Viral Shedding Rate Research Articles

Kinetics of Viral Shedding for Outbreak Surveillance of Emerging Infectious Diseases: Modeling Approach to SARS-CoV-2 Alpha and Omicron Infection.

Previous studies have highlighted the importance of viral shedding using cycle threshold (Ct) values obtained via reverse transcription polymerase chain reaction to understand the epidemic trajectories of SARS-CoV-2 infections. However, it is rare to elucidate the transition kinetics of Ct values from the asymptomatic or presymptomatic phase to the symptomatic phase before recovery using individual repeated Ct values. This study proposes a novel Ct-enshrined compartment model to provide a series of quantitative measures for delineating the full trajectories of the dynamics of viral load from infection until recovery. This Ct-enshrined compartment model was constructed by leveraging Ct-classified states within and between presymptomatic and symptomatic compartments before recovery or death among people with infections. A series of recovery indices were developed to assess the net kinetic movement of Ct-up toward and Ct-down off recovery. The model was applied to (1) a small-scale community-acquired Alpha variant outbreak under the "zero-COVID-19" policy without vaccines in May 2021 and (2) a large-scale community-acquired Omicron variant outbreak with high booster vaccination rates following the lifting of the "zero-COVID-19" policy in April 2022 in Taiwan. The model used Bayesian Markov chain Monte Carlo methods with the Metropolis-Hastings algorithm for parameter estimation. Sensitivity analyses were conducted by varying Ct cutoff values to assess the robustness of the model. The kinetic indicators revealed a marked difference in viral shedding dynamics between the Alpha and Omicron variants. The Alpha variant exhibited slower viral shedding and lower recovery rates, but the Omicron variant demonstrated swifter viral shedding and higher recovery rates. Specifically, the Alpha variant showed gradual Ct-up transitions and moderate recovery rates, yielding a presymptomatic recovery index slightly higher than 1 (1.10), whereas the Omicron variant had remarkable Ct-up transitions and significantly higher asymptomatic recovery rates, resulting in a presymptomatic recovery index much higher than 1 (152.5). Sensitivity analysis confirmed the robustness of the chosen Ct values of 18 and 25 across different recovery phases. Regarding the impact of vaccination, individuals without booster vaccination had a 19% higher presymptomatic incidence rate compared to those with booster vaccination. Breakthrough infections in boosted individuals initially showed similar Ct-up transition rates but higher rates in later stages compared to nonboosted individuals. Overall, booster vaccination improved recovery rates, particularly during the symptomatic phase, although recovery rates for persistent asymptomatic infection were similar regardless of vaccination status once the Ct level exceeded 25. The study provides new insights into dynamic Ct transitions, with the notable finding that Ct-up transitions toward recovery outpaced Ct-down and symptom-surfacing transitions during the presymptomatic phase. The Ct-up against Ct-down transition varies with variants and vaccination status. The proposed Ct-enshrined compartment model is useful for the surveillance of emerging infectious diseases in the future to prevent community-acquired outbreaks.

Influence of stocking density and interaction variability on disease progression of white spot syndrome virus-infected shrimp under different risk scenarios

