Virus Screening Research Articles

Nationwide Screening for Bee Viruses in Apis mellifera Colonies in Egypt

Honey bees are essential for crop and wild plant pollination. However, many countries have reported high annual colony losses caused by multiple possible stressors. Diseases, particularly those caused by viruses, are a major cause of colony losses. However, little is known about the prevalence of honey bee pathogens, particularly virus prevalence, in Egyptian honey bees. To address this shortfall, we determined the prevalence of widespread bee viruses in honey bee colonies in Egypt-whether it is affected by geography, the season, or infestation with Varroa destructor (varroa) mites. Honey bee worker samples were collected from 18 geographical regions across Egypt during two seasons: winter and summer of 2021. Three apiaries were chosen in each region, and a pooled sample of 150 worker bees was collected from five colonies in each apiary then screened by qPCR for 10 viral targets: acute bee paralysis virus (ABPV), black queen cell virus (BQCV), chronic bee paralysis virus (CBPV), deformed wing virus (DWV) genotypes A (DWV-A), B (DWV-B) and D (Egyptian bee virus), Israeli acute paralysis virus (IAPV), Kashmir bee virus (KBV), sacbrood virus (SBV), and slow bee paralysis virus (SBPV). Our results revealed that DWV-A was the most prevalent virus, followed by BQCV and ABPV; the DWV genotype now spreading across the world, DWV-B, was not detected. There was no difference in varroa infestation rates as well as virus prevalence between winter and summer. However, colonies infected with BQCV had a significantly higher varroa count (adjusted p < 0.05) in the winter season, indicating that there is a seasonal association between the intensity of infestation by varroa and the presence of this virus. We provide data on the current virus prevalence in Egypt, which could assist in the protection of Egypt's beekeeping industry. Moreover, our study aids in the systematic assessment of the global honey bee virome by filling a knowledge gap about the prevalence of honey bee viruses in Egypt.

Human cytomegalovirus pUL97 upregulates SOCS3 expression via transcription factor RFX7 in neural progenitor cells

Congenital human cytomegalovirus (HCMV) infection causes severe damage to the fetal brain, and the underlying mechanisms remain elusive. Cytokine signaling is delicately controlled in the fetal central nervous system to ensure proper development. Here we show that suppressor of cytokine signaling 3 (SOCS3), a negative feedback regulator of the IL-6 cytokine family signaling, was upregulated during HCMV infection in primary neural progenitor cells (NPCs) with a biphasic expression pattern. From viral protein screening, pUL97 emerged as the viral factor responsible for prolonged SOCS3 upregulation. Further, by proteomic analysis of the pUL97-interacting host proteins, regulatory factor X 7 (RFX7) was identified as the transcription factor responsible for the regulation. Depletion of either pUL97 or RFX7 prevented the HCMV-induced SOCS3 upregulation in NPCs. With a promoter-luciferase activity assay, we demonstrated that the pUL97 kinase activity and RFX7 were required for SOCS3 upregulation. Moreover, the RFX7 phosphorylation level was increased by either UL97-expressing or HCMV-infection in NPCs, suggesting that pUL97 induces RFX7 phosphorylation to drive SOCS3 transcription. We further revealed that elevated SOCS3 expression impaired NPC proliferation and migration in vitro and caused NPCs migration defects in vivo. Taken together, these findings uncover a novel regulatory mechanism of sustained SOCS3 expression in HCMV-infected NPCs, which perturbs IL-6 cytokine family signaling, leads to NPCs proliferation and migration defects, and consequently affects fetal brain development.

