SARS-CoV-2 Antiviral Prescribing Gaps Among Non-Hospitalized High-Risk Adults

Within a multi-state clinical cohort, SARS-CoV-2 antiviral prescribing patterns were evaluated from April 2022-June 2023 among non-hospitalized SARS-CoV-2-infected patients with risk factors for severe COVID-19. Among 3,247 adults, only 31.9% were prescribed an antiviral agent (87.6% nirmatrelvir/ritonavir, 11.9% molnupiravir, 0.5% remdesivir), highlighting the need to identify and address treatment barriers.

Risk scores' performance and their impact on operative decision-making in left-sided endocarditis: a cohort study

The accuracy of contemporary risk scores in predicting perioperative mortality in infective endocarditis (IE) remains controversial. The aim is to evaluate the performance of existent mortality risk scores for cardiovascular surgery in IE and the impact on operability at high-risk thresholds. A single-center retrospective review of adult patients diagnosed with acute left-sided IE undergoing surgery from May 2014 to August 2019 (n = 142) was done. Individualized risk calculation was obtained according to the available mortality risk scores: EuroScore I and II, PALSUSE, Risk-E, Costa, De Feo-Cotrufo, AEPEI, STS-risk, STS-IE, APORTEI, and ICE-PCS scores. A cross-validation analysis was performed on the score with the best area under the curve (AUC). The 30-day survival was 96.5% (95%CI 91-98%). The score with worse area under the curve (AUC = 0.6) was the STS-IE score, while the higher was for the RISK-E score (AUC = 0.89). The AUC of the majority of risk scores suggested acceptable performance; however, statistically significant differences in expected versus observed mortalities were common. The cross-validation analysis showed that a large number of survivors (> 75%) would not have been operated if arbitrary high-risk threshold estimates had been used to deny surgery. The observed mortality in our cohort is significantly lower than is predicted by contemporary risk scores. Despite the reasonable numeric performance of the analyzed scores, their utility in judging the operability of a given patient remains questionable, as demonstrated in the cross-validation analysis. Future guidelines may advise that denial of surgery should only follow a highly experienced Endocarditis Team evaluation.

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

BACKGROUND

Between November 2021 and February 2022, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events.

METHODS

We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant.

FINDINGS

We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5' end of the viral genome was from the Delta genome and the 3' end from Omicron, including the majority of the spike protein gene, though the breakpoints were different.

CONCLUSIONS

Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared with the circulating Omicron lineages.

FUNDING

This research was supported by the NIH RADx initiative and by the Centers for Disease Control Contract 75D30121C12730 (Helix).

Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative

Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.

Effect of feeding fresh forage plantain (Plantago lanceolata) or ryegrass-based pasture on methane emissions, total-tract digestibility, and rumen fermentation of nonlactating dairy cows

Plantain (Plantago lanceolata) is an herb used to reduce the forage deficit of ryegrass-based pastures during the summer. This herb is being promoted for its reduced environmental impact in terms of nitrogen emissions, particularly reducing urinary nitrogen. However, the effect of plantain on emissions of enteric CH₄, the main greenhouse gas produced from ruminant-based production systems, is not known. The aim of the present trial was to determine CH₄ emissions and rumen fermentation characteristics of nonlactating dairy cows fed 100% plantain (PLT) or 100% perennial ryegrass (RG; Lolium perenne) in 2 experiments (E1 and E2). The forages were in a vegetative growth stage in E1 and were in a reproductive growth stage in E2. Methane emissions from 16 cows in each experiment were measured in respiration chambers for 2 d. Methane emissions per unit of dry matter intake (CH₄ yield) were 15 and 28% less for cows fed PLT than those fed RG in E1 and E2, respectively. Dry matter digestibility of PLT was 7 and 27% less than that of RG in E1 and E2, respectively, and CH₄ per unit of dry matter digested was similar for PLT and RG in both experiments. There were only minor (but some significant) differences in rumen fermentation characteristics between cows fed PLT and RG in both experiments. In conclusion, CH₄ yield was lower for cows fed PLT compared with those fed RG in both experiments and this reduction was largely explained by the lesser dry matter digestibility of PLT.

SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads

We report on the sequencing of 74,348 SARS-CoV-2 positive samples collected across the United States and show that the Delta variant, first detected in the United States in March 2021, made up the majority of SARS-CoV-2 infections by July 1, 2021 and accounted for >99.9% of the infections by September 2021. Not only did Delta displace variant Alpha, which was the dominant variant at the time, it also displaced the Gamma, Iota, and Mu variants. Through an analysis of quantification cycle (Cq) values, we demonstrate that Delta infections tend to have a 1.7× higher viral load compared to Alpha infections (a decrease of 0.8 Cq) on average. Our results are consistent with the hypothesis that the increased transmissibility of the Delta variant could be due to the ability of the Delta variant to establish a higher viral load earlier in the infection as compared to the Alpha variant.

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Alpha was dominant in spring 2021 and went extinct in fall 2021 in the United States

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Delta also displaced Gamma, Iota, and Mu variants

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On average, viral load was ∼1.7× higher in Delta infections versus Alpha infections

Extracellular Polymeric Substances (EPS) produced by Streptomyces sp. biofilms: Chemical composition and anticancer properties

The extracellular polymeric substances (EPS) have shown free radical scavenging and antitumor activity against both breast and colon cell lines. In this regard, actinobacteria have become an increasingly popular sources of EPS. Therefore, in this study four Streptomyces strains isolated from contaminated soil (M7, A5, A14 and MC1) were evaluated for determining its biofilm-forming capacity including under pesticide stress. In addition, chemical composition of EPS and its cytotoxic effects over 4T1 breast cancer cell and Caco-2 human tumor colon cells were evaluated. The results demonstrated that Streptomyces sp. A5 had the highest capability to develop biofilm more than other strains tested, even under pesticide stress. Moreover, this strain produced EPS with a total protein/total polysaccharide rate of 1.59 ± 0.05. On the other hand, cytotoxicity assays of EPS showed that Streptomyces sp. A5 display a higher toxic effect against 4T1 Breast cancer cells (96.2 ± 13.5 %), Caco-2 (73.9 ± 6.4 %) and low toxicity (29.9 % ± 9.1 %) against non-transformed intestinal cells (IEC-18). Data do not show cytotoxic effect relationship with biofilm-forming capabilities of strains, nor the chemical composition of EPS matrix. The gene that codes for polysaccharide deacetylase, parB-like and transRDD proteins, were identified. These results contribute to the knowledge about the variability of chemical composition and potential cytotoxic properties of EPS produced by Streptomyces biofilms. It proposes interesting future challenges for linking Streptomyces-based pesticide remediation technology with the development of new antitumor drugs.

Predictive factors for requiring heart transplantation in patients with hypertrophic cardiomyopathy: data from a referral center

Background

Heart transplant (HT) remains the last treatment option for patients with non-obstructive hypertrophic cardiomyopathy (HCM) who develop end-stage heart failure (HF). Early identification of patients who may require a HT in the future is crucial in order to advise them, establish the appropriate follow-up and determine the appropriate time to include them in the waiting list.

Objectives

Our study sought to find predictive factors related with requiring HT during follow-up in patients with HCM.

Methods

Consecutive patients with HCM referred to a HCM monographic clinic from 2018 to 2020 (HCM controls) and transplanted patients due to HCM in the same tertiary HT hospital since 2003 (cases) were included. Baseline (on the date of HCM diagnosis) and longitudinal data regarding clinical, genetic, ECG and echocardiographic variables were retrospectively evaluated. Follow-up was registered from HCM diagnosis to HT (in cases) or last medical check up (controls).