White spot syndrome virus (WSSV), the causative agent of white spot disease (WSD), is the most significant viral pathogen affecting farmed shrimp. As the culture model for whiteleg shrimp has evolved into a higher-intensity model, the need to study the influence of stocking density on disease progression in pond culture systems has been reinforced. Therefore, we assessed WSD progression by deriving a direct correlation between seasonal disease outbreak risk, stocking density, and viral shedding rate (WSSV genome copies/L/g) using three different stocking densities: high (210 shrimp/m2), medium (140 shrimp/m2), and low (70 shrimp/m2). In Experiment 1 (three stocking densities at 25 °C) and Experiment 2 (stocking density × temperature conditions), shrimp showed relatively high cumulative mortality within the temperature range of optimal WSSV replication (23–29 °C). Notably, the mortality trend, peak viral loads, and viral shedding of WSSV-infected shrimp occurred earlier under high-density conditions, regardless of temperature. Thereafter, this study established WSD risk scenarios based on water temperature conditions and confirmed a significant difference in mortality trends between vulnerable and less vulnerable water temperature scenarios under high- and low-density conditions. The vulnerable water temperature scenario included constant (25 °C), shifting-up (20 °C to 30 °C), and shifting-down (30 °C to 20 °C) conditions, whereas the less vulnerable water temperature scenario included constant 20 °C and 30 °C conditions. Based on mortality trends, the WSD risk scenarios revealed that the times to 50 % mortality for shrimp at high, medium, and low densities were 4, 5, and 6 days post-infection (dpi) in the vulnerable water temperature scenario, and 6, 7, and 9 dpi in the less vulnerable water temperature scenario. Viral shedding variability was evaluated based on the correlation between viral loads and viral shedding rate, and linear regression analysis revealed a significant positive correlation between viral shedding rates and viral loads in shrimp, regardless of WSD risk scenarios or stocking density conditions. Notably, a relatively enhanced viral shedding rate was observed at higher stocking densities (from low- to high-density conditions) and under vulnerable water temperature scenarios. This study suggests that increased stocking density and vulnerable water temperature scenarios could induce greater interactions among WSSV-infected shrimp. It also confirmed the potential role of risk scenarios, stocking density, and viral shedding in WSD progression, providing insights into the disease outbreak mechanisms on shrimp farms.

Effect of SARS-CoV-2 shedding rate distribution of individuals during their disease days on the estimation of the number of infected people. Application of wastewater-based epidemiology to the city of Thessaloniki, Greece

During the COVID-19 pandemic, wastewater-based epidemiology has proved to be an important tool for monitoring the spread of a disease in a population. Indeed, wastewater surveillance was successfully used as a complementary approach to support public health monitoring schemes and decision-making policies. An essential feature for the estimation of a disease transmission using wastewater data is the distribution of viral shedding rate of individuals in their personal human wastes as a function of the days of their infection. Several candidate shapes for this function have been proposed in literature for SARS-CoV-2. The purpose of the present work is to explore the proposed function shapes and examine their significance on analyzing wastewater SARS-CoV-2 shedding rate data. For this purpose, a simple model is employed applying to medical surveillance and wastewater data of the city of Thessaloniki during a period of Omicron variant domination in 2022. The distribution shapes are normalized with respect to the total virus shedding and then their basic features are investigated. Detailed analysis reveals that the main parameter determining the results of the model is the difference between the day of maximum shedding rate and the day of infection reporting. Since the latter is not part of the distribution shape, the major feature of the distribution affecting the estimation of the number of infected people is the day of maximum shedding rate with respect to the initial infection day. On the contrary, the duration of shedding (total number of disease days) as well as the exact shape of the distribution are by far less important. The incorporation of such wastewater surveillance models in conventional epidemiological models - based on recorded disease transmission data- may improve predictions for disease spread during outbreaks.

The Use of Wastewater Surveillance to Estimate SARS-CoV-2 Fecal Viral Shedding Pattern and Identify Time Periods with Intensified Transmission.

