Deep mutational scanning identifies SARS-CoV-2 Nucleocapsid escape mutations of currently available rapid antigen tests.

The effects of mutations in continuously emerging variants of SARS-CoV-2 are a major concern for the performance of rapid antigen tests. To evaluate the impact of mutations on 17 antibodies used in 11 commercially available antigen tests with emergency use authorization, we measured antibody binding for all possible Nucleocapsid point mutations using a mammalian surface-display platform and deep mutational scanning. The results provide a complete map of the antibodies' epitopes and their susceptibility to mutational escape. Our data predict no vulnerabilities for detection of mutations found in variants of concern. We confirm this using the commercial tests and sequence-confirmed COVID-19 patient samples. The antibody escape mutational profiles generated here serve as a valuable resource for predicting the performance of rapid antigen tests against past, current, as well as any possible future variants of SARS-CoV-2, establishing the direct clinical and public health utility of our system.

Multisite Mpox Infection and Viral Dynamics Among Persons With HIV in Metro Atlanta.

The 2022 mpox outbreak primarily involved sexual transmission among men who have sex with men and disproportionately affected persons with human immunodeficiency virus (HIV). We examined viral dynamics and clinical features in a cohort evaluated for mpox infection at a comprehensive HIV clinic in Atlanta, Georgia. Viral DNA was found in 8 oropharyngeal and 5 anorectal specimens among 10 mpox cases confirmed by lesion swab polymerase chain reaction. Within-participant anatomic site of lowest cycle threshold (Ct) value varied, and lower Ct values were found in oropharyngeal and anorectal swabs when corresponding symptoms were present. This provides insight into mpox infection across multiple anatomic sites among people with HIV.

Liver-restricted deletion of the biliary atresia candidate gene Pkd1l1 causes bile duct dysmorphogenesis and ciliopathy.

BACKGROUND AND AIMS: A recent multicenter genetic exploration of the biliary atresia splenic malformation syndrome identified mutations in the ciliary gene PKD1L1 as candidate etiologic contributors. We hypothesized that deletion of Pkd1l1 in developing hepatoblasts would lead to cholangiopathy in mice. APPROACH AND RESULTS: CRISPR-based genome editing inserted loxP sites flanking exon 8 of the murine Pkd1l1 gene. Pkd1l1Fl/Fl cross-bred with alpha-fetoprotein-Cre expressing mice to generate a liver-specific intrahepatic Pkd1l1 -deficient model (LKO). From embryonic day 18 through week 30, control ( Fl/Fl ) and LKO mice were evaluated with standard serum chemistries and liver histology. At select ages, tissues were analyzed using RNA sequencing, immunofluorescence, and electron microscopy with a focus on biliary structures, peribiliary inflammation, and fibrosis. Bile duct ligation for 5 days of Fl/Fl and LKO mice was followed by standard serum and liver analytics. Histological analyses from perinatal ages revealed delayed biliary maturation and reduced primary cilia, with progressive cholangiocyte proliferation, peribiliary fibroinflammation, and arterial hypertrophy evident in 7- to 16-week-old LKO versus Fl/Fl livers. Following bile duct ligation, cholangiocyte proliferation, peribiliary fibroinflammation, and necrosis were increased in LKO compared with Fl/Fl livers. CONCLUSIONS: Bile duct ligation of the Pkd1l1 -deficient mouse model mirrors several aspects of the intrahepatic pathophysiology of biliary atresia in humans including bile duct dysmorphogenesis, peribiliary fibroinflammation, hepatic arteriopathy, and ciliopathy. This first genetically linked model of biliary atresia, the Pkd1l1 LKO mouse, may allow researchers a means to develop a deeper understanding of the pathophysiology of this serious and perplexing disorder, including the opportunity to identify rational therapeutic targets.

Farnesoid X receptor enhances epithelial ACE2 expression and inhibits virally induced IL-6 secretion: implications for intestinal symptoms of SARS-CoV-2.

