Patient Outcomes in CMV and SARS-CoV-2 Coinfection

This study examines clinical outcomes in patients with cytomegalovirus (CMV) and SARS-CoV-2 coinfection. Between June and November 2020, previously immunocompetent patients with SARS-CoV-2 and CMV coinfection were identified at Houston Methodist Hospital as part of routine clinical correlation by a molecular pathologist. SARS-CoV-2 nasopharyngeal specimens were analyzed by real time reverse-transcriptase polymerase chain reaction (RT-PCR). All CMV tests were performed on plasma or bronchoalveolar lavage (BAL) specimens and analyzed by competitive polymerase chain reaction. 65 previously immunocompetent patients with CMV and SARS-CoV-2 coinfection were identified. Patient demographics include 41 male patients (63%) and 24 female patients (37%) ranging in age from 34 to 86 years (mean: 66.04, median 68). Documented pre-existing conditions include 27 patients with hypertension 41.5%), 19 patients with diabetes mellitus (29.2%), 9 patients with coronary artery disease (13.8%), and 3 patients with asthma (4.6%). Eight patients (12.3%) had no documented pre-existing conditions. The plasma CMV viral load ranged from <300 to 21,566 IU/mL. The CMV PCR results from bronchoalveolar lavage and bronchial wash specimens ranged from <300 to 59,127 IU/mL. CMV PCR was initially negative in 10 patients then positive on serial testing. 60 patients were critically ill requiring ventilator support (92.3%). 47 patients (72.3%) expired, 7 patients (10.8%) were transferred to a long term acute care facility, 3 patients (4.6%) were discharged to a rehabilitation facility, 3 patients (4.6%) were discharged home, and 1 patient (1.5%) remained in-patient at the time of analysis. The prevalence of CMV seropositivity and medical comorbidities increases with age. Reactivation of latent CMV is a known occurrence in critically ill patients that is associated with poor outcomes. The majority of the patients in our cohort were 50 years old, and all were severely to critically ill with a mortality rate of 72.3% These findings suggest CMV portends a worse prognosis in patients with COVID-19. These findings also demonstrate the importance of clinical correlation in molecular testing.

The Value of Virtual Meetings during COVID-19 Pandemic in Healthcare Settings

Introduction/Objective The coronavirus pandemic led to an unprecedented rise in using virtual meeting technology in the healthcare sector for conferences, business meetings, and continuous medical education. This study aims to understand the practices and individual preferences and to highlight the benefits and challenges of virtual meetings compared to in-person ones. Methods/Case Report This cross-sectional study was disseminated via email as an online survey, using SurveyMonkey (Momentive Inc. San Mateo, California, USA) and targeted healthcare providers at the King Hussein Cancer Center-Amman, Jordan. Results (if a Case Study enter NA) A total of 342 healthcare providers took part in this questionnaire. 82.5% of respondents reported participating in virtual meetings;of those, only 33.5% preferred virtual over in-person meetings (PrV). Whether virtual meetings were equivalent to in-person ones, 33.2% of all participants (71.4% of the PrV) said virtual meetings were equivalent to in-person meetings in terms of participants' attention (p<0.001). Additionally 54.8% of all participants believed their gain level was less in virtual meetings compared to the conventional in-person ones;this percentage differs significantly between the participant's group who preferred in-person (PrP) over virtual meetings and the PV group who believed otherwise (75.0% vs 13.2%, p<0.001). Nonetheless, when respondents were asked about their meeting preferences in the event of a pandemic, 49.5% of all healthcare providers preferred virtual over in-person meetings (91.3% of the PrV group p<0.001). Almost half the participants (54.3%) reported that they tend to temporarily leave virtual meetings before it is over, yet, this percentage rockets to 70.0% if the meeting is over 2 hours long. On the other hand 43.3% of respondents admitted to leaving the meeting physically while keeping themselves logged in on their mobile/computer. An interesting result of the survey was that 58.3% of all respondents preferred to attend virtual meetings during working hours (85.7% of the PrV group, p<0.001). Finally, when asked about performing other tasks while in a virtual meeting, the vast majority (82.6%) of respondents confirmed either answering the phone, reading/sending emails, or checking a social media outlet at least once, which contributes to a lack of adequate concentration. Conclusion Healthcare providers still prefer and attach more value and benifit to in-person interactions