Wastewater-based surveillance is an important tool for monitoring the COVID-19 pandemic. However, it remains challenging to translate wastewater SARS-CoV-2 viral load to infection number, due to unclear shedding patterns in wastewater and potential differences between variants. We utilized comprehensive wastewater surveillance data and estimates of infection prevalence (i.e., the source of the viral shedding) available for New York City (NYC) to characterize SARS-CoV-2 fecal shedding pattern over multiple COVID-19 waves. We collected SARS-CoV-2 viral wastewater measurements in NYC during August 31, 2020 - August 29, 2023 ( N = 3794 samples). Combining with estimates of infection prevalence (number of infectious individuals including those not detected as cases), we estimated the time-lag, duration, and per-infection fecal shedding rate for the ancestral/Iota, Delta, and Omicron variants, separately. We also developed a procedure to identify occasions with intensified transmission. Models suggested fecal viral shedding likely starts around the same time as and lasts slightly longer than respiratory tract shedding. Estimated fecal viral shedding rate was highest during the ancestral/Iota variant wave, at 1.44 (95% CI: 1.35 - 1.53) billion RNA copies in wastewater per day per infection (measured by RT-qPCR), and decreased by ∼20% and 50-60% during the Delta wave and Omicron period, respectively. We identified around 200 occasions during which the wastewater SARS-CoV-2 viral load exceeded the expected level in any of 14 sewersheds. These anomalies disproportionally occurred during late January, late April - early May, early August, and from late-November to late-December, with frequencies exceeding the expectation assuming random occurrence ( P < 0.05; bootstrapping test). These estimates may be useful in understanding changes in underlying infection rate and help quantify changes in COVID-19 transmission and severity over time. We have also demonstrated that wastewater surveillance data can support the identification of time periods with potentially intensified transmission.

Viral genomic variation and the severity of genital HSV-2 infection as quantified by shedding rate: a viral genome-wide association study.

The clinical severity of genital HSV-2 infection varies widely among infected persons with some experiencing frequent genital lesions while others are asymptomatic. The viral genital shedding rate is closely associated with and has been established as a surrogate marker of clinical severity. To assess the relationship between viral genetics and shedding, we assembled a set of 145 persons who had the severity of their genital herpes quantified through determination of their HSV genital shedding rate. An HSV-2 sample from each person was sequenced and biallelic variants among these genomes were identified. We found no association between metrics of genome-wide variation in HSV-2 and shedding rate. A viral genome-wide association study (vGWAS) identified the minor alleles of three individual unlinked variants as significantly associated with higher shedding rate (p<8.4x10-5): C44973T (A512T), a non-synonymous variant in UL22 (glycoprotein H); A74534G, a synonymous variant in UL36 (large tegument protein); and T119283C, an intergenic variant. We also found an association between the total number of minor alleles for the significant variants and shedding rate (p=6.6x10-7). These results add to a growing body of literature for HSV suggesting a connection between viral genetic variation and clinically important phenotypes of infection.

Investigation of the presence of the virus in the urine and fecal samples of COVID-19 diagnosed and suspected patients by RT-PCR method: A different perspective on fecal-oral transmission theory

With the sudden COVID-19 outbreak in 2019 which has taken over the whole world, drastic changes have taken place on a global level from the understanding of hygiene to living conditions. Although the disease is often detected using respiratory tract samples with PCR tests, many publications state that the virus can also be traced in various body wastes. In our study, we aimed to determine the frequency of the virus in 50 urine and 50 stool samples and to reveal the relationship between the patients' stool PCR results according to Computed tomography (CT), biochemical tests, and the positivity of respiratory PCR test with microbiological samples. The presence of SARS-CoV2 RNA in the urine and stool samples of the patients was detected by qRT-PCR methods. Shapiro-Wilk normality test was applied to the CT, respiratory tract PCR and biochemistry results of the patients. As shown by the results, while none of the 50 patients had positive urine samples, we detected COVID-19 viral shedding in the stool specimens of 15 patients. Respiratory PCR test was negative in 4 of the stool-positive patients. No significant correlation was found between CT results and the biochemistry results of 15 patients with positive stools. In our study, the rate of viral shedding in feces was found to be 30%, which we think may be a finding to demonstrate how the pandemic rapidly progresses in cities due to the viability of the virus outside the body.

Genetic Characterization and Pathogenesis of H5N1 High Pathogenicity Avian Influenza Virus Isolated in South Korea during 2021-2022.

