Characterizing fitness and immune escape of SARS-CoV-2 EG.5 sublineage using elderly serum and nasal organoid.

SARS-CoV-2 Omicron variant has evolved into sublineages. Here, we compared the neutralization susceptibility and viral fitness of EG.5.1 and XBB.1.9.1. Serum neutralization antibody titer against EG.5.1 was 1.71-fold lower than that for XBB.1.9.1. However, there was no significant difference in virus replication between EG.5.1 and XBB.1.9.1 in human nasal organoids and TMPRSS2/ACE2 over-expressing A549 cells. No significant difference was observed in competitive fitness and cytokine/chemokine response between EG.5.1 and XBB.1.9.1. Both EG.5.1 and XBB.1.9.1 replicated more robustly in the nasal organoid from a younger adult than that from an older adult. Our findings suggest that enhanced immune escape contributes to the dominance of EG.5.1 over earlier sublineages. The combination of population serum susceptibility testing and viral fitness evaluation with nasal organoids may hold promise in risk assessment of upcoming variants. Utilization of serum specimens and nasal organoid derived from older adults provides a targeted risk assessment for this vulnerable population.

[METATARSUS ADDUCTUS - A COMMON DEFORMITY - WHAT TO DO AND WHEN?]

INTRODUCTION: The most common foot deformity in newborns is the forefoot adduction deformity (FAD), where the hindfoot foot is in a normal position. The diagnosis for this problem is mainly based on a physical examination. The use of imaging methods has been described, but no advantage was shown with their utilization in determining the diagnosis and guiding treatment. Several classification systems have been proposed to characterize the degree of severity. The classifications are based on the degree of deviation and the flexibility of the foot. Early diagnosis and early treatment, if necessary, are extremely important to improve the chances of treatment success. Treatment depends on the severity of the deformity. For mild deformities the treatment is conservative - follow-up or stretching of the foot. The usual treatment for severe deformities is serial casting. Several orthoses have recently been proposed to address the problem and these demonstrated similar results, higher comfort and satisfaction, lower cost and a similar side effect profile. Surgical treatments to correct the deformity are reserved for cases where conservative treatment failed and for older children. This review aims to summarize the current knowledge on the subject, describe the ways to diagnose and classify the deformity, and present the variety of ways to treat the problem including the use of innovative braces. In addition, we will offer a protocol for the treatment of the deformity that is accepted in our institution. The protocol will assist primary care physicians to both diagnose and treat appropriate deformities, and know when a specialist referral is necessary.

Review of Current Concepts in Metatarsus Adductus.

Metatarsus adductus (MA), the most common congenital foot deformity, involves adduction of the forefoot at the tarsometatarsal joint, with normal hindfoot alignment. Early diagnosis is important because treatment is more successful if initiated before age 9 months. Treatment of MA depends on deformity severity, in which mild to moderate deformity can be treated conservatively. Current standard of care for severe or rigid deformity involves referral by primary care physicians to specialists for management by casting and splinting. Recently, several orthoses have demonstrated equal effectiveness to casting and may allow for primary care physicians to treat MA without the need for referral. In this review article, we provide an overview of MA and discuss diagnosis and treatment. We also discuss novel devices and suggest how they may affect the future management of severe and rigid MA. [Pediatr Ann. 2024;53(4):e152-e156.].

Development and Evaluation of an In-House Real-Time RT-PCR Targeting nsp10 Gene for SARS-CoV-2 Detection.

The emergence of SARS-CoV-2 mutations poses significant challenges to diagnostic tests, as these mutations can reduce the sensitivity of commonly used RT-PCR assays. Therefore, there is a need to design diagnostic assays with multiple targets to enhance sensitivity. In this study, we identified a novel diagnostic target, the nsp10 gene, using nanopore sequencing. Firstly, we determined the analytical sensitivity and specificity of our COVID-19-nsp10 assay. The COVID-19-nsp10 assay had a limit of detection of 74 copies/mL (95% confidence interval: 48-299 copies/mL) and did not show cross-reactivity with other respiratory viruses. Next, we determined the diagnostic performance of the COVID-19-nsp10 assay using 261 respiratory specimens, including 147 SARS-CoV-2-positive specimens belonging to the ancestral strain and Alpha, Beta, Gamma, Delta, Mu, Eta, Kappa, Theta and Omicron lineages. Using a LightMix E-gene RT-PCR assay as the reference method, the diagnostic sensitivity and specificity of the COVID-19-nsp10 assay were found to be 100%. The median Cp values for the LightMix E-gene RT-PCR and our COVID-19-nsp10 RT-PCR were 22.48 (range: 12.95-36.60) and 25.94 (range 16.37-36.87), respectively. The Cp values of the COVID-19-nsp10 RT-PCR assay correlated well with those of the LightMix E-gene RT-PCR assay (Spearman's ρ = 0.968; p < 0.0001). In conclusion, nsp10 is a suitable target for a SARS-CoV-2 RT-PCR assay.