Screening for Hepatitis C Among Community Health Center Patients by Ethnicity and Language Preference

Hepatitis C virus is associated with high morbidity and mortality-chronic liver disease is a leading cause of death among Latinos in the U.S. Screening for hepatitis C virus in community health center settings, which serve a disproportionate percentage of Latinos, is essential to eradicating hepatitis C virus infection. We assessed hepatitis C virus screening disparities in adults served by community health centers by ethnicity and language preference. This was an observational cohort study (spanning 2013-2017) of adults born in 1945-1965 in the Accelerating Data Value Across a National Community Health Center Network electronic health record data set. Our exposure of interest was race/ethnicity and language preference (non-Hispanic White, Latino English preferred, Latino Spanish preferred). Our primary outcome was the relative hazard of hepatitis C virus screening, estimated using multivariate Cox proportional hazards regression. A total of 182,002 patients met the study criteria and included 60% non-Hispanic Whites, 29% Latino Spanish preferred, and 11% Latino English preferred. In total, 9% received hepatitis C virus screening, and 2.4% were diagnosed with hepatitis C virus. Latino English-preferred patients had lower rates of screening than both non-Hispanic Whites and Latino Spanish preferred (5.5% vs 9.4% vs 9.6%, respectively). Latino English preferred had lower hazards of hepatitis C virus screening than non-Hispanic Whites (adjusted hazard ratio=0.56, 95% CI=0.44, 0.72), and Latino Spanish preferred had similar hazards of hepatitis C virus screening (adjusted hazard ratio=1.11, 95% CI=0.88, 1.41). We found that in a large community health center network, adult Latinos who preferred English had lower hazards of hepatitis C virus screening than non-Hispanic Whites, whereas Latinos who preferred Spanish had hazards of screening similar to those of non-Hispanic Whites. The overall prevalence of hepatitis C virus screening was low. Further work on the role of language preference in hepatitis C virus screening is needed to better equip primary care providers to provide this recommended preventive service in culturally relevant ways.

Eliminating Potential Effects of Other Infections during Selection of Nonhuman Primates for COVID-19 Research.

The study of nonhuman primates (NHP) can provide significant insights into our understanding numerous infectious agents. The etiological agent of COVID-19, SARS-CoV-2 virus, first emerged in 2019 and has so far been responsible for the deaths of over 4 million people globally. In the frenzied search to understand its pathogenesis and immunology and to find measures for prevention and control of this pandemic disease, NHP, particularly macaques, are the preferred model because they manifest similar clinical signs and immunologic features as humans. However, possible latent, subclinical, and opportunistic infections not previously detected in animals participating in a study may obscure experimental results and confound data interpretations in testing treatments and vaccine studies for COVID-19. Certain pathophysiologic changes that occur with SARS-CoV-2 virus infection are similar to those of simian pathogens. The current review discusses numerous coinfections of COVID-19 with other diseases and describes possible outcomes and mechanisms in COVID-19 studies of NHP that have coinfections. Due to the urgency triggered by the pandemic, screening that is more rigorous than usual is necessary to limit background noise and maximize the reliability of data from NHP COVID-19 studies. Screening for influenza virus, selected respiratory bacteria, and regional endemic pathogens such as vector-borne agents, together with the animal's individual exposure history, should be the main considerations in selecting a NHP for a COVID-19 study. In addition, because NHP are susceptible to the SARS-CoV-2 virus, management and surveillance measures should be established to prevent transmission to healthy animals from infected colony animals and husbandry staff. This review presents compiled data on the use of NHP in COVID-19 studies, emphasizing the need to create the most reliable NHP model for those studies by extensive screening for other pathogens.

Rapid virus detection using magnetic second harmonics of superparamagnetic iron oxide nanoparticles

Virus detection methods based on nonlinear magnetic response of magnetic nanoparticles have been investigated, and magnetic detection methods using the third harmonic are widely applied, owing to their high sensitivity and short measurement time. This paper proposes a virus detection method based on the second harmonic because of its larger signal component. We found that the second harmonic signal is superior to the third harmonic signal for small nanobeads and a large change of the second harmonic signal in the signal-to-noise ratio (SNR) with nanobeads concentration. In addition, a virus detection limit of 100 pg/ml is achieved. Therefore, the proposed method can potentially be utilized for rapid screening of viruses.

How Frequently Should We Screen for Hepatitis C in US Hemodialysis Centers? Evaluating the Cost-Effectiveness of Different Strategies.