High pathogenicity avian influenza (HPAI) viruses of clade 2.3.4.4 H5Nx have been circulating in poultry and wild birds worldwide since 2014. In South Korea, after the first clade 2.3.4.4b H5N1 HPAI viruses were isolated from wild birds in October 2021, additional HPAIV outbreaks occurred in poultry farms until April 2022. In this study, we genetically characterized clade 2.3.4.4b H5N1 HPAIV isolates in 2021-2022 and examined the pathogenicity and transmissibility of A/mandarin duck/Korea/WA585/2021 (H5N1) (WA585/21) in chickens and ducks. Clade 2.3.4.4b H5N1 HPAI viruses caused 47 outbreaks in poultry farms and were also detected in multiple wild birds. Phylogenetic analysis of HA and NA genes indicated that Korean H5N1 HPAI isolates were closely related to Eurasian viruses isolated in 2021-2022. Four distinct genotypes of H5N1 HPAI viruses were identified in poultry, and the majority were also found in wild birds. WA585/21 inoculated chickens showed virulent pathogenicity with high mortality and transmission. Meanwhile, ducks infected with the virus showed no mortality but exhibited high rates of transmission and longer viral shedding than chickens, suggesting that they may play an important role as silent carriers. In conclusion, consideration of both genetic and pathogenic traits of H5N1 HPAI viruses is required for effective viral control.

Evaluation of the Horizontal Transmission of White Spot Syndrome Virus for Whiteleg Shrimp (Litopenaeus vannamei) Based on the Disease Severity Grade and Viral Shedding Rate.

White spot syndrome virus (WSSV) is the most problematic pathogen in crustaceans. In this study, we investigated the horizontal transmission model of WSSV based on the correlation between the disease severity grade and viral shedding rate and determined the minimum infective dose of WSSV via the waterborne route. Intramuscular injection challenges at different doses and water temperatures revealed that the thresholds of viral shedding and mortality were G1 (3.1 × 103 copies/mg) and G2 (8.5 × 104 copies/mg), respectively. Furthermore, a positive linear correlation was observed between viral copies of pleopods and viral shedding rate (y = 0.7076x + 1.414; p < 0.001). Minimum infective doses of WSSV were determined via an immersion challenge. Infection was observed within 1, 3, and 7 d in 105-, 103-, and 101 copies/mL of seawater, respectively. In the cohabitation challenge, infection was observed within six days with viral loads of 101 to 102 copies/mL of seawater, which further increased in the recipient group. Our results indicate a positive correlation between disease severity grade and viral shedding rate of infected shrimp and suggest that the waterborne transmission of WSSV depends on the viral load and exposure period.

In vitro and in vivo evaluation of the antiviral activity of arctigenin, ribavirin, and ivermectin against viral hemorrhagic septicemia virus infection

Viral hemorrhagic septicemia virus (VHSV) causes a severe and often lethal infection in olive flounder (Paralichthys olivaceus) in Korea, resulting in mass mortality and substantial economic loss. As a potential prevention strategy for infectious viral diseases, this study aimed to evaluate the antiviral activity of three compounds (arctigenin [ARG], ribavirin [RBV], and ivermectin [IVM]) against VHSV infection in vitro and in vivo. In epithelioma papulosum cyprini cells, the expression of both VHSV glycoprotein (G) and nucleoprotein (N) genes were significantly suppressed by the three compounds in a dose-dependent manner (P < 0.05). Also, cell morphology and viability were maintained at the following concentrations: ARG 1.5 mg/L, RBV 2.5 mg/L, and IVM 10 mg/L. The fish that were treated with RBV (8.33 mg/kg) and IVM (0.25 mg/kg) before VHSV infection and those treated with IVM (0.25 mg/kg) after VHSV infection showed significant improvements in the survival rate, a reduction in the viral shedding rate, and downregulation of viral gene expression compared to those seen in fish with naïve VHSV infections. Furthermore, among the innate immune genes studied, persistent expression of Mx and upregulation of tumor necrosis factor-α gene expression in VHSV-infected fish treated with RBV and IVM revealed that these compounds might induce an immunostimulatory effect as one of their antiviral activities. Overall, this study supports the use of RBV and IVM as antiviral agents to control VHSV infections in olive flounder.