Intestinal inflammation and diarrhea are often associated with SARS-CoV-2 infection. The angiotensin converting enzyme 2 (ACE2) receptor plays a key role in SARS-CoV-2 pathogenesis, facilitating entry of the virus into epithelial cells, while also regulating mucosal inflammatory responses. Here, we investigated roles for the nuclear bile acid receptor farnesoid X receptor (FXR) in regulating ACE2 expression and virally mediated inflammatory responses in intestinal epithelia. Human colonic or ileal enteroids and cultured T84 and Caco-2 monolayers were treated with the FXR agonists, obeticholic acid (OCA) or GW4064, or infected with live SARS-CoV-2 (2019-nCoV/USA_WA1/2020). Changes in mRNA, protein, or secreted cytokines were measured by qPCR, Western blotting, and ELISA. Treatment of undifferentiated colonic or ileal enteroids with OCA increased ACE2 mRNA by 2.1 ± 0.4-fold (n = 3; P = 0.08) and 2.3 ± 0.2-fold (n = 3; P < 0.05), respectively. In contrast, ACE2 expression in differentiated enteroids was not significantly altered. FXR activation in cultured epithelial monolayers also upregulated ACE2 mRNA, accompanied by increases in ACE2 expression and secretion. Further experiments revealed FXR activation to inhibit IL-6 release from both Caco-2 cells infected with SARS-CoV-2 and T84 cells treated with the viral mimic, polyinosinic:polycytidylic acid, by 46 ± 12% (n = 3, P < 0.05) and 35 ± 6% (n = 8; P < 0.01), respectively. By virtue of its ability to modulate epithelial ACE2 expression and inhibit virus-mediated proinflammatory cytokine release, FXR represents a promising target for the development of new approaches to prevent intestinal manifestations of SARS-CoV-2.NEW & NOTEWORTHY Activation of the nuclear bile acid receptor, farnesoid X receptor (FXR), specifically upregulates ACE2 expression in undifferentiated colonic epithelial cells and inhibits virus-induced proinflammatory cytokine release. By virtue of these actions FXR represents a promising target for the development of new approaches to prevent intestinal manifestations of SARS-CoV-2 infection.

Sensitivity of rapid antigen tests against SARS-CoV-2 Omicron and Delta variants.

Rapid antigen tests (RATs) have become an invaluable tool for combating the COVID-19 pandemic. However, concerns have been raised regarding the ability of existing RATs to effectively detect emerging SARS-CoV-2 variants. We compared the performance of 10 commercially available, emergency use authorized RATs against the Delta and Omicron SARS-CoV-2 variants using both individual patient and serially diluted pooled clinical samples. The RATs exhibited lower sensitivity for Omicron samples when using PCR cycle threshold (CT) value (a rough proxy for RNA concentration) as the comparator. Interestingly, however, they exhibited similar sensitivity for Omicron and Delta samples when using quantitative antigen concentration as the comparator. We further found that the Omicron samples had lower ratios of antigen to RNA, which offers a potential explanation for the apparent lower sensitivity of RATs for that variant when using C T value as a reference. Our findings underscore the complexity in assessing RAT performance against emerging variants and highlight the need for ongoing evaluation in the face of changing population immunity and virus evolution.

Photobiomodulation invigorating collagen deposition, proliferating cell nuclear antigen and Ki67 expression during dermal wound repair in mice.

The present investigation focuses on understanding the role of photobiomodulation in enhancing tissue proliferation. Circular excision wounds of diameter 1.5 cm were created on Swiss albino mice and treated immediately with 2 J/cm2 and 10 J/cm2 single exposures of the Helium-Neon laser along with sham-irradiated controls. During different days of healing progression (day 5, day 10, and day 15), the tissue samples upon euthanization of the animals were taken for assessing collagen deposition by Picrosirius red staining and cell proliferation (day 10) by proliferating cell nuclear antigen (PCNA) and Ki67. The positive influence of red light on collagen synthesis was found to be statistically significant on day 10 (P < 0.01) and day 15 (P < 0.05) post-wounding when compared to sham irradiation, as evident from the image analysis of collagen birefringence. Furthermore, a significant rise in PCNA (P < 0.01) and Ki67 (P < 0.05) expression was also recorded in animals exposed to 2 J/cm2 when compared to sham irradiation and (P < 0.01) compared to the 10 J/cm2 treated group as evidenced by the microscopy study. The findings of the current investigation have distinctly exhibited the assenting influence of red laser light on excisional wound healing in Swiss albino mice by augmenting cell proliferation and collagen deposition.

Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern.

To provide an accessible and inexpensive method to surveil for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations, we developed a multiplex real-time reverse transcription-PCR (rRT-PCR) assay, the Spike single-nucleotide polymorphism (SNP) assay, to detect specific mutations in the spike receptor binding domain. A single primer pair was designed to amplify a 348-bp region of spike, and probes were initially designed to detect K417, E484K, and N501Y. The assay was evaluated using characterized variant sample pools and residual nasopharyngeal samples. Variant calls were confirmed by SARS-CoV-2 genome sequencing in a subset of samples. Subsequently, a fourth probe was designed to detect L452R. The lower limit of 95% detection was 2.46 to 2.48 log10 genome equivalents (GE)/ml for the three initial targets (∼1 to 2 GE/reaction). Among 253 residual nasopharyngeal swabs with detectable SARS-CoV-2 RNA, the Spike SNP assay was positive in 238 (94.1%) samples. All 220 samples with threshold cycle (CT) values of <30 for the SARS-CoV-2 N2 target were detected, whereas 18/33 samples with N2 CT values of ≥30 were detected. Spike SNP results were confirmed by sequencing in 50/50 samples (100%). Addition of the 452R probe did not affect performance for the original targets. The Spike SNP assay accurately identifies SARS-CoV-2 mutations in the receptor binding domain, and it can be quickly modified to detect new mutations that emerge.

Organic solute transporter-ß (SLC51B) deficiency in two brothers with congenital diarrhea and features of cholestasis.

Primary bile acid malabsorption is associated with congenital diarrhea, steatorrhea, and a block in the intestinal return of bile acids in the enterohepatic circulation. Mutations in the ileal apical sodium-dependent bile acid transporter (ASBT; SLC10A2) can cause primary bile acid malabsorption but do not appear to account for most familial cases. Another major transporter involved in the intestinal reclamation of bile acids is the heteromeric organic solute transporter alpha-beta (OSTα-OSTß; SLC51A-SLC51B), which exports bile acid across the basolateral membrane. Here we report the first patients with OSTß deficiency, clinically characterized by chronic diarrhea, severe fat soluble vitamin deficiency, and features of cholestatic liver disease including elevated serum gamma-glutamyltransferase activity. Whole exome sequencing revealed a homozygous single nucleotide deletion in codon 27 of SLC51B, resulting in a frameshift and premature termination at codon 50. Functional studies in transfected cells showed that the SLC51B mutation resulted in markedly reduced taurocholic acid uptake activity and reduced expression of the OSTα partner protein. CONCLUSION: The findings identify OSTß deficiency as a cause of congenital chronic diarrhea with features of cholestatic liver disease. These studies underscore OSTα-OSTß's key role in the enterohepatic circulation of bile acids in humans. (Hepatology 2017).

Role of MDCT as an effective imaging tool in detection of complications amongst oncological patients in a tertiary care oncology institute.

OBJECTIVES: The objectives of the study are to evaluate the role of multidetector computed tomography (MDCT), its sensitivity and specificity in recognizing the complications related to oncology, and its treatment in patients with known malignancies and to determine how clinician's diagnosis, diagnostic dilemma, and management decisions are affected by the results of computed tomography (CT) in a tertiary care oncology setup. MATERIALS AND METHODS: A thorough retrospective search of the database of 1 year in the Department of Radiology was done at our tertiary oncology center, of patients who were diagnosed or suspected with complications associated with cancer. In addition, patients, in whom acute emergencies were detected by the MDCT, were also included as these were mostly part of the complications related to the malignancies. A total of 207 patients were included after excluding patients in whom the final diagnosis was uncertain or in patients who died before a definitive diagnosis was made. Clinical details were noted and compared with the CT diagnosis of the complication. RESULTS: Out of the 207 patients, majority of complications were related to cardiovascular system [22.2%]. Gastrointestinal malignancies constituted the next most common [20.7%], followed by genitourinary [17.8%], central nervous system [9.6%], and respiratory system complications [8.2%]. The musculoskeletal and head and neck complications were seen in 4.8% of the total patients. The iatrogenic complications and those complications arising due to chemotherapy or radiotherapy were separated constituting about 5.3% of the total number of patients in the study. CT showed a sensitivity of 96.4%, specificity of 66.6%, positive predictive value of 98.4%, and negative predictive value of 46.1% in detecting these complications. Overall, CT detected 96.6% of complications which were not suspected clinically and detected 83% of complications supporting the clinical suspicion. CONCLUSION: MDCT plays an important role in detecting the complications associated with malignancies. It helps in definitive diagnosis of those complications which are clinically suspected and also in recognizing those complications which may not be apparent clinically and thus can change the management strategies. This is probably the first comprehensive study in the English literature evaluating and highlighting the role of MDCT in recognizing various complications in patients with known malignancies.