NfL reliability across laboratories, stage-dependent diagnostic performance and matrix comparability in genetic FTD: a large GENFI study.

BACKGROUND: Blood neurofilament light chain (NfL) is increasingly considered as a key trial biomarker in genetic frontotemporal dementia (gFTD). We aimed to facilitate the use of NfL in gFTD multicentre trials by testing its (1) reliability across labs; (2) reliability to stratify gFTD disease stages; (3) comparability between blood matrices and (4) stability across recruiting sites. METHODS: Comparative analysis of blood NfL levels in a large gFTD cohort (GENFI) for (1)-(4), with n=344 samples (n=148 presymptomatic, n=11 converter, n=46 symptomatic subjects, with mutations in C9orf72, GRN or MAPT; and n=139 within-family controls), each measured in three different international labs by Simoa HD-1 analyzer. RESULTS: NfL revealed an excellent consistency (intraclass correlation coefficient (ICC) 0.964) and high reliability across the three labs (maximal bias (pg/mL) in Bland-Altman analysis: 1.12±1.20). High concordance of NfL across laboratories was moreover reflected by high areas under the curve for discriminating conversion stage against the (non-converting) presymptomatic stage across all three labs. Serum and plasma NfL were largely comparable (ICC 0.967). The robustness of NfL across 13 recruiting sites was demonstrated by a linear mixed effect model. CONCLUSIONS: Our results underline the suitability of blood NfL in gFTD multicentre trials, including cross-lab reliable stratification of the highly trial-relevant conversion stage, matrix comparability and cross-site robustness.

Humoral and cellular immunity against different SARS-CoV-2 variants in patients with chronic kidney disease.

Chronic kidney disease (CKD) patients are at higher risk of severe COVID-19. Humoral and cellular immunity from prior infection or vaccination are important for protection, but the neutralizing antibody (nAb) response against SARS-CoV-2 variants is impaired. We investigated the variant-specific nAb and T cell immunity among CKD patients. Adult CKD patients were recruited between August and October 2022. nAb against the SARS-CoV-2 (ancestral strains and four Omicron sublineages) and T cell response were measured using the live virus neutralization assay and interferon-gamma release assay (IGRA). The correlation between nAb/T-cell response and subsequent infection after recruitment were also determined. Among the 88 recruited patients, 95.5% had prior infection or had completed the primary vaccine series. However, only 77.3% had detectable nAb against at least one SARS-CoV-2 strains, 59.1% tested positive in IGRA, and 52.3% had detectable nAb and tested positive in the IGRA. The nAb geometic mean titers (GMTs) against XBB.1, BA.5 and BA.2.3.20 were significantly lower than those against BA.2 and ancestral strain. Prior SARS-CoV-2 infection was associated with elevated nAb and T cell response. More kidney transplant recipients (KTRs) showed absent nAb and T cell response (36.8% vs. 10.1%), despite a higher prevalence of vaccine booster in this population (94.7% vs. 50.7%). Lower levels of nAb titer and T cell response were significantly associated with subsequent infection. A considerable proportion of CKD patients, especially KTRs, showed absence of humoral and cellular protective immunity against SARS-CoV-2. Strategies to improve immunogenicity in this population are urgently needed.

Nephrology in Veterinary Medicine.