Exhaled Breath Aerosol Shedding of Highly Transmissible Versus Prior Severe Acute Respiratory Syndrome Coronavirus 2 Variants.

Aerosol inhalation is recognized as the dominant mode of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Three highly transmissible lineages evolved during the pandemic. One hypothesis to explain increased transmissibility is that natural selection favors variants with higher rates of viral aerosol shedding. However, the extent of aerosol shedding of successive SARS-CoV-2 variants is unknown. We aimed to measure the infectivity and rate of SARS-CoV-2 shedding into exhaled breath aerosol (EBA) by individuals during the Delta and Omicron waves and compared those rates with those of prior SARS-CoV-2 variants from our previously published work. Individuals with coronavirus disease 2019 (COVID-19) (n = 93; 32 vaccinated and 20 boosted) were recruited to give samples, including 30-minute breath samples into a Gesundheit-II EBA sampler. Samples were quantified for viral RNA using reverse-transcription polymerase chain reaction and cultured for virus. Alpha (n = 4), Delta (n = 3), and Omicron (n = 29) cases shed significantly more viral RNA copies into EBAs than cases infected with ancestral strains and variants not associated with increased transmissibility (n = 57). All Delta and Omicron cases were fully vaccinated and most Omicron cases were boosted. We cultured virus from the EBA of 1 boosted and 3 fully vaccinated cases. Alpha, Delta, and Omicron independently evolved high viral aerosol shedding phenotypes, demonstrating convergent evolution. Vaccinated and boosted cases can shed infectious SARS-CoV-2 via EBA. These findings support a dominant role of infectious aerosols in transmission of SARS-CoV-2. Monitoring aerosol shedding from new variants and emerging pathogens can be an important component of future threat assessments and guide interventions to prevent transmission.