Potential imaging findings following assisted reproduction: complications and clinical implications.

Recent rapid advances in assisted reproduction (ART) have led to global increase in usage of in vitro fertilization. This in turn has resulted in clinicians and imaging specialists encountering increase in complications associated with ART. The specialists dealing with infertility should be aware of potential complications associated with ART. Early diagnosis of these problems is based on clinician's suspicion and radiologist's awareness of these complications. Many of these conditions may be life threatening. Hence, early diagnosis and treatment of these complications can safeguard the fetal and maternal health.

Photo-biomodulatory response of low-power laser irradiation on burn tissue repair in mice.

The present work reports the photo-biomodulatory effect of red (632.8 nm) and near infrared (785 and 830 nm) lasers on burn injury in Swiss albino mice. Animals were induced with a 15-mm full thickness burn injury and irradiated with various fluences (1, 2, 3, 4, and 6 J/cm2) of each laser wavelength under study having a constant fluence rate (8.49 mW/cm2). The size of the injury following treatment was monitored by capturing the wound images at regular time intervals until complete healing. Morphometric assessment indicated that the group treated with 3-J/cm2 fluence of 830 nm had a profound effect on healing as compared to untreated controls and various fluences of other wavelengths under study. Histopathological assessment of wound repair on treatment with an optimum fluence (3 J/cm2) of 830 nm performed on days 2, 6, 12, and 18 post-wounding resulted in enhanced wound repair with migration of fibroblasts, deposition of collagen, and neovascularization as compared to untreated controls. The findings of the present study have clearly demonstrated that a single exposure of 3-J/cm2 fluence at 830-nm enhanced burn wound healing progression in mice, which is equivalent to 5 % povidone iodine treatment (reference standard), applied on a daily basis till complete healing.

Rare Presentation of Pseudomyxoma Retroperitonei: Stretching the Limits.

A 55-year-old woman presented with a mucopurulent sinusal discharge from the right supragluteal region, with symptoms over the previous five months. This abscess began as a slowly swelling growth, which eventually turned into a discharging sinus, and she was diagnosed with a gluteal abscess. The patient underwent incisional drainage, and intra-operatively, the sinus tract could be seen extending to the retroperitoneum. A subsequent CT scan and an MRI of the abdomen revealed a large heterogeneous retroperitoneal cystic mass on the right side of midline, extending inferiorly into the anterior thigh along the iliopsoas. Superiorly, a tubular projection extended from the lesion, indenting the ileocaecal junction, while a fluid filled cutaneous fistulous tract was seen, extending to the right flank. A diagnosis of pseudomyxoma retroperitonei, likely of retrocaecal appendicular origin, was proposed. An explorative laparotomy with an appendectomy, and the evacuation of the retroperitoneal collection were completed. The subsequent histopathology confirmed the diagnosis of appendicular mucinous cystadenoma, with pseudomyxoma retroperitonei.

Slc10a2-null mice uncover colon cancer-promoting actions of endogenous fecal bile acids.