1Department of Pharmaceutical and Health Economics, School of Pharmacy, University of Southern California, Los Angeles, California 2The Leonard D. Schaeffer Center for Health Policy & Economics, University of Southern California, Los Angeles, California 3Department of Medicine, Division of Nephrology, Keck School of Medicine of the University of Southern California, Los Angeles, California 4Sol Price School of Public Policy, University of Southern California, Los Angeles, California Correspondence: Dr. Eugene Lin, University of Southern California, 1333 San Pablo St., MMR 622, Los Angeles, CA 90033. Email: [email protected] See related article, “A Microsimulation Study of the Cost-Effectiveness of Hepatitis C Virus Screening Frequencies in Hemodialysis Centers,” on pages 205–219.

DOP17 HIV infection is associated with a less aggressive phenotype of inflammatory bowel disease. A multicenter study based on the ENEIDA registry.

Abstract Background The coexistence of immune-mediated diseases and non-pharmacological immunosuppression states are rare and might determine the natural history of the disease and therapeutic decisions of the physician. IBD guidelines recommend screening for human immunodeficiency virus (HIV) before starting immunosuppressive treatment, but data on the impact of HIV infection on IBD and its management in the era of biological drugs are scarce. Therefore, our aim was to describe IBD phenotype, immunosuppressive requirements, and prevalence of opportunistic infections (OI) in patients with IBD and coexistent HIV infection. Methods Case-control, retrospective, multicenter study including all IBD patients with available HIV serology on the ENEIDA registry (a large, prospectively maintained database of the Spanish Working Group in IBD –GETECCU). IBD patients with positive HIV serology were selected (HIV+) and compared to HIV seronegative IBD patients (controls), matched 1:3 by year of IBD diagnosis, age, gender and type of IBD). Demographic, clinical IBD characteristics, therapeutic requirements, OI and IBD complications were registered. Results Eighty-eight HIV+ IBD patients and 264 controls were included. In the whole cohort, 81% were men, 56.8% had ulcerative colitis (UC), 36.4% Crohns’ disease (CD) and 6.8% IBD unclassified. Median age at IBD diagnosis was 38 years (IQR 30-47), median age at HIV infection diagnosis was 36 years (IQR 30-42), 46.3% being were firstly diagnosed of IBD. Among UC patients, HIV+ had a lower proportion of extensive disease (24.5% vs 44.8%; P=0.002), and a higher proportion of proctitis (38.8% vs. 16.6%; P=0.002) than controls, without differences on disease proximal progression (7.7% vs 7.9%). Among CD patients, HIV+ presented a higher proportion of colonic involvement than controls (40.6% vs 12,6%, P=0.002) and lower penetrating behavior (10.7% vs 25%; ns). HIV+ had a lower proportion of extraintestinal manifestations (10.7% vs 25.4%; P=0.005). Although it was not statistically significant, a trend towards a lower proportion of hospitalizations (25.6% vs 35.3%) and IBD complications (6.3% vs. 9.2%) in HIV+ was observed. Regarding IBD therapeutic requirements, immunosuppressant (40.5% vs 58.7%; P=0.003) and biological drugs (28.3% vs 42.8%; P=0.020) were used less frequently among HIV+ than among controls. Conversely, HIV+ had a higher rate of OI (38.3% vs 17.8%; P&amp;lt;0.001) and malignancies (12.5% vs 8.3%, ns) than controls. Conclusion The coexistence of IBD and HIV infection seems to be associated with a less aggressive IBD phenotype and a lower use of immunosuppressants and biologicals but with a remarkable rate of OI.

Machine Learning Approaches for the Prediction of Hepatitis B and C Seropositivity.

(1) Background: The identification of patients at risk for hepatitis B and C viral infection is a challenge for the clinicians and public health specialists. The aim of this study was to evaluate and compare the predictive performances of four machine learning-based models for the prediction of HBV and HCV status. (2) Methods: This prospective cohort screening study evaluated adults from the North-Eastern and South-Eastern regions of Romania between January 2022 and November 2022 who underwent viral hepatitis screening in their family physician's offices. The patients' clinical characteristics were extracted from a structured survey and were included in four machine learning-based models: support vector machine (SVM), random forest (RF), naïve Bayes (NB), and K nearest neighbors (KNN), and their predictive performance was assessed. (3) Results: All evaluated models performed better when used to predict HCV status. The highest predictive performance was achieved by KNN algorithm (accuracy: 98.1%), followed by SVM and RF with equal accuracies (97.6%) and NB (95.7%). The predictive performance of these models was modest for HBV status, with accuracies ranging from 78.2% to 97.6%. (4) Conclusions: The machine learning-based models could be useful tools for HCV infection prediction and for the risk stratification process of adult patients who undergo a viral hepatitis screening program.