Results

A total of 157 patients (24 HCM-HT cases and 133 HCM controls) were included (45±19 yo; 57% male). At the time of MCH diagnosis (Table), cases were significantly younger than controls, were more frequently symptomatic and showed significantly higher BNP levels and more advanced diastolic dysfunction (larger left atrium, higher E/A ratio and lower e'); also, HCM-HT reported more family history and had higher proportion of pathogenic mutations (being MYH7 the most frequently involved). Left ventricular (LV) systolic function was slightly reduced in HCM-HT cases. In contrast, HCM controls were more frequently diagnosed by casual findings or family screening and had more LV outflow tract obstruction at first medical evaluation. LV maximal wall thickness (MWT) did not differ between groups. During a median follow-up since HCM diagnosis of 6.2 years (median follow-up of 8.9 and 7.1 years in cases and controls, respectively), HCM-HT cases presented a higher incidence of sustained ventricular tachycardia or ICD therapy (HR=4.0; CI95%:1.6–10.0 p=0.03) and HF admissions (HR=3.9; CI95%:1.8–8.1 p<0.001). There were no cardiovascular deaths during follow-up.

Conclusions

The presence of symptoms in a young non-obstructive HCM patient, along with family history and a pathogenic mutation, should advice clinicians a closer follow-up and early transfer to a HT referral center, especially if associated with diastolic dysfunction and high BNP values.

Funding Acknowledgement

Type of funding sources: None. Table 1

SEDAR/SECCE ECMO management consensus document

ECMO is an extracorporeal cardiorespiratory support system whose use has been increased in the last decade. Respiratory failure, postcardiotomy shock, and lung or heart primary graft failure may require the use of cardiorespiratory mechanical assistance. In this scenario perioperative medical and surgical management is crucial. Despite the evolution of technology in the area of extracorporeal support, morbidity and mortality of these patients continues to be high, and therefore the indication as well as the ECMO removal should be established within a multidisciplinary team with expertise in the area. This consensus document aims to unify medical knowledge and provides recommendations based on both the recent bibliography and the main national ECMO implantation centres experience with the goal of improving comprehensive patient care.

Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing, we investigated the prevalence and dynamics of this variant in the United States (US), tracking it back to its early emergence. We found that, while the fraction of B.1.1.7 varied by state, the variant increased at a logistic rate with a roughly weekly doubling rate and an increased transmission of 40%–50%. We revealed several independent introductions of B.1.1.7 into the US as early as late November 2020, with community transmission spreading it to most states within months. We show that the US is on a similar trajectory as other countries where B.1.1.7 became dominant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.

COVID-19: from epidemiology to treatment

The COVID-19 pandemic has greatly impacted the daily clinical practice of cardiologists and cardiovascular surgeons. Preparedness of health workers and health services is crucial to tackle the enormous challenge posed by SARS-CoV-2 in wards, operating theatres, intensive care units, and interventionist laboratories. This Clinical Review provides an overview of COVID-19 and focuses on relevant aspects on prevention and management for specialists within the cardiovascular field.

Genome-wide rare variant analysis for thousands of phenotypes in over 70,000 exomes from two cohorts

Understanding the impact of rare variants is essential to understanding human health. We analyze rare (MAF < 0.1%) variants against 4264 phenotypes in 49,960 exome-sequenced individuals from the UK Biobank and 1934 phenotypes (1821 overlapping with UK Biobank) in 21,866 members of the Healthy Nevada Project (HNP) cohort who underwent Exome + sequencing at Helix. After using our rare-variant-tailored methodology to reduce test statistic inflation, we identify 64 statistically significant gene-based associations in our meta-analysis of the two cohorts and 37 for phenotypes available in only one cohort. Singletons make significant contributions to our results, and the vast majority of the associations could not have been identified with a genotyping chip. Our results are available for interactive browsing in a webapp (https://ukb.research.helix.com). This comprehensive analysis illustrates the biological value of large, deeply phenotyped cohorts of unselected populations coupled with NGS data.

Population-based association analyses of rare genetic variants with complex traits are limited by the availability of data from sufficiently large cohorts. Here, Cirulli et al. report gene-based collapsing analysis of exomes from 49,960 participants of the UK Biobank and 21,866 participants of the Healthy Nevada Project over a total of 4377 traits.