The Pandemic as a Catalyst for Digital Pathology Adoption as an LDT

Whole-slide images (WSI) are the basis for the application of artificial intelligence/machine learning and other informatics methods to histological diagnosis and will further blur the line separating anatomic and clinical pathology. FDA classified WSI systems for primary diagnosis as class III (highest risk) medical devices until 2017. This discouraged anatomic pathology laboratories at risk-averse domestic institutions like mine from investing in these digital pathology (DP) platforms. In 2017, FDA downgraded WSI to class II (moderate risk) when they de-novo approved a system marketed by Philips. We were not interested in that system at my institution, but the downgrade caused us to reset our perception of the risk of validating a RUO system for primary diagnosis. Cost remained a barrier. In April 2020, FDA issued temporary guidance stating they would not enforce premarket approval of WSI systems to facilitate pathologists working remotely during the SARS-CoV-2 pandemic. The guidance included a statement that "laboratories and hospitals consider performing a validation study.” In January 2021, FDA proposed making the temporary non-enforcement guidance permanent. So, in a little more than three years, WSI for primary diagnosis had gone from class III to exempted from pre-market approval! This nicely aligned the approval framework for WSI with the approval framework for our conventional optical microscopes, which are statutorily exempted from approval, and further reset our perception of risk. In April 2021, FDA withdrew the proposal to make non-enforcement permanent, but the temporary non-enforcement guidance is still in effect at the time of writing. Amid all this FDA activity, the College of American Pathologists updated and reissued their consensus guidelines for validating WSI systems for diagnostic purposes in March 2021. The narrative mentions the FDA's recent approval of a few WSI systems and anticipates more, but the expert panel recommendations do not include any related to the approval status of systems. The reissue of this document reminded us that, as clinical laboratorians, we are capable of safely validating WSI as a laboratory-developed test and are supported in doing so by consensus guidelines from one of our leading professional organizations. In early 2021 we committed to funding a DP initiative to make WSI part of our routine histological process for 10% of our anatomic pathology cases. The initial capital investment is $1.5M. When realized, the microscope slides for designated pathology services will be transported directly from the cover slipper to a slide scanner and electronically distributed to pathologists using a clinical-grade image management system that we share with our radiology department. We made the decision to fund this in the context of the regulatory (decreased perception of risk), sociological (demand for remote telepathology), and technological (availability of scalable WSI systems) changes that occurred during the pandemic.

The Spectrum of Pulmonary Histomorphology Changes in COVID-19 Cases

Introduction/Objective Pulmonary specimens following COVID-19 virus infection demonstrate a spectrum of pulmonary histomorphology. Six patients with a history of COVID-19 infection are summarized in this review. The purpose of our study is to elucidate any possible correlations between clinical, laboratory, radiographic, and pathologic findings in COVID-19 patients. Further, we aim to characterize both non-specific and specific histomorphology and cytomorphology in COVID-19 patients. Methods/Case Report Six patients with known COVID-19 infection and lung biopsies/resections are identified. A chart review is performed to collect clinical histories, the results of COVID-19 PCR testing, radiographic impressions, pathologic interpretations of histology, and clinical outcomes. Information is summarized and tabulated. Results (if a Case Study enter NA) The most common, non-specific histological findings are focal/diffuse acute lung injury, organizing lung injury, or a combination of both patterns. Unique features of COVID-19 infection are identified in three cases, which illustrate viral cytopathic changes within hyperplastic pneumocytes. These include basophilic, vacuolated, granular cytoplasm and variably sized cytoplasmic/nuclear inclusions. Virus-loaded pneumocytes are typically identified in the organizing phase, and rarely in the acute lung injury phase. Immunohistochemical staining of anti-nuclear capsule antibody with appropriate controls shows focal positive staining in one case. SARS-CoV-2 PCR is positive in formalin-fixed paraffin-embedded (FFPE) tissue, while a serum PCR assay is negative. Conclusion The severity of clinical symptoms and clinical outcome are unrelated to the degree of lung involvement. Viral cytopathic changes are identified in three cases, with these specific findings associated with the organizing phase of lung injury, and either concurrent PCR positivity or positive immunohistochemical staining.

Minimal Change Disease Secondary to Either COVID-19 Infection or Pfizer-BioNTech COVID-19 Vaccination

Introduction/Objective Kidney injury has now become one of the known complications following COVID-19 infection and vaccination. Only few cases of minimal change disease following administration of COVID-19 vaccination and infection have been reported. This study was to highlight incidence of minimal change disease following COVID-19 infection or vaccination. Methods/Case Report Case 1:15 year-old female with past medical history of asthma and hypercholesterolemia presented for evaluation of periorbital edema, nephrotic-range proteinuria, hypoalbuminemia, elevated serum creatinine, elevated blood pressures, and hematuria after COVID-19 infection. Renal biopsy after 1 week of infection showed unremarkable glomeruli and negative immunofluorescent stains in glomeruli, and 20-30% fusion of foot processes. The biopsy was consistent with a minimal change disease with features of natural remission (her nephrotic-range proteinuria resolved soon after). Case 2: 18 year-old female with no significant past medical history presented with a chief complaint of generalized swelling, which started around the same time she received her 1st dose of Pfizer COVID vaccine (the 2nd dose 2 months later). She had a nephrotic range proteinuria and hypoalbuminemia, but normal level of serum creatinine. A renal biopsy after 4 months of vaccination showed unremarkable glomeruli by light microscopy, negative immunofluorescent study, but diffuse effacement of foot processes involving more than 80% of the examined loops by electron microscopy. This biopsy findings were consistent with a minimal change disease. Both patients did not receive any treatment before the renal biopsies. Results (if a Case Study enter NA) NA Conclusion Minimal change disease can be a rare complication following COVID-19 infection or Pfizer COVID-19 vaccination, raising a question if there are similar antigens induced by the infection or by the vaccination that trigger the minimal change disease. Further studies are needed to determine the incidence and pathophysiology of minimal change disease either post COVID-19 vaccines or following COVID-19 infections.