Developing broad-spectrum resistance in cassava against viruses causing the cassava mosaic and the cassava brown streak diseases.

Growing cassava in Africa requires resistance against the viruses causing cassava mosaic disease (CMD) and the viruses causing cassava brown streak disease (CBSD). A dominant CMD2 resistance gene from a West African cassava landrace provides strong resistance against the cassava mosaic viruses. However, resistance against cassava brown streak viruses is limited to cassava varieties that show tolerance to the disease. A recently identified cassava germplasm that cannot be infected with cassava brown streak viruses provides a new source of the resistance required to protect cassava from CBSD. We present a synopsis of the status of virus resistance in cassava and report on the research to combine resistance against CBSD and CMD. We improve the lengthy and erratic screening for CBSD resistance by proposing a virus infection and screening protocol for the viruses causing CBSD and CMD, which allows a rapid and precise assessment of cassava resistance under controlled conditions. Using this approach, we classified the virus responses of cassava lines from Africa and South America and identified truly virus-resistant clones that cannot be infected with any of the known viruses causing CBSD even under the most stringent virus infections. A modification of this protocol was used to test seedlings from cassava crosses for resistance against both diseases. A broad-spectrum resistance was identified in a workflow that lasted 9 months from seed germination to the identification of virus resistance. The workflow we propose dramatically reduces the evaluation and selection time required in a classical breeding workflow to reach the advanced field trial stage in only 9 months by conducting selections for virus resistance and plant multiplication in parallel. However, it does not bypass field evaluations; cassava resistance assessment prior to the field limits the evaluation to candidates with virus resistance defined as the absence of symptoms and the absence of the virus. The transfer of our virus screening workflow to cassava breeding programs enhances the efficiency by which resistance against viruses can be selected. It provides a precise definition of the plant's resistance response and can be used as a model system to tackle resistance in cassava against other diseases.

Hepatitis C Virus Screening among Baby Boomers: The Positive Benefits of Health Education and Outreach during the COVID-19 Pandemic.

In 2019, 2020, and 2021, Sendero Health Plans, an ACA health insurance company, implemented Hepatitis C Virus (HCV) health education and outreach screening campaigns. Chi-square goodness-of-fit and tests of independence were performed to assess and compare the uptake of HCV screening among baby boomers in 2019, 2020, and 2021. In 2019, 2020, and 2021, 17.9% (308/1,718), 10.9% (93/852), and 8.5% (37/435) of eligible members were screened, respectively. Individuals were more likely to be screened for HCV in 2019 than in 2020 and 2021 (p < 0.0001). In 2019, 2020, and 2021, 39.9%, 26.9%, and 48.6% of annual screenings occurred during the health campaign months, respectively. Annual HCV screening rates were lower during the COVID-19 pandemic period than in the pre-pandemic cohort. However, screening rates during the months of outreach and education contributed to nearly 50% of annual screenings in the pandemic year 2021, thus representing a positive impact on preventive screening uptake despite the pandemic. Missed screening opportunities affect HCV transmission, diagnosis, and treatment. Yet, health education and outreach continue to work, even during a pandemic.

