes available for hydroxyl radical formation is increased. It is also proposed that at higher iron levels, the disinfection rate falls because electron hole recombination at iron centres in the lattice reduces the number of holes which reach the surface. Our conclusion that the optimum electrode performance is a balance between surface and bulk effects is consistent with the proposal, of earlier authors for photocatalytic reactions, that the optimum dopant level depends on the TiO(2).

A novel electrochemical device for the disinfection of fluids by OH radicals

This paper describes a novel, composite device, based not on optical excitation but on the transfer of holes from Si to the TiO(2)/air or TiO(2)/water interface, for the disinfection and detoxification of fluid streams.

Electrochemical hydrodehalogenation of 2,4-dibromophenolin paraffin oil using a solid polymer electrolyte reactor

A new technology for remediation of halogenated organics-oil systems, which can cause serious environmental problems, has been demonstrated using the electrochemical hydrodehalogenation of 2,4-dibromophenol (DBP) in paraffin oil in a solid polymer electrolyte reactor. The reactor has been evaluated in terms of cathode materials and structure and the ratio of the cathode surface area to the solution volume. A cathode of titanium minimesh with a palladium electrocatalyst produced by electrodeposition was particularly effective. Current efficiencies of up to 85% and percentage of DBP removal of up to 62%, space-time yields of up to 7.6 kg DBP m(-3) h(-1), and energy consumption as low as 1.6 kW h (kg of DBP)(-1) were achieved. The reactor showed stable operation for periods of up to 170 h. The results demonstrated that electroreduction could be an alternative technology to electrooxidation forthe treatment of wastes and toxic halogenated compounds, making the process simpler in comparison to electrooxidation.

In situ FTIR studies on the electrochemical reduction of halogenated phenols

Electrochemical reduction of a variety of mono- and di-chloro- and bromo- phenols at a palladised titanium electrode afforded phenolate in all cases according to in situ FTIR studies, with the same intermediate species being observed in some cases.

In situ FTIR studies on the effect of temperature on the electro-oxidation of small organic molecules at the Ru(0001) electrode

The adsorption and electro-oxidation of formaldehyde, formic acid and methanol at the Ru(0001) electrode in perchloric acid solution have been studied as a function of temperature, potential and time using in situ FTIR spectroscopy, and the results interpreted in terms of the surface chemistry of the Ru(000 1) electrode and compared to those obtained during our previous studies on the adsorption of CO under the same conditions. It was found that no dissociative adsorption or electro-oxidation of methanol takes place at Ru(0001) at potentials < 900 mV vs. Ag/AgCl, and at all three temperatures employed, 10, 25 and 50 degrees C. However, both formaldehyde and formic acid did undergo dissociative adsorption, even at -200 mV, to form linear (CO(L)) and 3-fold-hollow (COH) binding CO adsorbates. In contrast to the adsorption of CO, it was found that increasing the temperature to 50 degrees C markedly increased the amount of CO adsorbates formed on the Ru(0001) surface from the adsorption of both formaldehyde and formic acid. On increasing the potential, the electro-oxidation of the CO adsorbates to CO2 took place via reaction with the active (1 x 1)-O oxide. Formic acid was detected as a partial oxidation product during formaldehyde electro-oxidation. At all three temperatures employed, it was found that adsorbed CO species were formed from the adsorption of both formic acid and formaldehyde, and were oxidised to CO2 faster than was observed in the experiments involving CO adsorbed from CO(g), suggesting a higher mobility of the CO adsorbates formed from the adsorption of the HCOOH and HCHO. At potentials > 1000 mV, both the oxidation of formic acid to CO2 and the oxidation of formaldehyde to both CO2 and formic acid were significantly increased, and the oxidation of methanol to CO2 and methyl formate was observed, all of which were attributed to the formation of an active RuO2 phase on the Ru(0001) surface.

Fate of Cryptosporidium oocysts in an immobilised titanium dioxide reactor with electric field enhancement

We have undertaken simple proof of principle experiments to find out if electric field enhanced photo-oxidation using immobilised titanium dioxide will damage Cryptosporidium oocysts. Using a simple Petri dish reactor and two forms of immobilised titanium catalyst (sol-gel and thermal-film) we have tested the ability of this technology to affect Cryptosporidium oocysts permeability assessed by propidium iodide exclusion. Test and control reactor runs were significantly different (P = 0.007). The thermal-film reactor had the greatest effect (approximately 27% of the seed) and was statistically distinguishable from the sol-gel reactor and the controls. The sol-gel reactor showed an increase in oocyst permeability, but was not statistically distinguishable from one of the controls. The enhanced performance of the thermal film reactor is attributed to the superior conversion of photochemical holes to hydroxyl radicals at the surface of this catalyst.