MO672: Covid-19 in Patients on Peritoneal Dialysis: A Case-Series

BACKGROUND AND AIMSA great amount of information has been divulged on the epidemiology and outcome of coronavirus disease 2019 (COVID-19) in patients with ESRD. The majority of the studies have been conducted in patients on maintenance hemodialysis (HD) and kidney transplant recipients. Unfortunately, few studies focused on the outcome of peritoneal dialysis (PD) patients. Information regarding this subset of the population has been extrapolated from aggregated data including a higher percentage of HD patients. As a result, the impact of COVID-19 is indefinite in patients receiving PD. We conducted a study to better understand how patients on PD have been affected by COVID-19.METHODWe conducted a single-center retrospective analysis of 141 PD patients followed at the University Hospital of Modena, Italy from 1 March 2020 to 31 December 2021. The diagnosis of COVID-19 was performed through nasopharyngeal swab RT–PCR testing. Duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding measured the time elapsed from diagnosis of COVID-19 to one or two (if available) negative nasopharyngeal PCR tests. Median and interquartile range or mean and standard deviation were used for continuous variables and percentage for categorical variables. A P-value <0.05 was considered statistically significant.RESULTSDuring the pandemic, 18 out of 141 (12.7%) patients receiving PD dialysis contracted COVID-19. Median age was 60 (50.2–66.5) years with a predominance of males (72.2%)The percentage of patients on APD accounted for 33.3%.The infection was symptomatic in out of 18 (94.4%) patients. Fever (94.4%) and cough (55.6%) were the most common symptoms. Viral shedding, traced with nasopharyngeal swabs lasted 26 (14.5–3.5) days. Two patients were inactive on the waiting list for kidney transplantation for a mean of 43 ± 1.4 days.COVID-19 caused hospital admission of seven (38.9%) patients. During hospitalization two (11.1%) patients switched from PD to HD for ultrafiltration failure and inadequate solute clearance and two (11.1%) died for septic shock with multiorgan failure. In our cohort of patients, excess death due to COVID-19 was 22.2%.Half of the patients contracted the infection before the availability of SARS-CoV-2 vaccine. There were no statistically significant differences between vaccinated and unvaccinated patients in terms of symptoms, viral shedding and hospital admission or (Table 1). We underline that COVID-19 was fatal only in two unvaccinated patients.Table 1.Demographic and clinical characteristics of patients on PD with COVID-19VariablesAllpatientsUnvaccinated patientsVaccinated patientsP-value(n. 18)(n. 9)(n. 9)Age, years60 (50.2–66.5)54 (52–65)62 (39–73)0.96Male, n. (%)13 (72.2)8 (88.8)5 (55.5)0.29Dialysis vintage, years0.9 (0.7–2.4)1.2 (0.5–2.9)0.94 (0.7–2)0.85CAPD, n. (%)6 (33.3)2 (33.3)4 (44.4)0.6Immunosuppressive therapy6 (33.3)1 (16.7)5 (55.5)0.13Etiology of ESRD0.59 Hypertensive nephropathy6 (33.3)4 (44.4)2 (22.2) Diabetic nephropathy3 (16.7)2 (22.2)1 (11.1) IgA nephropathy2 (11.1)1 (11.1)1 (11.1) Lupus nephritis2 (11.1)0 (0)2 (22.2) Others5 (27.8)2 (22.2)3 (33.3)Comorbidities Diabetes6 (33.3)3 (33.3)3 (33.3)1 CVD7 (38.9)4 (44.4)3 (33.3)1 Obesity5 (27.8)2 (22.2)3 (33.3)1 Cancer3 (16.7)2 (22.2)1 (11.1)1Symptoms Cough10 (55.6)7 (77.7)3 (33.3)0.15 Fever17(94.4)9 (100)8 (88.8)1 Dyspnea6 (33.3)3 (33.3)3 (33.3)1Asymptomatic, n. (%)1 (5.6)0 (0)1 (11.1)1Viral shedding, day26 (14.5–33.5)26 (15–35)27.5 (11.5–33)0.51Switch to HD2 (11.1)1 (11.1)1 (11.1)1Hospitalization, n. (%)7 (38.9)3 (33.3)4 (44.4)1Death, n. (%)2 (11.1)2 (22.2)0 (0)0.47CONCLUSIONThis study reports the monocentric experience of a large PD center during the COVID-19 pandemic. COVID-19 was symptomatic in the majority of patients and led to hospitalization of about 40% of the patients. The rate of symptoms, viral shedding and hospital admission was similar between vaccinated and unvaccinated patients. Two unvaccinated patients died for the severe consequence of COVID-19.

11 NEWLY-DIAGNOSED HYPERTENSION DURING ADMISSION FOR COVID-19 CARE AND ITS SUBSEQUENT EFFECT ON OUTCOME OF TREATMENT: A PROSPECTIVE COHORT STUDY

Background: Recent evidences shown that majority of hypertension case in Indonesia were unrecognized, undiagnosed, and left untreated. Hypertension is among the most prevalent comorbidity of COVID-19 infection and being associated with poor outcome following standard treatment. This study aimed to describe newly-diagnosed hypertension among COVID-19 subject and its outcome following treatment Material &amp; Methods: This cohort study enroll subject admitted to Gelora Joko Samudro Centre for COVID-19 Care, confirmed by Nucleic Acid Amplification Test (NAAT) for COVID-19, with no or mild symptom. Newly-diagnosed hypertension was confirmed by manual blood pressure examination as required by JNC VII criteria for hypertension, without previous history of hypertension. Non-hypertensive COVID-19 subject was enrolled as paired control group. Results: Among 62 subjects admitted with hypertension as presenting comorbidities, 20 subjects (32.26%) were newly-diagnosed. They were predominantly male, with average age of 47.2±9.65 years old. Newly-diagnosed hypertension group has significant longer day of admission (p 0.001) compared to the control group (Mean difference 5.5 95%CI 2.48-8.41). Newly-diagnosed hypertension group also has significant duration of viral shedding (p&lt;0.001) compared to the control group (Mean difference 6.6 95%CI 3.68-9.52). At the end of treatment the newly-diagnosed hypertension group has significant reduced proportion of subject achieving negative conversion (p 0.002) compared to the control group (HR 0.3, 95%CI 0.12-0.63). Conclusion: Newly-diagnosed hypertension were quite prevalent in COVID-19 care, and had been associated with longer day of admission, longer duration of viral shedding and lower rate of negative conversion at the end of treatment compared with control group.