Identification of novel RNA mycoviruses from wild mushroom isolates in Japan

The characterization of viruses from environmental samples could aid in our understanding of their ecological significance and potential for biotechnological exploitation. While there has been much focus on pathogenic fungi or commercially cultivated mushrooms, attention to viruses from wild Basidiomycota mushrooms is lacking. Therefore, in this study, we conducted viral screening of fungal mycelia isolated from wild basidiocarps using agarose gel electrophoresis (AGE) and fragmented and primer-ligated dsRNA sequencing (FLDS). Among the 51 isolates, seven isolates were detected with virus-like bands during the initial screening with AGE, but only five isolates were detected with viruses after long-term storage. Using the FLDS method, we obtained seven viral genome sequences, including five double-stranded RNA (dsRNA) viruses belonging to Partitiviridae and Curvulaviridae, one positive-sense single-stranded RNA (ssRNA) virus belonging to Endornaviridae and one negative-sense ssRNA virus belonging to Tulasviridae (Bunyavirales). All viruses characterized in this study are novel species. These findings greatly expanded our knowledge of the diversity of RNA viruses from environmental samples.

An integrated dual-layer microfluidic platform for multiple respiratory viruses screening

Currently, the coronavirus disease 2019 (COVID-19) caused by the outbreak of a novel coronavirus (SARS-CoV-2) is spreading rapidly worldwide. Due to the high incidence of influenza coinciding with SARS-CoV-2, rapid detection is crucial to prevent spreading. Here, we present an integrated dual-layer microfluidic platform for specific and highly sensitive SARS-CoV-2, influenza viruses A (FluA) H1N1, H3N2, and influenza virus B (FluB) simultaneous detection. The platform includes a dual microchip (Dμchip) and a portable detection device for real-time fluorescence detection, temperature control and online communication. The Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) and Cas12a cleavage were performed on the Dμchip. The limit of detection (LoD) of the Dμchip assay was 10 copies for SARS-CoV-2, FluA H1N1, H3N2, and FluB RNAs. The Dμchip assay yielded no cross-reactivity against other coronaviruses, so it was suitable for the screening of multiple viruses. Moreover, the positive percentage agreement (PPA) and negative percentage agreement (NPA) of the assay were 97.9% and 100%, respectively, in 75 clinical samples compared to data from RT-PCR-based assays. Furthermore, the assay allowed the detection SARS-CoV-2 and influenza viruses in spiked samples. Overall, the present platform would provide a rapid method for the screening of multiple viruses in hospital emergency, community and primary care settings and facilitate the remote diagnosis and outbreak control of the COVID-19.

Efficacy of a Primary Care-Based Mobile Application to Increase Hepatitis C Screening Among Asian Americans: A Secondary Analysis of a Randomized Clinical Trial.

Hepatitis C virus (HCV) screening remains suboptimal. We assessed the efficacy of a mobile application and provider alert in enhancing HCV screening among Asian Americans. A secondary analysis of a cluster-randomized clinical trial was performed during the birth cohort screening era to assess the efficacy of a Hepatitis App (intervention), a multilingual mobile application delivering interactive video education on viral hepatitis and creating a Provider Alert printout, at primary care clinics within 2 healthcare systems in San Francisco from 2015 to 2017. A comparison group received usual care and a similar intervention on nutrition and physical activity. The outcome was electronic health record (EHR) documentation of HCV screening along with patient-provider communication about testing and test ordering. Four hundred fifty-two participants (mean age 57 years, 36% male, 80% foreign-born) were randomized by provider clusters to the intervention (n = 270) or comparison groups (n = 182). At 3-month follow up, the intervention group was more likely than the comparison group to be aware of HCV (75% vs 59%, P = .006), to discuss HCV testing with their providers (63% vs 13%, P < .001), to have HCV testing ordered (39% vs 10%, P < .001), and to have EHR-verified HCV testing (30% vs 6%, P < .001). Within the intervention group, being born between 1945 and 1965 (odds ratio, 3.15; 95% confidence interval, 1.35-7.32) was associated with increased HCV testing. The Hepatitis App delivered in primary care settings was effective in increasing HCV screening in a socioeconomically diverse Asian American cohort. This highlights the importance of mobile technology as a patient-centered strategy to address gaps in HCV care.