Trending the Variants of SARS-CoV-2 in the Veteran Population: How Things Have Changed from Before to the Interesting Present

Introduction/Objective In both the past and for the foreseeable future, SARS-CoV-2 (the coronavirus that causes COVID-19 disease) will continue to evolve. This evolution has already and will lead to new variants that will then cause surges of infection. These outbreaks in the past with the variant responsible have previously been reported individually. However, a timeline perspective on the changing SARS-CoV-2 variant landscape is sparse in the literature, particularly for testing performed at a Veteran Affairs Medical Center (VAMC). The Veteran population has increased comorbidities compared to the general population leading to susceptibility to infection including SARS-CoV-2. Hence, it is of utmost importance to explore the trending variants of SARS-CoV-2 in the veteran population as this epidemiological information may help in preventing transmission, which remains key in the management of COVID-19. Methods/Case Report Samples from selected patients from March 2021 to June 2022 who tested positive for SARS- CoV-2 by reverse transcriptase polymerase chain reaction with a cycle threshold or number <30 (required for sequencing) were sent for SARS-CoV-2 sequencing analysis. Results (if a Case Study enter NA) There were a total of 19 VAMC patients who were sequenced during the entire study period (March 2021 to June 2022). From March to May 2021, there were 8 patients, from which 6 demonstrated Pango Lineage B.1.1.7, 1 demonstrated Pango Lineage B.1.526.1, and 1 demonstrated Pango Lineage B.1. Later in 2021 (August to October 2021), there were 4 patients all of which demonstrates the Delta variant;2 of these 4 demonstrated the Delta subvariant Pango Lineage AY.25 and the other 2 demonstrated Pango Lineage AY.44. By May to June 2022, there were 7 patients, all of whom demonstrated infection by the Omicron variant. Interestingly, 6 of these 7 patients demonstrated the newly emerging subvariant BA.2.12.1 and the remaining 1 demonstrated BA.2.9. Conclusion SARS-CoV-2 has continued to evolve throughout the course of the pandemic, which has led to variants and subvariants that have predominated for a time to cause an outbreak only to be replaced later by a different strain. This timeline epidemiological perspective demonstrates that the Veteran population has also been affected by the variants that have led to outbreaks in the past within the general population.

Application of the Jhala Risk Scoring System (JRSS) to a SARS-CoV-2 Sequenced Population

Introduction/Objective Much was unknown initially regarding the triaging of scarce resources to manage the COVID-19 disease, particularly for prognosticating hospital admission needs, which contributed to the healthcare resource supply crisis. Thus, the authors developed the simple Jhala Risk Scoring System (JRSS). There is no report in the English literature that has explored a risk scoring system in patients with a SARS-CoV-2 sequencing result demonstrating different SARS-CoV-2 strains;hence, presented here is a first report. Methods/Case Report The JRSS assesses risk factor points based on patient's age, ethnicity, pulmonary medical history, cardiovascular medical history, diabetes history, smoking history, and laboratory parameters. From the veteran patients who had been sequenced for COVID-19 from March 2021 to June 2022 with available clinical notes or follow-up, the JRSS was applied to obtain a JRSS score. This JRSS score was then compared with the patient's admission status, SARS-CoV-2 sequence result, and survival. A JRSS score of 7 or greater would designate higher risk. Results (if a Case Study enter NA) There were a total of 11 COVID-19 positive patients meeting the inclusion criteria during the study period. 4 of these 11 patients were from March to May 2021. The patient ages ranged from 55-80 years of age and consisted of 2 Caucasian Americans and 2 African Americans. Of these 4 patients, 1 was treated as an outpatient (JRSS score 2), 2 were treated in the intensive care unit within which 1 expired (both JRSS score 9), and 1 was treated on the medical floor (JRSS score 7). All 4 patients from March to May 2021 sequenced to have Pango Lineage B.1.1.7. 7 of the 11 patients were from May to June 2022. The patient ages ranged from 69-86 years of age and consisted of 4 Caucasian Americans, 2 African Americans, and 1 decline to state. Of these 7 patients, 1 patient expired in the CLC (JRSS score 10). 5 recovered within the CLC with JRSS scores of 5, 7, and 8 for 2, 1, and 2 patients respectively. One patient required hospitalization (JRSS of 6 based clinically only as lab parameters were not performed). All 7 patients except for 1 sequenced for BA.2.12.1, a subvariant of Omicron. The 1 patient who sequenced with a different Omicron subvariant (BA.2.9) was one of the 5 patients who recovered from infection within the CLC. Conclusion The JRSS, developed early in the pandemic, is a very simple and highly successful system that helps in prognostication even with the Omicron outbreak.