Veterinary nephrology is a specialized field of veterinary medicine providing a high level of care for animals with all types of kidney disease. Veterinarians complete extensive training to become board-certified in veterinary nephrology-urology. Companion animal nephrology is the most advanced field; however, all species are afflicted by a variety of renal disorders. Most naturally occurring animal kidney diseases have similar disorders found in people; where veterinary research is lacking, clinical management is often modified from standard of care in people. Veterinarians have become adept at scaling down procedures to safely perform them on dogs and cats weighing only a few kilograms. Advanced diagnostics (renal biopsy, cystoscopy, fluoroscopic studies, etc. ) and therapeutics (renal replacement therapy, interventional endourology, etc. ) are commonly performed within the practice of veterinary nephrology-urology. Collaboration between veterinary and human nephrologists may advance both disciplines and improve care for people and animals alike.

The T1 Ratio of Marrow (TROM) as a Novel Tool to Identify Metastatic from Nonmalignant Marrow Lesions of the Spine: A Pilot Study.

Objective The purpose of this study was to analyze quantitative values of normal and abnormal marrow on T1-weighted images of spine, to propose a ratio for T1 values of abnormal to normal vertebrae, and to assess whether this ratio could be helpful in predicting presence of neoplastic lesions in the spine. Materials and Methods One-hundred randomly selected magnetic resonance imagings of lumbar spine without infection, fracture, and tumor were selected to form normal cohort. A second cohort of 100 metastasis of lumbar spine was identified. Ratio of T1 value of vertebral body to the T1 value of the inferior vertebral body was performed for normal cohort from D11 to L5. Ratio of T1 value of metastasis to adjacent normal vertebral body was done for metastatic cohort. Data was analyzed using standard t -test and kappa was performed for intra- and inter-observer reliability. Results A decline in T1 value of abnormal to normal marrow was seen in patients with metastasis that was statistically significant. We call this the T1 ratio of marrow (TROM). The sensitivity and accuracy with the cutoff value of TROM at 0.7 (92% sensitivity, 97.1% accuracy) are better than at 0.6 (75% sensitivity, 96.2% accuracy) or 0.5 (47% sensitivity, 93.2% accuracy). A subset analysis of the other T1 hypointense benign lesions including atypical hemangiomas and focal marrow hyperplasia, however, revealed overlapping TROM values with the metastatic cohort. Conclusion Using the TROM on T1-weighted images could not confidently differentiate malignant from benign T1 hypointense lesions of the spine.

Transparency films: intraoperative templating to prevent limb deformity.

Operative management of fractures and malunions can be challenging when restoring native anatomy is not straightforward. Comminuted fractures and managing deformity correction in the setting of osteolysis, callus, and even complete fracture healing must include careful planning. Preoperative planning has been popularized and taught as an integral part of a surgeon's skill set, with critical evaluation and assessment of the implemented plan being the final step in the process. We present a robust, reproducible, and cost-effective technique for intraoperative fracture fixation assessment with case examples, used routinely at our institution.

Measurement Analysis of Ice Ball Size during CT-Guided Cryoablation Procedures for Better Prediction of Final Ice Ball Size and Avoidance of Complications.

Introduction Cryoablation is the destruction of living tissue by the application of extreme freezing temperature. There has been an increase in the use of cryoablation in the management of musculoskeletal lesions, in particular fibromatosis. Aim This study aimed to measure the average and relative increase in size of the cryoablation ice ball after the first (10 minutes) and second freeze cycles (20 minutes) to accurately predict the size of the ice ball between first and second freezes to help prevent any unwanted damage of the nearby skin and neurovascular structures. This is especially important when ablating in relatively small body parts such as in the appendicular skeleton. Material and Methods Eight patients treated with cryoablation over a 12-month period for fibromatosis were, included in the study. The size and volume of the ice ball were measured during the first and second cycle of cryoablation. Results The average patient age of the cohort was 35.6 years old (min 28 and max 43). There was female predominance in the study (3:2, F:M). There was a significant increase (26%) in the linear dimensions and almost doubling in the volume of the ice ball between freeze cycles ( p -value = 0.0037 for dimensions and p -value = 0.0002 for volumes). Conclusion This pilot study is a preliminary attempt to predict the eventual size of the ice ball during cryoablation procedures when treating cases of fibromatosis. This should help in planning cryoablation to ensure decrease morbidity by preventing injury to adjacent critical structures (neurovascular bundle and skin).