Immunogenetic determinants of HSV-2 infection and disease

Abstract Herpes simplex virus-2 (HSV-2) is one of the most prevalent sexually transmitted infections, and can result in life-long, chronic disease. Disease severity, frequency of reactivation, and shedding rates vary between individuals, though little is known about how host genes regulate tissue-specific immune responses. We have previously used the Collaborative Cross (CC) mouse model system, which incorporates the extent of genetic variation found in the human genome, to better model the diversity of outcomes found in human viral infections, so we next probed the CC to identify host genetic regions that regulate viral shedding and disease following HSV-2 infection, as well as tissue-specific immune responses. We performed a screen of mice from different CC strains to assess viral titers and disease following vaginal HSV-2 infection, and then used this data to perform quantitative trait loci (QTL) mapping to identify chromosomal regions linked to vaginal viral shedding rates and levels, as well as virus-associated clinical disease. In parallel experiments, we assessed lymphoid, nervous system, and mucosal immune cell frequencies at innate, adaptive, and memory response timepoints. We observed a distinctive suppressive signature on vaginal Tregs compared to lymph node Tregs, at various times following HSV-2 infection. Additionally, these suppressive responses varied in mice with either higher viral titers, or more tissue inflammation, highlighting the interplay between host immune response and viral infection kinetics. Understanding host factors that contribute to HSV shedding, clinical disease, and immune responses may provide critical insights for developing new preventive strategies or interventions to HSV-2 infection. Supported by grant R21 AI152559-01 from the NIH

SARS-COV-2 viral load in tears of patients with COVID-19 in the early symptomatic stages: comparison of two different tear sampling methods.

PurposeTo evaluate the presence of SARS-CoV-2 virus in tears of patients with COVID-19 in the early symptomatic stages and to compare two different sampling methods.Materials and methodIn this cross-sectional study, tears sampling was performed in COVID-19 patients admitted within the first 7 days of symptom onset. The samples were collected with both conjunctival swabs and Schirmer strips. Each specimen was analyzed via RT-PCR. The viral load was evaluated in terms of the cycle threshold value. Ocular and systemic symptoms and comorbidities of the patients were also recorded.ResultsForty patients were included. The average time from the initiation of symptoms was 3.15 days. Unilateral conjunctivitis has been observed in 5% of patients and foreign body sensation in 7.5% of patients. No viral RNA was detected in the tear samples of the patients with ocular findings. The positivity rate for SARS-CoV-2 in tears was 2.5% (n = 1). None of the samples collected by Schirmer test strips yielded positive polymerase chain reaction result for SARS-COV-2. The Ct value of the positive conjunctival swab was 36.03 and the nasopharyngeal Ct value of the same patient was 25.68.ConclusionThe SARS-CoV-2 viral shedding rate has been determined as 2.5% in the tears of early symptomatic stage COVID-19 patients. The viral load of the tears was lower than the naso-oropharynx. The conjunctival swab method is recommended in tear collection to evaluate the presence of SARS-CoV-2 by RT-PCR analysis in low viral load tears.