COVID Cholangiopathy Can Occur Despite Mild COVID

Introduction/Objective Post-COVID-19 cholangiopathy is a novel entity first noted in patients recovering from critical COVID-19 infection. Since its initial description in May 2021, all cases reported to date have been in patients with a history of critical COVID-19, defined as requiring ICU admission, the development of respiratory or circulatory failure requiring intubation or ECMO, or vasopressor support. Here we report three cases of post-COVID-19 cholangiopathy arising in patients who recovered from non-severe COVID-19. Methods/Case Report Six cases of COVID-19-related cholangiopathy were identified by retrospective review, three of which involved patients who verifiably did not develop critical COVID-19. Histology slides for each case were reviewed and all showed features of secondary sclerosing cholangitis. Patient 1 is a 41yo female who developed COVID-19 after liver transplant (LT). Despite administration of monoclonal antibodies, she required re-transplantation 6 weeks later. Explant histology showed bile infarcts, severe hepatocytic and canalicular cholestasis, ductular reaction, organizing portal vein thrombi, and necrotic bile ducts accompanied by bile lakes. Patient 2 is a 47yo male with alcoholic cirrhosis who was diagnosed with COVID-19 at the time of LT workup, and underwent LT 90 days later. In addition to alcohol-related cirrhosis, explant histology showed dilated bile ducts with periductal fibrosis, as well as severe ductular reaction with proliferating ductules containing thick, inspissated bile. Patient 3 is a 54yo male with history of LT for PSC who developed mild COVID-19 five years after LT. Allograft function subsequently worsened and biopsy 6 months later showed bile duct damage and loss of ~35% of bile ducts;repeat biopsy 14 months after his COVID diagnosis showed periportal fibrosis with edema, ductular reaction, marked hepatocellular and canalicular cholestasis, and ductopenia with loss of 60% bile ducts. Average time between COVID-19 diagnosis and onset of COVID-related cholangiopathy was 3 months (range: 6 weeks-6 months). These patients were also all immunocompromised with two due to prior LT and one being cirrhotic. Results (if a Case Study enter NA) NA. Conclusion Although previously reported only in patients with severe COVID-19, the cases described represent the first evidence that cholangiopathy, manifested by sclerosing cholangitis, can arise even in patients who were not critically ill, although this may require an immunocompromised state to develop.

SARS-CoV-2 Detection by Extraction-free qRT-PCR for Massive and Rapid COVID-19 Diagnosis During a Pandemic

Introduction/Objective COVID-19 pandemic severely impacted the healthcare and economy on a global scale. It is widely recognized that mass testing is an efficient way to contain the spread of SARS-CoV-2 infection as well as aid in the development of informed policies for disease management. Here we optimized two different protocols for qRT- PCR with direct samples and systematically compared them with the laboratory standard qRT-PCR detection assay. Methods/Case Report RNA samples from 270 subjects collected in two phases at 2020-2021. The groups consisted from positive (n = 240) and negative (n = 30) samples. We compared the performance of qRT-PCR in direct heat- inactivated (95 °C for 5 min, H), heat-inactivated and pelleted (95 °C for 5 min and centrifuged for 10 min at 12,000 g, HC) against standard laboratory protocol for SARS-CoV-2 qRT-PCR (targeting ORF1ab and N genes). Accuracy, sensitivity, and specificity for PCR assays were calculated using caret and epiR packages available in the R software environment for statistical computing. The Wilcoxon matched rank test was used to compare differences in Ct values. Results (if a Case Study enter NA) Our study suggests that HC samples show higher accuracy for SARS-CoV-2 detection PCR assay compared to direct H (89 % (95 % CI: 80–95 %) vs 83 % (95 % CI: 74–91 %) of the detection in RNA). The median ΔCt was lower by 1.55 and 2.29 cycles (Wilcoxon signed-rank test p = 0.0018 and < 0.0001 for ORF1ab and N genes, accordingly) in HC samples compared to H samples. Conclusion Our results suggest that purified RNA provides more accurate results;heat-inactivated and pelleted sample testing with qRT-PCR showed a slight drop in accuracy. However, the latter could also help to significantly increase testing capacity. Switching to the direct sample testing is justified if the number of tests is doubled at least.