Although epidemiological evidence in humans and bile acid feeding studies in rodents implicate bile acids as tumor promoters, the role of endogenous bile acids in colon carcinogenesis remains unclear. In this study, we exploited mice deficient in the ileal apical sodium-dependent bile acid transporter (ASBT, encoded by SLC10A2) in whom fecal bile acid excretion is augmented more than 10-fold. Wild-type and Asbt-deficient (Slc10a2 (-/-) ) male mice were treated with azoxymethane (AOM) alone to examine the development of aberrant crypt foci, the earliest histological marker of colon neoplasia and a combination of AOM and dextran sulfate sodium to induce colon tumor formation. Asbt-deficient mice exhibited a 54% increase in aberrant crypt foci, and 70 and 59% increases in colon tumor number and size, respectively. Compared to littermate controls, Asbt-deficient mice had a striking, 2-fold increase in the number of colon adenocarcinomas. Consistent with previous studies demonstrating a role for muscarinic and epidermal growth factor receptor signaling in bile acid-induced colon neoplasia, increasing bile acid malabsorption was associated with M3 muscarinic and epidermal growth factor receptor expression, and activation of extracellular signal-related kinase, a key post-receptor signaling molecule.

Intestine-specific deletion of SIRT1 in mice impairs DCoH2-HNF-1α-FXR signaling and alters systemic bile acid homeostasis.

BACKGROUND & AIMS: Sirtuin 1 (SIRT1), the most conserved mammalian oxidized nicotinamide adenine dinucleotide-dependent protein deacetylase, is an important metabolic sensor in many tissues. However, little is known about its role in the small intestine, which absorbs and senses nutrients. We investigated the functions of intestinal SIRT1 in systemic bile acid and cholesterol metabolism in mice. METHODS: SIRT1 was specifically deleted from the intestines of mice using the flox-Villin-Cre system (SIRT1 iKO mice). Intestinal and hepatic tissues were collected, and bile acid absorption was analyzed using the everted gut sac experiment. Systemic bile acid metabolism was studied in SIRT1 iKO and flox control mice placed on standard diets, diets containing 0.5% cholic acid or 1.25% cholesterol, or lithogenic diets. RESULTS: SIRT1 iKO mice had reduced intestinal farnesoid X receptor (FXR) signaling via hepatocyte nuclear factor 1α (HNF-1α) compared with controls, which reduced expression of the bile acid transporter genes Asbt and Mcf2l (encodes Ost) and absorption of ileal bile acids. SIRT1 regulated HNF-1α/FXR signaling partially through dimerization cofactor of HNF-1a (Dcoh2) Dcoh2, which increases dimerization of HNF-1α. SIRT1 was found to deacetylate Dcoh2, promoting its interaction with HNF-1α and inducing DNA binding by HNF-1α. Intestine-specific deletion of SIRT1 increased hepatic bile acid biosynthesis, reduced hepatic accumulation of bile acids, and protected animals from liver damage from a diet high in levels of bile acids. CONCLUSIONS: Intestinal SIRT1, a key nutrient sensor, is required for ileal bile acid absorption and systemic bile acid homeostasis in mice. We delineated the mechanism of metabolic regulation of HNF-1α/FXR signaling. Reagents designed to inhibit intestinal SIRT1 might be developed to treat bile acid-related diseases such as cholestasis.

Visualization of nerve fibers and their relationship to peripheral nerve tumors by diffusion tensor imaging.

OBJECT The majority of growing and/or symptomatic peripheral nerve tumors are schwannomas and neurofibromas. They are almost always benign and can usually be resected while minimizing motor and sensory deficits if approached with the proper expertise and techniques. Intraoperative electrophysiological stimulation and recording techniques allow the surgeon to map the surface of the tumor in an effort to identify and thus avoid damaging functioning nerve fibers. Recently, MR diffusion tensor imaging (DTI) techniques have permitted the visualization of axons, because of their anisotropic properties, in peripheral nerves. The object of this study was to compare the distribution of nerve fibers as revealed by direct electrical stimulation with that seen on preoperative MR DTI. METHODS The authors conducted a retrospective chart review of patients with a peripheral nerve or nerve root tumor between March 2012 and January 2014. Diffusion tensor imaging and intraoperative data had been prospectively collected for patients with peripheral nerve tumors that were resected. Preoperative identification of the nerve fiber location in relation to the nerve tumor surface as seen on DTI studies was compared with the nerve fiber's intraoperative localization using electrophysiological stimulation and recordings. RESULTS In 23 patients eligible for study there was good correlation between nerve fiber location on DTI and its anatomical location seen intraoperatively. Diffusion tensor imaging demonstrated the relationship of nerve fibers relative to the tumor with 95.7% sensitivity, 66.7% specificity, 75% positive predictive value, and 93.8% negative predictive value. CONCLUSIONS Preoperative DTI techniques are useful in helping the peripheral nerve surgeon to both determine the risks involved in resecting a nerve tumor and plan the safest surgical approach.