Abstract A131: The effective of mHealth intervention on hepatitis B virus screening among Asian Americans: A scoping review

Abstract Introduction. Hepatitis B virus (HBV) is one of the major health threats causing cancer. Asian Americans are especially vulnerable to HBV infection risk compared to other racial/ethnic groups in America. New mHealth interventions have promising potential to save lives by increasing HBV screening among racial/ethnic minority groups, but its scope, range, and uptake among Asian Americans are not clear. This study aims to scope the literature describing the research of mHealth interventions on HBV screening among Asian Americans. Methods. A scoping systematic review search is conducted in PubMed and Embase. Eligible studies focus on Asian Americans aged 18 years or older who have participated in an mHealth Hepatitis B screening. All types of mHealth interventions on HBV are relevant (e.g., health apps and text messages). Studies not published in the English language will be excluded. Results. A review protocol is developed. Next. We will covert our search strategy to Embase, Medline, and other databases to get more records. At present, title and abstract screening are under development. After that, full-text screening, data extraction, data management, quality assessment, and data synthesis and analysis will be conducted. Initial results will be discussed. Potential impact. The results of this scoping and systematic review could improve our understanding of mHealth HBV screening use and uptake among Asian Americans and inform the development of a future intervention to encourage mHealth HBV screening for this patient population. In the long run, it could encourage the development of a future tailored mHealth intervention to facilitate the HBV screening uptake among Asian Americans Citation Format: Di Zhu, Yarra Zisman-Ilani, Stephanie Roth, Lin Zhu, Grace X. Ma. The effective of mHealth intervention on hepatitis B virus screening among Asian Americans: A scoping review [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr A131.

A Vermont Statewide Educational Intervention to Improve Access to Hepatitis C Virus Treatment in a Rural State.

Improved knowledge of hepatitis C virus (HCV) screening, linkage to care, and treatment is needed among nonspecialist medical professionals to combat the HCV epidemic. The authors sought to implement and analyze the impact of an HCV curriculum for primary care professionals (PCPs) across the state of Vermont, USA. This investigation was a retrospective analysis of uptake of a Vermont HCV educational curriculum and its impact on HCV direct-acting antiviral (DAA) prescribing rates within the state before and after the study period. The curriculum was delivered online and in-person over 2 years from 2019 to 2020. The primary outcome was health care professional performance on a pre- and post-curriculum short-term knowledge assessment exam. The secondary outcome was assessing the number of unique healthcare professionals within a single payor database prescribing DAA treatment for HCV in Vermont before and after the study intervention, from January 1, 2017 until December 1, 2021. There were 31 unique respondents on the pre- and post-intervention examinations, which represented 9% of known participants. Respondents included physicians (n = 15), nurse practitioners (n = 8), and nurses (n = 8). Pre- and post-intervention knowledge scores increased significantly across all provider groups, from 3.2 (SD 0.6) to 4.5 (SD 0.4) 1 to 5 scale (P = .01). The total number of unique HCV DAA therapy prescribers decreased over the study period, from 17 in 2017 to 9 in 2021. A Vermont statewide HCV curriculum for PCPs was successful at increasing short-term HCV-related knowledge. However, this did not obviously translate to an increase in new professionals treating HCV.

Leveraging COVID-19 vaccination to promote hepatitis C screening.

Health care initiatives, such as hepatitis C virus (HCV) screening, have been greatly overshadowed by the corona virus disease 2019 (COVID-19) pandemic. However, COVID-19 vaccination programs also provide an opportunity to engage with a high volume of people in a health care setting. We collaborated with a large COVID vaccination center to offer HCV point-of-care testing followed by dried blood spot collection for HCV RNA. Additionally, this opportunity was used to evaluate the practical significance of a 5-minute version of the OraQuick HCV antibody test in lieu of the standard 20-minute test. We tested 2317 individuals; 31 were HCV antibody positive and six were RNA positive of which four were treated and reached sustained virological response. Over a third of those surveyed said they would not have participated had the test required 20 minutes. Conclusion : Colocalizing HCV testing and linkage to care at a COVID vaccination clinic was found to be highly feasible; furthermore, a shortened antibody test greatly improves the acceptance of testing.

Establishing Bipotential Human Lung Organoid Culture System and Differentiation to Generate Mature Alveolar and Airway Organoids.