Systemic and Local Disease Manifestations Following COVID-19 Vaccination

Introduction/Objective COVID-19 vaccine-related lymphadenopathy, particularly in the ipsilateral axilla, is a relatively well-known side effect of mRNA vaccines with many reports in radiology, but less is known regarding histopathology and additional sites of lymphadenopathy, as well as other localized potential vaccine-related mass manifestations. In addition to a case of minimal change disease, we report two cases here with associated systemic and local pathologic changes related to COVID-19 vaccination. Methods/Case Report In case #1, a 17-year-old male presented with a 2.4 cm left postauricular mass. He had originally noticed the mass six months prior and thought that it had recently been growing. The mass was soft, nonfluctuant, and nontender to palpation. Given the risk of malignancy, a resection was performed. Histology showed an enlarged lymph node composed of mixed inflammatory cell components consistent with lymphoid hyperplasia and no evidence of malignancy. On further chart review, the patient had received his second COVID-19 vaccination just prior to noticing the mass enlarging. A SARS-CoV-2 Anti-Spike IgG assay was as high as 24,396 AU/ml, suggesting that this benign lymphadenopathy was most likely related to his vaccination. For case #2, a 47-year-old male developed a painless right deltoid mass shortly after receiving his vaccination at the same area that subsequently increased in size over seven months to 6.5 cm. Imaging showed a heterogeneous mass within the deltoid muscle concerning for malignancy and a biopsy was performed. Sections showed wavy, bland spindle cells with nuclei staining diffusely positive for beta-catenin, consistent with fibromatosis at his vaccination site. Results (if a Case Study enter NA) NA. Conclusion In summary, these case reports show potential systemic and local reactive effects in response to COVID-19 vaccination.

Thermal Shock Viral RNA Release in COVID-19 Testing

Introduction/Objective The public health emergency of the COVID-19 pandemic emphasized the crucial role of medical laboratory professionals and scientists in molecular diagnostics laboratories to ensure success in infection control strategies. The demand for laboratory testing using nucleic acid amplification tests to detect SARS-CoV-2 RNA imposed strains in laboratory supplies. Here, we explored an alternative cost-effective solution that will simplify the pre-PCR steps by using a simple heating method to release viral RNA. Methods/Case Report Samples tested using the reference automated extraction method were used:100 samples identified as positive for SARS-CoV-2 RNA and 500 samples tested negative for SARS-CoV-2 RNA were used for the study and sorted with equal distribution according to Ct values of (a) <20, (b) 20–30, and (c) >30.100 ul from swab preserved in Universal Transport Medium was treated with 30 μg of proteinase K, and another set was tested without proteinase K pre-treatment. All samples with or without proteinase K were diluted to minimize PCR inhibitors. The thermal shock protocol was set at (98°C, 5 minutes;4°C, 2 minutes) and screened for purity. Performance and method verification studies were performed. Internal extraction, positive template, and no template controls were markers used for testing quality. The experimental study was performed by qualified testing personnel and all under the same experimental conditions. Results (if a Case Study enter NA) The Ct values from the thermal shock RNA release were compared to the automated extraction method and statistically analyzed.The criteria for acceptability for validation of this new RNA extraction proceeding were set to 100% concordance compared to the commercial kit using an automated extraction. PCR efficiency was at 98% and a slope of -3.3. Within run precision of 2% and limits of detection from 200 to 20,000 copies/uL The method 100% (50/50) concordance on samples previously identified as negative by automated methods and identified 86% (86/100) with a mean difference of 3 Ct. Conclusion Our findings suggest that the thermal shock treatment of nasopharyngeal swabs in viral transport media can successfully extract viral nucleic acid for nucleic acid amplification and is a reasonable alternative for chemical extraction methods when molecular diagnostic laboratories persistently encounter supply chain issues.

Barotrauma in a Previously Healthy and Young COVID-19 Patient: an Autopsy Case Report

Introduction/Objective Since the emergence of a novel SARS-CoV-2 virus caused coronavirus disease 2019 (COVID-19), a great number of autopsy studies have been published. However, histopathologic studies focused on pulmonary barotrauma are very rare. Here we report an autopsy confined to the lungs on a young COVID-19 patient. Methods/Case Report The patient was a 37-year-old male, non-smoker, with no significant past medical history, and a body mass index of 24.1, who presented with shortness of breath and cough. A computerized tomography (CT) showed features of atypical pneumonia. The main abnormal laboratory data included elevated partial thromboplastin time, fibrinogen, and D-Dimer. The patient had been on mechanical ventilation for 35 days, and was complicated by recurrent pneumothoraces, hypotension, and worsening hypoxia. An autopsy limited to the lungs was performed after the patient expired. Grossly, the lungs showed increased weight, adhesions on visceral pleural surface, patchy consolidation and dilated subpleural cysts. Histological examination revealed cystically dilated/remodeled airspaces with extensive coagulative necrosis, focal alveolar hemorrhage and edema, focal confluent fibrosis, and subpleural blebs. Fresh fibrinous thrombi were seen in small- and medium-sized vessels. Viral cytopathic changes or significant inflammation were not observed. The findings in the lungs were consistent with barotrauma in COVID-19. Results (if a Case Study enter NA) NA. Conclusion This case demonstrates various histopathologic changes of the lungs in a previously healthy and young COVID-19 patient with prolonged hospital course of mechanical ventilation. The features of diffuse alveolar damage with inflammation usually seen in the early stage of barotrauma are not identified. Our findings in the lungs may represent the histopathologic characteristics of the later stage of barotrauma in COVID-19.