Fibroblastic reticular cell tumor of eyelid: Rare case report and review of literature.

Fibroblastic reticular cell tumours (FRCT) originate from the fibroblastic reticular cells (FBRC) which are histiocytic cells, belonging to the dendritic cell family. These tumours are extremely rare, with only a few cases reported in literature. Histomorphologically, they resemble follicular dendritic cell sarcoma (FDCS); however, they differ immunophenotypically. Extranodal presentations are rare. We report a case of malignant FBRC tumour of the left eyelid, in a 23-year-old woman, who had presented with a recurrent swelling over left lower eyelid. Microscopy revealed an ill circumbscribed tumour composed of oval to spindle cells in storiform pattern, sprinkled with lymphocytes. Immunohistochemistry was performed and diagnosis of FRCT was offered. To the best of our knowledge, this is the first report of malignant FBRC tumour arising in the eyelid region. Here we present this extremely rare case with review of the available literature.

Protocol for the creation and characterization of SARS-CoV-2 variant testing panels using remnant clinical samples for diagnostic assay testing.

The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Alpha variant in 2020 demonstrated the need for reanalysis of diagnostic tests to ensure detection of emerging variants. Here, we present a protocol for creating and characterizing SARS-CoV-2 variant testing panels using remnant clinical samples for diagnostic assay testing. We describe steps for characterizing SARS-CoV-2 remnant clinical samples and preparing them into pools and their use in preparing varying quantities of virus. We then detail procedures for verifying variant detection using the resulting sample panel. For complete details on the use and execution of this protocol, please refer to Rao et al.1,2.

Performance of the Xpert™ Mpox PCR assay with oropharyngeal, anorectal, and cutaneous lesion swab specimens.

Anorectal and oropharyngeal exposures are implicated in sexual transmission of mpox, but authorized assays in the United States are only validated with cutaneous lesion swabs. Diagnostic assays for anorectal and oropharyngeal swabs are needed to address potential future outbreaks. The Cepheid Xpert® Mpox is the first point-of-care assay to receive FDA emergency use authorization in the United States and would be a valuable tool for evaluating these sample types. Our exploratory study demonstrates 100 % positive agreement with our in-house PCR assay for natural positive anorectal and oropharyngeal specimens and 92 % sensitivity with low-positive spiked specimens. The Xpert® assay detected viral DNA in specimens not detected by our reference PCR assay from four participants with mpox DNA at other sites, suggesting it may be more sensitive at low viral loads. In conclusion, the validation of the Xpert® for oropharyngeal and anorectal sample types can be rapidly achieved if clinical need returns and prospective samples become available.

Comparison of RT-PCR and antigen test sensitivity across nasopharyngeal, nares, and oropharyngeal swab, and saliva sample types during the SARS-CoV-2 omicron variant.

Limited data highlight the need to understand differences in SARS-CoV-2 omicron (B.1.1.529) variant viral load between the gold standard nasopharyngeal (NP) swab, mid-turbinate (MT)/anterior nasal swabs, oropharyngeal (OP) swabs, and saliva. MT, OP, and saliva samples from symptomatic individuals in Atlanta, GA, in January 2022 and longitudinal samples from a small familial cohort were tested by both RT-PCR and ultrasensitive antigen assays. Higher concentrations in the nares were observed in the familial cohort, but a dominant sample type was not found among 39 cases in the cross-sectional cohort. The composite of positive MT or OP assay for both RT-PCR and antigen assay trended toward higher diagnostic yield but did not achieve significant difference. Our data did not identify a singular preferred sample type for SARS-CoV-2 testing, but higher levels of saliva nucleocapsid, a trend toward higher yield of composite OP/MT result, and association of apparent MT or OP predominance with symptoms warrant further study.