Does acetabular coverage influence the clinical outcome of arthroscopically treated cam-type femoroacetabular impingement (FAI)?

Aims

What represents clinically significant acetabular undercoverage in patients with symptomatic cam-type femoroacetabular impingement (FAI) remains controversial. The aim of this study was to examine the influence of the degree of acetabular coverage on the functional outcome of patients treated arthroscopically for cam-type FAI.

Patients and Methods

Between October 2005 and June 2016, 88 patients (97 hips) underwent arthroscopic cam resection and concomitant labral debridement and/or refixation. There were 57 male and 31 female patients with a mean age of 31.0 years (17.0 to 48.5) and a mean body mass index (BMI) of 25.4 kg/m² (18.9 to 34.9). We used the Hip2Norm, an object-oriented-platform program, to perform 3D analysis of hip joint morphology using 2D anteroposterior pelvic radiographs. The lateral centre-edge angle, anterior coverage, posterior coverage, total femoral coverage, and alpha angle were measured for each hip. The presence or absence of crossover sign, posterior wall sign, and the value of acetabular retroversion index were identified automatically by Hip2Norm. Patient-reported outcome scores were collected preoperatively and at final follow-up with the Hip Disability and Osteoarthritis Outcome Score (HOOS).

Results

At a mean follow-up of 2.7 years (1 to 8, sd 1.6), all functional outcome scores significantly improved overall. Radiographically, only preoperative anterior coverage had a negative correlation with the improvement of the HOOS symptom subscale (r = -0.28, p = 0.005). No significant difference in relative change in HOOS subscale scores was found according to the presence or absence of radiographic signs of retroversion.

Discussion

Our study demonstrated the anterior coverage as an important modifier influencing the functional outcome of arthroscopically treated cam-type FAI. Cite this article: Bone Joint J 2018;100-B:831-8.

Sheep from low-methane-yield selection lines created on alfalfa pellets also have lower methane yield under pastoral farming conditions

Selection lines of sheep with low and high CH yield (g/kg DMI; CH/DMI) are being developed on the basis of feeding pelleted alfalfa hay at 2.0 times maintenance ME requirements in respiration chambers, but their divergence under predominant grazing conditions, as in New Zealand, is not known. The objectives of this study were to determine CH emissions and rumen fermentation characteristics in sheep from low and high CH/DMI selection lines while grazing pasture. Two grazing experiments were conducted with 42 selection line ewes in March 2013 (Exp. 1) and 98 selection line progeny ewe hoggets in October/November 2014 (Exp. 2), with CH emissions estimated by the SF tracer technique and DMI estimated by titanium oxide in combination with natural long-chain -alkanes. Total daily CH production (g/d) was similar between high and low CH/DMI selection line sheep in Exp. 1 and lower for low CH/DMI progeny compared with high CH/DMI progeny in Exp. 2 ( < 0.05). The CH/DMI tended to be 20% lower for low CH/DMI line sheep compared with high CH/DMI selection line sheep in Exp. 1 ( < 0.10) and was 15% lower for the low CH/DMI line in Exp. 2 ( < 0.01). Total VFA concentration and concentrations (m) of acetate, butyrate, and isobutyrate plus isovalerate were lower ( < 0.05) for low CH/DMI line sheep compared with high CH/DMI selection line sheep in both experiments. The current study indicates that differences in CH/DMI and VFA concentrations in selection line sheep, previously established on alfalfa pellets, are also present to a similar magnitude when grazing pasture.