HLA-B evolutionary divergence is associated with poor outcomes after SARS-CoV-2 infection

Objectives Human leukocyte antigens (HLA) are highly diverse transmembrane proteins that present viral peptides to T cells and launch pathogen-specific immune responses. We aim to investigate the correlation between HLA evolutionary divergence (HED), a surrogate for the capacity to present different peptides, and the outcomes of SARS-CoV-2 infection in a cohort from the St. Louis Metropolitan area. Methods We enrolled adult patients with SARS-CoV-2 infection confirmed by RT-PCR who were hospitalized at two tertiary hospitals in St. Louis between March and July 2020. Genomic DNA was extracted from peripheral blood and genotyped by next-generation sequencing (NGS). HLA alleles were assigned based on key-exon sequences (G group) and limited to the 2-field resolution. HED was calculated by Grantham distance, which considers the difference in composition, polarity, and molecular volume between each pair of amino acids from maternal and paternal HLA. The HED score was obtained for HLA class I (HLA-A, -B, and -C) genotypes using the HLAdivR package in R. Clinical data were collected retrospectively from electronic medical records. A poor outcome was defined as an admission to the intensive care unit (ICU), a need for mechanical ventilation, or death. A favorable outcome was defined as the absence of the above poor outcomes. Results A total of 234 patients were enrolled in this study, 96 being females (41%). The median age and BMI were 66 years old and 28.30 kg/m2, respectively. African Americans comprised 71.4% of the cohort. Only 19 patients (8.1%) presented with no comorbidity;the rest had one or more comorbidities, with cardiovascular diseases being the most common. A total of 137 (58.5%) patients had poor outcomes from SARS-CoV-2 infection, while 97 (41.5%) patients had a favorable outcome. We detected a significant association between higher HLA-B HED and favorable outcomes, with each 1-point increase in HLA-B HED associated with 8% increased probability for the composite endpoint (OR 1.08, 95% CI=1.01-1.16, P = 0.04). The HED scores calculated for HLA-A or HLA-C were not significantly different between patients with favorable or poor outcomes. In a multivariate logistic regression analysis, increased HLA-B HED score, younger age, and no comorbidity were independently associated with favorable outcomes (P = 0.02, P = 0.01, and P = 0.05, respectively). Conclusion Our study shows a significant correlation between lower HLA-B HED scores and poor outcomes after SARS-CoV-2 infection. This finding suggests that maximizing the presentation of diverse SARS-CoV-2 peptides by HLA-B alleles may improve the clearance of SARS-CoV-2. Further studies are warranted to understand the functional and mechanistic implications of this finding.

Trends in Viral Respiratory Culture: Impacts of the SARS-CoV-2 Pandemic

Introduction Due to the increasing ease and availability of molecular assays, viral culture is rarely employed for the diagnosis of respiratory illnesses. Despite lower sensitivity than molecular techniques, viral culture may detect a wider array of viral pathogens at a lower cost relative to multiplex molecular panels. In this study, we examined the effects of the SARS-CoV-2 pandemic on viral respiratory culture ordering and trends in the rates of pathogen detection. Methods Viral respiratory culture results from Jan 1st, 2017 to February 28th, 2022 were analyzed for changes in the number of monthly orders, positivity rate, and incidence of individual pathogens. To determine changes in seasonal incidence and viral etiology, a comparison was made between winter (Dec-Feb) and summer (June-Aug) months as well as acute (Influenza A/B, RSV) and chronic (HSV, CMV) infections. Given SARS-CoV-2's classification as a BSL-3 pathogen, our viral culture assay was not designed to detect this virus. As a surrogate method to measure rates of SARS-CoV-2 in viral culture specimens, we performed NAAT testing with the ThermoFisher TaqPath COVID-19, Flu A/B, RSV assay on negative specimens. Results Following the pandemic, testing volume decreased by 46.7% with the overall positivity rate decreasing from 6.67% to 4.85%. Among the 46 states for which more than ten orders were placed, monthly testing decreased in 38 states. Of the eight states with increased average monthly testing, the greatest increases were seen in Rhode Island, Nevada, and Montana. During the pre-pandemic timeframe, acute respiratory pathogens demonstrated a typical winter peak with low summer detection. Post-pandemic, there was an atypical increase of acute respiratory pathogens, driven primarily by RSV. The positivity rate for chronic viral infections increased from 3.43% pre-pandemic to 4.09% post-pandemic. Following the pandemic, HSV has replaced influenza as the most commonly detected pathogen during winter months. Molecular studies of 229 negative viral culture specimens identified 36 (15.7%) samples positive for SARS-CoV-2, 9 (3.9%) for RSV, and none for influenza A or B. Median cycle threshold values for SARS-CoV-2 samples were 21.3 (range: 9.1-36.5). Conclusions Following the SARS-CoV-2 pandemic, the number of respiratory virus cultures ordered significantly decreased. There has also been a statistically significant decrease in the positivity rate driven by the absence of acute viral respiratory pathogens, including influenza A/B and RSV. We also observed an offseason increase of RSV during the summer months of 2021. Detection rates of chronic viral pathogens including CMV and HSV have remained relative stable. The presence of SARS-CoV-2 in negative specimens raises concerns for inappropriate test utilization. While less sensitive than molecular methods, viral culture has the potential to offer a lower cost alternative for monitoring a broad range of viral pathogens.