A robust in vitro model of the human respiratory epithelium, including the alveolar and the airway epithelium, is essential for understanding the biology and pathology of the human respiratory system. We previously described a protocol to derive human lung organoids from primary lung tissues. We now describe a protocol to induce bidirectional differentiation to generate mature alveolar or airway organoids. The lung organoids are consecutively expanded for over one year with high stability, while the differentiated alveolar and airway organoids morphologically and functionally simulate the human alveolar and airway epithelium to a near-physiological level. Thus, we establish a robust organoid culture system of the entire human respiratory epithelium, the first two-phase bipotential organoid culture system that enables long-term expansion and bidirectional differentiation of respiratory epithelial cells. The long-term expandable lung organoids and differentiated organoids generate a stable and renewable source of respiratory epithelial cells, enabling scientists to reconstruct and expand the human respiratory epithelium in culture dishes. The respiratory organoid system provides a unique and physiologically active in vitro model of the human respiratory epithelium for various applications, including studying respiratory viral infection, disease modeling, drug screening, and pre-clinical testing. Graphical abstract.

A clinico-epidemiological profile, coinfections and outcome of patients with Influenza Like Illnesses (ILI) presenting to the emergency department during the COVID-19 pandemic.

During the COVID-19 pandemic, many patients presented to the emergency department (ED) with features of Influenza-like illnesses (ILI) and with other atypical presentations. This study was done to determine the etiology, co-infections, and clinical profile of patients with ILI. This prospective observational study included all patients presenting to the ED with fever and/or cough, breathing difficulty, sore throat, myalgia, gastrointestinal complaints (abdominal pain/vomiting/diarrhea), loss of taste and altered sensorium or asymptomatic patients who resided in or travelled from containment zones, or those who had contact with COVID-19 positive patients during the first wave of the pandemic between April and August 2020. Respiratory virus screening was done on a subset of COVID-19 patients to determine co-infection. During the study period, we recruited 1462 patients with ILI and 857 patients with the non-ILI presentation of confirmed COVID-19 infection. The mean age group of our patient population was 51.4 (SD: 14.9) years with a male predominance (n-1593; 68.7%). The average duration of symptoms was 4.1 (SD: 2.9) days. A sub-analysis to determine an alternate viral etiology was done in 293 (16.4%) ILI patients, where 54 (19.4%) patients had COVID 19 and co-infection with other viruses, of which Adenovirus (n-39; 14.0%) was the most common. The most common symptoms in the ILI-COVID-19 positive group (other than fever and/or cough and/or breathing difficulty) were loss of taste (n-385; 26.3%) and diarrhea (n- 123; 8.4%). Respiratory rate (27.5 (SD: 8.1)/minute: p-value < 0.001) and oxygen saturation (92.1% (SD: 11.2) on room air; p-value < 0.001) in the ILI group were statistically significant. Age more than 60 years (adjusted odds ratio (OR): 4.826 (3.348-6.956); p-value: <0.001), sequential organ function assessment score more than or equal to four (adjusted OR: 5.619 (3.526-8.957); p-value: <0.001), and WHO critical severity score (Adjusted OR: 13.812 (9.656-19.756); p-value: <0.001) were independent predictors of mortality. COVID-19 patients were more likely to present with ILI than atypical features. Co-infection with Adenovirus was most common. Age more than 60 years, SOFA score more than or equal to four and WHO critical severity score were independent predictors of mortality.

Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study

Symptomatic patients who test negative for common viruses are an important possible source of unrecognised or emerging pathogens, but metagenomic sequencing of all samples is inefficient because of the low likelihood of finding a pathogen in any given sample. We aimed to determine whether nasopharyngeal CXCL10 screening could be used as a strategy to enrich for samples containing undiagnosed viruses. In this pathogen surveillance and detection study, we measured CXCL10 concentrations from nasopharyngeal swabs from patients in the Yale New Haven health-care system, which had been tested at the Yale New Haven Hospital Clinical Virology Laboratory (New Haven, CT, USA). Patients who tested negative for a panel of respiratory viruses using multiplex PCR during Jan 23-29, 2017, or March 3-14, 2020, were included. We performed host and pathogen RNA sequencing (RNA-Seq) and analysis for viral reads on samples with CXCL10 higher than 1 ng/mL or CXCL10 testing and quantitative RT-PCR (RT-qPCR) for SARS-CoV-2. We used RNA-Seq and cytokine profiling to compare the host response to infection in samples that were virus positive (rhinovirus, seasonal coronavirus CoV-NL63, or SARS-CoV-2) and virus negative (controls). During Jan 23-29, 2017, 359 samples were tested for ten viruses on the multiplex PCR respiratory virus panel (RVP). 251 (70%) were RVP negative. 60 (24%) of 251 samples had CXCL10 higher than 150 pg/mL and were identified for further analysis. 28 (47%) of 60 CXCL10-high samples were positive for seasonal coronaviruses. 223 (89%) of 251 samples were PCR negative for 15 viruses and, of these, CXCL10-based screening identified 32 (13%) samples for further analysis. Of these 32 samples, eight (25%) with CXCL10 concentrations higher than 1 ng/mL and sufficient RNA were selected for RNA-Seq. Microbial RNA analysis showed the presence of influenza C virus in one sample and revealed RNA reads from bacterial pathobionts in four (50%) of eight samples. Between March 3 and March 14, 2020, 375 (59%) of 641 samples tested negative for 15 viruses on the RVP. 32 (9%) of 375 samples had CXCL10 concentrations ranging from 100 pg/mL to 1000 pg/mL and four of those were positive for SARS-CoV-2. CXCL10 elevation was statistically significant, and a distinguishing feature was found in 28 (8%) of 375 SARS-CoV-2-negative samples versus all four SARS-CoV-2-positive samples (p=4·4 × 10-5). Transcriptomic signatures showed an interferon response in virus-positive samples and an additional neutrophil-high hyperinflammatory signature in samples with high amounts of bacterial pathobionts. The CXCL10 cutoff for detecting a virus was 166·5 pg/mL for optimal sensitivity and 1091·0 pg/mL for specificity using a clinic-ready automated microfluidics-based immunoassay. These results confirm CXCL10 as a robust nasopharyngeal biomarker of viral respiratory infection and support host response-based screening followed by metagenomic sequencing of CXCL10-high samples as a practical approach to incorporate clinical samples into pathogen discovery and surveillance efforts. National Institutes of Health, the Hartwell Foundation, the Gruber Foundation, Fast Grants for COVID-19 research from the Mercatus Center, and the Huffman Family Donor Advised Fund.

Universal admission laboratory screening for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) asymptomatic infection across a large health system

Admission laboratory screening for asymptomatic coronavirus disease 2019 (COVID-19) has been utilized to mitigate healthcare-associated severe acute respiratory coronavirus virus 2 (SARS-CoV-2) transmission. An understanding of the impact of such testing across a variety of patient populations is needed. SARS-CoV-2 nucleic acid amplification admission testing results for all asymptomatic patients across 4 distinct inpatient facilities between April 20, 2020, and June 14, 2021, were analyzed. Positivity rates and the number needed to test (NNT) to identify 1 asymptomatic infected patient were calculated. Admission results were compared to COVID-19 community incidence rates for the system's surrounding metropolitan service area. Using a national survey of hospital epidemiologists, a clinically meaningful NNT of 1:100 was identified. In total, 51,187 tests were collected (positivity rate, 1.8%). During periods of high transmission, the NNT met the clinically relevant threshold in all populations. The NNT approached or met the threshold for most locations during periods of lower transmission. For all transmission levels, the NNT for fully vaccinated patients did not meet the threshold. Implementing an asymptomatic patient admission testing program can provide clinically relevant data based on the NNT, even during periods of lower transmission and among different patient populations. Limiting admission testing to non-fully vaccinated patients during periods of lower transmission may be a strategy to address resource concerns around this practice. Although the impact of such testing on healthcare-associated COVID-19 among patients and healthcare workers could not be clearly determined, these data provide important information as facilities weigh the costs and benefits of such testing.