Methane emissions differ between sheep offered a conventional diploid, a high-sugar diploid or a tetraploid perennial ryegrass cultivar at two allowances at three times of the year

Elevated water-soluble carbohydrate (WSC) concentration in the diet may affect rumen fermentation and consequently reduce methane (CH4) emissions. The objective of the present study was to determine CH4 emissions from male sheep (8 per treatment) in respiration chambers for 48 h and fed either a conventional diploid (CRG), a high-sugar diploid (HSG) or a tetraploid (TRG) perennial ryegrass cultivar, each offered at 0.7 or 1.0 kg dry matter (DM)/day during periods in early spring 2013 (P1), early autumn 2014 (P2) and late spring 2014 (P3). There was a significant (P < 0.001) interaction between cultivar and period for CH4 yield (g/kg DM intake). In P1 yield was 9% lower (P = 0.007) for sheep fed HSG than for sheep fed CRG or TRG, in P2 yield was 16% lower (P < 0.001) for sheep fed TRG than that for sheep fed CRG or HSG, and in P3 yield was 15% lower (P < 0.001) for sheep fed TRG than that for sheep fed CRG, with HSG-fed sheep being intermediate and not significantly different from either CRG or TRG. Despite there being a cultivar × period interaction, overall, CH4 yield was lower for sheep fed HSG or TRG than for sheep fed CRG (P < 0.001). There were no cultivar × level of feed offer interactions and, overall, yield of CH4 was 9% higher (P = 0.003) for sheep offered 0.7 than for sheep offered 1.0 kg DM/day. In each period, one or other of the high-WSC diploid (HSG) or tetraploid cultivars (TRG) gave lower CH4 yields than did the control diploid (CRG), suggesting that CH4 yield is reduced by characteristics of these cultivars. However, the effect was not consistently associated with either cultivar and could not be attributed to higher forage water-soluble carbohydrate concentrations.

Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells

In this study, we used whole-genome sequencing and gene expression profiling of 215 human induced pluripotent stem cell (iPSC) lines from different donors to identify genetic variants associated with RNA expression for 5,746 genes. We were able to predict causal variants for these expression quantitative trait loci (eQTLs) that disrupt transcription factor binding and validated a subset of them experimentally. We also identified copy-number variant (CNV) eQTLs, including some that appear to affect gene expression by altering the copy number of intergenic regulatory regions. In addition, we were able to identify effects on gene expression of rare genic CNVs and regulatory single-nucleotide variants and found that reactivation of gene expression on the X chromosome depends on gene chromosomal position. Our work highlights the value of iPSCs for genetic association analyses and provides a unique resource for investigating the genetic regulation of gene expression in pluripotent cells.

Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics

Induced pluripotent stem cells (iPSCs) show variable methylation patterns between lines, some of which reflect aberrant differences relative to embryonic stem cells (ESCs). To examine whether this aberrant methylation results from genetic variation or non-genetic mechanisms, we generated human iPSCs from monozygotic twins to investigate how genetic background, clone, and passage number contribute. We found that aberrantly methylated CpGs are enriched in regulatory regions associated with MYC protein motifs and affect gene expression. We classified differentially methylated CpGs as being associated with genetic and/or non-genetic factors (clone and passage), and we found that aberrant methylation preferentially occurs at CpGs associated with clone-specific effects. We further found that clone-specific effects play a strong role in recurrent aberrant methylation at specific CpG sites across different studies. Our results argue that a non-genetic biological mechanism underlies aberrant methylation in iPSCs and that it is likely based on a probabilistic process involving MYC that takes place during or shortly after reprogramming.

Prolonged incubation time does not increase sensitivity for the diagnosis of implant-related infection using samples prepared by sonication of the implants

We have designed a prospective study to evaluate the usefulness of prolonged incubation of cultures from sonicated orthopaedic implants. During the study period 124 implants from 113 patients were processed (22 osteosynthetic implants, 46 hip prostheses, 54 knee prostheses, and two shoulder prostheses). Of these, 70 patients had clinical infection; 32 had received antibiotics at least seven days before removal of the implant. A total of 54 patients had sonicated samples that produced positive cultures (including four patients without infection). All of them were positive in the first seven days of incubation. No differences were found regarding previous antibiotic treatment when analysing colony counts or days of incubation in the case of a positive result. In our experience, extending incubation of the samples to 14 days does not add more positive results for sonicated orthopaedic implants (hip and knee prosthesis and osteosynthesis implants) compared with a conventional seven-day incubation period.

Cite this article: Bone Joint J 2013;95-B:1001–6.