Incidence of Heparin Induced Thrombocytopenia (HIT) in patients with severe COVID-19

Introduction To prevent and treat thrombotic complications in patients hospitalized with severe COVID-19 infection, anticoagulation treatments primarily with heparin and low molecular weight heparin have been recommended. Heparin-induced thrombocytopenia (HIT) is a rare but conceivably fatal reaction to heparin that is characterized by a sudden drop in platelet count accompanied by new onset of thrombosis 4-10 days after heparin exposure. The purpose of this retrospective study was to investigate the prevalence of thrombocytopenia and HIT in hospitalized COVID-19 patients, as well as their association with mortality. Methods 3,672 plasma samples were collected from patients admitted to the first wave of COVID-19 in our institution at New York City (March to May 2020). All patients admitted with a platelet count of less than 150 k/ul were assigned to the thrombocytopenic group. In addition, two groups with similar demographics and normal platelet counts were randomly selected based on discharge outcome: alive vs. deceased (n= 88 per group). PF4 IgG Elisa and heparin neutralization were carried out in accordance with the manufacturer's instructions. A positive HIT result required an optical density (OD) greater than 0.4 and heparin neutralization greater than 50%. Statistical analysis was done in R studio (V.1.4.1717) to analyze demographics (age, gender, ethnicity), initial laboratory data, anticoagulation on admission, and thrombosis. Results Only 86 of the 3,672 (2.3%) patients admitted had thrombocytopenia. Only 1 of the 86 patients tested positive for HIT (1.1%). 4 cases of the non-survivors (4.5%) tested positive for HIT compared to none of the survivors in the two groups with normal platelet counts. One of these 4 cases had a history of thrombosis (DVT). Interestingly, the PF4 Elisa ODs in non-survivors were significantly higher than in survivors (0.09 vs. 0.06, p-value< 0.001). Although the platelet count did not differ significantly between the two groups, the mean platelet volume (MPV) on admission and its maximum peak during hospitalization were significantly higher in non-survivors than in survivors. Conclusions We only found HIT positive cases among non-survivors, implying that HIT is associated with COVID severity. The incidence of HIT in severe COVID-19 patients appears to be higher than the pre-COVID-19 historical rates of HIT in hospitalized patients (<1%). Although thrombocytopenia is relatively uncommon in COVID-19 patients, the MPV was significantly higher in non-survivors, suggesting that platelet activation and destruction may explain the higher rate of HIT in COVID-19.

Detection of Mutations in SARS-CoV-2 Genomic Clades using COVIDSeq-NGS among International Travelers

Introduction/Objective Numerous SARS-CoV-2 variants/lineages have been identified based on genome sequencing. As of June 15, 2022 almost 11,399,573 whole genome sequences have been deposited in the GISAID-database. Severity and spread of COVID19 is based on their efficiency of infection and to multiply in host. That largely depend upon the structural mutation in spike, ORF and N proteins etc. That happens due to translation of genomic mutations during polypeptide synthesis. Also, the mutations are region/country specific. Specific mutation and combination of mutation causes the emergence of new strains. However, the strains can migrate from one region to other through travelers. The main objective of the current study is profiling of mutations in the genome of SARSCoV2 using Next- Generation-Sequencing (NGS) in international travelers and phylogenetic analysis of the sequences to find out different clades of SARSCoV2. Methods/Case Report A total of 557 SARSCoV2 genomes were sequenced on S4-sequencing flow-cell on NovaSeq 6000. For NGS of SARS-CoV-2 genome, Illumina, COVIDSeq kits and the protocols will be used strictly as recommended by the manufacturer. After NGS the analysis was done followed by FASTA sequences retrieval, mutations recording and phylogeny. Results (if a Case Study enter NA) This study reports 11 clades (19A, B, 20A, B, C, D, 20E;EU1, 20G, 20H;Beta V2, 20I: Alpha V1, 21D;and Eta) for the first time in international travelers. To best of our knowledge, this is the first report of the COVIDSeq approach for detection of mutation in SARSCoV2 genomic clades. The study revealed some dominants mutations was (Orf1a: P2018Q, K1053R, E176V, Orf1b: A520V, T2165A, S: D1127G, D614G, L18F etc. in other genes). Conclusion Profiling of common mutations among travelers could fill some gaps about the existence of SARS-CoV-2 variants information. However, further studies are needed to consolidate these findings before to be utilized for development of a potential therapeutic strategy.