Global prevalence of SARS-CoV-2 3CL protease mutations associated with nirmatrelvir or ensitrelvir resistance.

BACKGROUND: Nirmatrelvir-ritonavir (Paxlovid) and ensitrelvir are 3-chymotrypsin-like cysteine protease (3CLpro) inhibitors which have been approved for the treatment of COVID-19 in 2021 and 2022, respectively. Previous studies have identified 3CLpro mutations that are associated with reduced susceptibility to these antivirals. The aim of the current study was to estimate the global prevalence of 3CLpro inhibitor-resistant SARS-CoV-2 strains. METHODS: We compiled a list of 3CLpro mutations which have been associated with nirmatrelvir or ensitrelvir resistance based on either viral replication or 3CLpro activity assays, and determined their prevalence among 13.4 million sequences deposited in GISAID as of December 14, 2022, about 1 year after the approval of nirmatrelvir-ritonavir. We analyzed the prevalence for different time periods, SARS-CoV-2 lineages and geographical locations. FINDINGS: Overall, 0.5% (67,095/13,446,588) of the sequences contained at least one mutation that was shown to affect the inhibitory activity of nirmatrelvir or ensitrelvir on viral replication or 3CLpro activity. We did not observe any increasing trend of resistance after the widespread clinical use of nirmatrelvir-ritonavir. G15S (2070 per million) and T21I (1386 per million) were the most prevalent mutations, and these mutations were dominant in some SARS-CoV-2 lineages. E166V and S144E, previously shown to affect the inhibitory activity of nirmatrelvir on viral replication or protease activity by > 100-folds, were found in <1 per million sequences. INTERPRETATION: Our data suggest that 3CLpro inhibitor resistance is currently rare. However, continuous global genotypic and phenotypic surveillance would be crucial in the early detection of resistant mutants. FUNDING: Richard and Carol Yu, May Tam Mak Mei Yin, The Shaw Foundation Hong Kong, Michael Tong, Marina Lee, Government Consultancy Service, the Emergency Key Program of Guangzhou Laboratory (See acknowledgements for full list).

Disrupting N-Glycosylation Using Type I Mannosidase Inhibitors Alters B-Cell Receptor Signaling.

Kifunensine is a known inhibitor of type I α-mannosidase enzymes and has been shown to have therapeutic potential for a variety of diseases and application in the expression of high-mannose N-glycan bearing glycoproteins; however, the compound's hydrophilic nature limits its efficacy. We previously synthesized two hydrophobic acylated derivatives of kifunensine, namely, JDW-II-004 and JDW-II-010, and found that these compounds were over 75-fold more potent than kifunensine. Here we explored the effects of these compounds on different mice and human B cells, and we demonstrate that they affected the cells in a similar fashion to kifunensine, further demonstrating their functional equivalence to kifunensine in assays utilizing primary cells. Specifically, a dose-dependent increase in the formation of high-mannose N-glycans decorated glycoproteins were observed upon treatment with kifunensine, JDW-II-004, and JDW-II-010, but greater potency was observed with the acylated derivatives. Treatment with kifunensine or the acylated derivatives also resulted in impaired B-cell receptor (BCR) signaling of the primary mouse B cells; however, primary human B cells treated with kifunensine or JDW-II-004 did not affect BCR signaling, while a modest increase in BCR signaling was observed upon treatment with JDW-010. Nevertheless, these findings demonstrate that the hydrophobic acylated derivatives of kifunensine can help overcome the mass-transfer limitations of the parent compound, and they may have applications for the treatment of ERAD-related diseases or prove to be more cost-effective alternatives for the generation and production of high-mannose N-glycan bearing glycoproteins.

Development and Validation of a Novel COVID-19 nsp8 One-Tube RT-LAMP-CRISPR Assay for SARS-CoV-2 Diagnosis.