Spectroelectrochemical characterisation of poly[Ni(saltMe)]-modified electrodes

Electrogenerated polymers based on the nickel(II) complex 2,3-dimethyl-N,N'-bis(salicylidene)butane-2,3-diaminatonickel(II), poly[Ni(saltMe)], were characterised by in situ FTIR and UV/Vis spectroscopy and ex-situ EPR spectroscopy in order to gain insights into film structure, electronic states and charge conduction. The role of the nickel ions during film oxidation was probed by using EPR to study naturally abundant Ni and 61Ni-enriched polymers. The data from all the spectroscopic techniques are consistent, and clearly indicate that polymerisation and redox switching are associated with oxidative ligand based processes; coulometry suggests that one positive charge was delocalised through each monomer unit. EPR provided evidence for the non-direct involvement of the metal in polymer oxidation: the polymer is best described as a polyphenylene-type compound (conducting polymer), rather than an aggregation of nickel complexes (redox polymer), and the main charge carriers are identified as polarons. An explanation for the high electrochemical stability and conductivity of poly[Ni(saltMe)] with respect to that of poly[Ni(salen)] is proposed. based on stereochemical repulsion between monomeric units; this can impose a less compact supramolecular structure on polymers with bulkier substituents.

Specific binding of alpha-macroglobulin to complement-type repeat CR4 of the low-density lipoprotein receptor-related protein

The low-density lipoprotein receptor-related protein (LRP) is a large surface receptor that mediates binding and internalization of a large number of structurally and functionally unrelated ligands. The ligand binding sites are located in clusters of complement-type repeats (CR), where the general absence of mutual binding competition suggests that different ligands map to distinct sites. Binding of alpha(2)-macroglobulin-protease complexes to the LRP is mediated by the receptor binding domain (RBD) of alpha(2)-macroglobulin (alpha(2)M). To determine the major binding epitope(s) in the LRP, we generated a complete set of tandem CR proteins spanning the second cluster of CR domains, and identified a binding site for alpha(2)M in the N-terminal part of the cluster comprising CR3-CR6, using ligand blotting and surface plasmon resonance (SPR) analysis. The specific site involved in alpha(2)M recognition resides in the fourth CR domain, CR4, whereas another site is identified in CR5. An acidic epitope in CR4 is identified as important for binding alpha(2)M by mutagenesis and SPR analysis. The formation of the complex between the rat alpha(1)-macroglobulin RBD and CR domain pairs is characterized by analytical size-exclusion chromatography, which demonstrates a sufficiently strong interaction between the alpha(1)M RBD and CR34 or CR45 for the isolation of a complex.

Identification of the minimal functional unit in the low density lipoprotein receptor-related protein for binding the receptor-associated protein (RAP). A conserved acidic residue in the complement-type repeats is important for recognition of RAP

The low density lipoprotein receptor-related protein (LRP), a member of the low density lipoprotein receptor family, mediates the internalization of a diverse set of ligands. The ligand binding sites are located in different regions of clusters consisting of approximately 40 residues, cysteine-rich complement-type repeats (CRs). The 39-40-kDa receptor-associated protein, a folding chaperone/escort protein required for efficient transport of functional LRP to the cell surface, is an antagonist of all identified ligands. To analyze the multisite inhibition by RAP in ligand binding of LRP, we have used an Escherichia coli expression system to produce fragments of the entire second ligand binding cluster of LRP (CR3-10). By ligand affinity chromatography and surface plasmon resonance analysis, we show that RAP binds to all two-repeat modules except CR910. CR10 differs from other repeats in cluster II by not containing a surface-exposed conserved acidic residue between Cys(IV) and Cys(V). By site-directed mutagenesis and ligand competition analysis, we provide evidence for a crucial importance of this conserved residue for RAP binding. We provide experimental evidence showing that two adjacent complement-type repeats, both containing a conserved acidic residue, represent a minimal unit required for efficient binding to RAP.

Behçet's syndrome presenting with peripheral arterial aneurysms

A case of Behçet's syndrome is described presenting with several peripheral arterial aneurysms. The diagnostic criteria are discussed and the need for increased vigilance of this disease is stressed due to an increasing number of immigrants.

Electroacupuncture in anaesthesia for hysterectomy

We have studied the effects of electroacupuncture at classical acupuncture points, applied before and during surgery in patients undergoing hysterectomy, on postoperative pain and metabolic stress responses in a prospective, randomized and patient-blinded manner. Fifty otherwise healthy women were allocated randomly to receive or not receive electroacupuncture. Electroacupuncture was begun 20 min before skin incision and continued to the end of surgery. All patients received similar general anaesthesia and all received patient-controlled analgesia (PCA) after operation. Postoperative pain in the two groups was evaluated by recording analgesic requirements by PCA and by pain-rating performed by patients and nursing staff. There were no significant differences between the two groups in postoperative analgesic requirements, pain-rating or metabolic stress responses.