SUBPOPULATION COMPOSITION OF PERIPHERAL BLOOD LYMPHOCYTES IN COVID-19.

The pathogenesis of severe coronavirus infection COVID-19 is associated with activation of immune system, cytokine storm, impaired blood clotting, microvascular thrombosis, organ ischemia and multiple organ dysfunction syndrome. The role of various lymphocyte subpopulations in COVID-19 is still debated. The aim of our study was to analyze the subpopulational profile of peripheral blood lymphocytes in COVID-19 patients as compared with healthy donors. The study included 20 COVID-19 patients (11 males and 9 females,) and 26 healthy donors. Average age of the patients was 52 and 56 years, respectively. Clinical examinations were performed by standard laboratory methods. Peripheral blood lymphocytes were isolated in the Ficoll gradient. The cells were stained with antibodies to specific antigens of main lymphocyte populations, endothelial cells, and apoptotic cell markers. The analysis was performed by flow cytometry. The results showed that all patients had elevated C-reactive protein (14- to 35-fold), ferritin (1.2- to 13-fold), D-dimers (1.2- to 90-fold). 55% of men had a decrease in the absolute number of lymphocytes, in women this index was at the low normal limit. Cytometric analysis showed that, among peripheral blood lymphocytes, the proportion of functional cells expressing the CD45 marker ranged from 2 to 12% in 70% of patients, as compared with 80-99% among the donors. The proportion of CD45+ lymphocytes significantly correlated with the level of hemoglobin, but not with the levels of inflammatory biochemical markers. Among the functional lymphocytes of patients, there was a decrease in the proportion of CD3+, CD4+, CD8+T cells, increased proportion of natural killer CD56+ and the apoptotic (AnnexinV+) cell contents, but the proportion of CD19 and HLA-DR+B cells was not changed. Analysis of the lymphocyte (LC) subpopulations that did not express CD45 marker showed that this fraction contained different lymphocyte subsets with reduced expression of CD4, CD8, CD19, CD56 etc. in the blood of patients and donors. Higher percentage of endothelial cells expressing CD62P marker made the difference between patients and donors. Laboratory determination of lymphocyte subsets in blood samples of COVID-19 patients does not reflect the real severity pattern of the disease, thus requiring studies of the CD45-expressing functional cell populations.Copyright © Svirshchevskaya E.V. et al., 2023 The article can be used under the Creative Commons Attribution 4.0 License.

SCIENCE DIGEST

Needlestick injuries (3.1%) were associated with mental health problems presumably related to the transmission of infectious diseases and liquid nitrogen related injuries were reported in 3.1% of respondents. Overall the survey concluded that embryologists experienced a number of occupational health problems of which musculoskeletal and mental health and work stress issues were the dominate issues emerging from the survey which appeared to be linked to lack of control of workflow and irregular breaks as well as workplace stress. [...]these have been difficult to describe but with the ability to sequence multiple genes in a single assay decisions will have to be made on which genes should be identified as being responsible for susceptibility to breast cancer. Recently two high quality major studies (4,5) have identified a number of genes that are statistically associated with breast cancer risk.

Pathology Education Powered by Virtual and Digital Transformation: Now and the Future

[...]standing on the crest of yet another wave of change, driven by artificial intelligence (AI) and machine learning,2 pathology educators may soon be challenged to convey the best ways to apply these tools to the problems of diagnostic pathology for the coming generation of learners and the present corps of practitioners.3 Hence, this collaborative effort aims to describe the genetic code governing the transmission of pathology knowledge to subsequent generations of medical professionals.4 We aim to expose not just the code but also the supporting array of catalysts, enhancers, and other cofactors now in place to ensure we have a robust and potent supply of pathologists. APPLYING DP IN UNDERGRADUATE MEDICAL, DENTAL, VETERINARY, AND ALLIED HEALTH EDUCATION Beginning in 1985, this technology has been progressively more widely implemented in undergraduate medical, dental, veterinary, and allied health (nursing, pharmacy, medical technology, etc) education platforms in the United States and internationally.5,11-26 As noted above, virtual microscopy laboratories, available on personal devices or in school-based computer labs, have replaced fixed laboratories housing gross specimens, boxes of glass slides, and student microscopes. WSI with links to supplementary resources, such as gross and radiologic images and additional study material, provide enrichment for the teaching and learning experience in the new virtual environment. [...]significant exposure to microanatomy and the laboratory methods of pathology underpinning so much of diagnosis, therapy, and management is foundational.