Accurate and simple diagnostic tests for coronavirus disease 2019 (COVID-19) are essential components of the pandemic response. In this study, we evaluated a one-tube reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay coupled with clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein-mediated endpoint detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in clinical samples. RT-LAMP-CRISPR is fast and affordable, does not require bulky thermocyclers, and minimizes carryover contamination risk. Results can be read either visually or with a fluorometer. RT-LAMP-CRISPR assays using primers targeting a highly expressed nsp8 gene and previously described nucleocapsid (N) gene primers were designed. The analytical characteristics and diagnostic performance of RT-LAMP-CRISPR assays were compared to those of a commercial real-time RT-PCR E gene assay. The limits of detection (LODs) of the nsp8 and N RT-LAMP-CRISPR assays were 750 and 2,000 copies/mL, which were higher than that of the commercial real-time RT-PCR assay (31.3 copies/mL). Despite the higher LOD, RT-LAMP-CRISPR assays showed diagnostic sensitivity and specificity of 98.6% and 100%, respectively, equivalent to those of the real-time RT-PCR assay (P = 0.5). The median fluorescence reading from the nsp8 assay (378.3 raw fluorescence unit [RFU] [range, 215.6 to 592.6]) was significantly higher than that of the N gene assay (342.0 RFU [range, 143.0 to 576.6]) (P < 0.0001). In conclusion, we demonstrate that RT-LAMP-CRISPR assays using primers rationally designed from highly expressed gene targets are highly sensitive, specific, and easy to perform. Such assays are a valuable asset in resource-limited settings. IMPORTANCE Accurate tests for the diagnosis of SARS-CoV-2, the virus causing coronavirus disease 2019 (COVID-19), are important for timely treatment and infection control decisions. Conventional tests such as real-time reverse transcription-PCR (RT-PCR) require specialized equipment and are expensive. On the other hand, rapid antigen tests suffer from a lack of sensitivity. In this study, we describe a novel assay format for the diagnosis of COVID-19 that is based on principles of loop-mediated isothermal amplification (LAMP) and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas chemistry. A major advantage of this assay format is that it does not require expensive equipment to perform, and results can be read visually. This method proved to be fast, easy to perform, and inexpensive. The test compared well against an RT-PCR assay in terms of the ability to detect SARS-CoV-2 RNA in clinical samples. No false-positive test results were observed. The new assay format is ideal for SARS-CoV-2 diagnosis in resource-limited settings.

Risk Factors for Slow Viral Decline in COVID-19 Patients during the 2022 Omicron Wave.

Formulating termination of isolation (de-isolation) policies requires up-to-date knowledge about viral shedding dynamics. However, current de-isolation policies are largely based on viral load data obtained before the emergence of Omicron variant. In this retrospective cohort study involving adult patients hospitalised for COVID-19 between January and February 2022, we sought to determine SARS-CoV-2 viral shedding kinetics and to investigate the risk factors associated with slow viral decline during the 2022 Omicron wave. A total of 104 patients were included. The viral load was highest (Ct value was lowest) on days 1 post-symptom-onset (PSO) and gradually declined. Older age, hypertension, hyperlipidaemia and chronic kidney disease were associated with slow viral decline in the univariate analysis on both day 7 and day 10 PSO, while incomplete or no vaccination was associated with slow viral decline on day 7 PSO only. However, older age was the only risk factor that remained statistically significant in the multivariate analysis. In conclusion, older age is an independent risk factor associated with slow viral decline in this study conducted during the Omicron-dominant 2022 COVID-19 wave. Transmission-based precaution guidelines should take age into consideration when determining the timing of de-isolation.

Contribution of low population immunity to the severe Omicron BA.2 outbreak in Hong Kong.

Monitoring population protective immunity against SARS-CoV-2 variants is critical for risk assessment. We hypothesize that Hong Kong's explosive Omicron BA.2 outbreak in early 2022 could be explained by low herd immunity. Our seroprevalence study using sera collected from January to December 2021 shows a very low prevalence of neutralizing antibodies (NAb) against ancestral virus among older adults. The age group-specific prevalence of NAb generally correlates with the vaccination uptake rate, but older adults have a much lower NAb seropositive rate than vaccination uptake rate. For all age groups, the seroprevalence of NAb against Omicron variant is much lower than that against the ancestral virus. Our study suggests that this BA.2 outbreak and the exceptionally high case-fatality rate in the ≥80 year-old age group (9.2%) could be attributed to the lack of protective immunity in the population, especially among the vulnerable older adults, and that ongoing sero-surveillance is essential.