Saliva is superior over nasopharyngeal swab for detecting SARS-CoV2 in COVID-19 patients

Scaling up of diagnostic capacity is needed to mitigate the global pandemic of SARS-CoV2. However, there are challenges including shortage of sample collection swabs and transport medium. Saliva has been recommended as a simple, low-cost, non-invasive option. However, data from different populations and settings are limited. Here, we showed that saliva could be a good alternative sample to diagnose COVID-19 patients. Pair of NPS-saliva samples was collected from 152 symptomatic; confirmed COVID-19 patients, and compared their positivity rate, viral load, and duration of viral shedding. From 152 patients, 80 (52.63%) tested positive and 72 (47.37%) were negative for SARSA-CoV2 in NPS sample. In saliva, 129 (92.14%) were tested positive and 11 (7.86%) were negative on the day of admission to hospital. The overall percent agreement of RT-PCR result of Saliva to NPS was 70% (196/280). A comparison of viral load from 72 NPS-saliva pair samples on day of admission shows saliva contains significantly higher viral load (P < 0.001). In conclusion, saliva has higher yield in detecting SARS-CoV2, and COVID-19 patients show higher viral load and prolonged period of viral shedding in saliva. Therefore, we recommend saliva as a better alternative sample to NPS to diagnose COVID-19 patients.

Enumerating asymptomatic COVID-19 cases and estimating SARS-CoV-2 fecal shedding rates via wastewater-based epidemiology

Wastewater-based epidemiology (WBE) was utilized to monitor SARS-CoV-2 RNA in sewage collected from manholes specific to individual student dormitories (dorms) at the University of Arizona in the fall semester of 2020, which led to successful identification and reduction of SARS-CoV-2 transmission events. Positive wastewater samples triggered clinical testing of residents within that dorm; thus, SARS-CoV-2 infected individuals were identified regardless of symptom expression. This current study examined clinical testing data to determine the abundance of asymptomatic versus symptomatic cases in these defined communities. Nasal and nasopharyngeal swab samples processed via antigen and PCR tests indicated that 79.2% of SARS-CoV-2 infections were asymptomatic, and only 20.8% of positive cases reported COVID-19 symptoms at the time of testing. Clinical data was paired with corresponding wastewater virus concentrations, which enabled calculation of viral shedding rates in feces per infected person. Mean shedding rates averaged from positive wastewater samples across all dorms were 7.30 ± 0.67 log10 genome copies per gram of feces (gc/g-feces) based on the N1 gene. Quantification of SARS-CoV-2 fecal shedding rates from infected individuals has been the critical missing component necessary for WBE models to measure and predict SARS-CoV-2 infection prevalence in communities. The findings from this study can be utilized to create models that can be used to inform public health prevention and response actions.

Estimation of foot-and-mouth disease windborne transmission risk from USA beef feedlots

Windborne spread of foot-and-mouth disease (FMD) requires specific epidemiological and meteorological conditions, thus modeling the risk of windborne spread involves integrating epidemiological and meteorological models. The objective of this study was to investigate the potential risk of windborne spread of FMD from an infected US feedlot using an integrated modeling approach, and to identify factors that determine this risk.To address this objective, we integrated a within-herd epidemiological model and an advanced atmospheric dispersion model, and calculated infection risk dependent on exposed herd size. A previously developed epidemiological model was used to simulate the spread of FMD through a typical U.S. feedlot, while the National Oceanic and Atmospheric Administration’s (NOAA) HYSPLIT atmospheric dispersion model, which has been validated for FMD modeling, was used to model virus dispersion. Infection risk for exposed herds was calculated as a binomial probability accounting for dose and exposed herd size. We modeled risk of windborne spread from a typical 4000 head feedlot in the U.S. state of Iowa (IA), and a typical 48,000 head feedlot in the U.S. state of Kansas (KS) during winter and summer seasons.The risk of windborne spread of FMD varied based on weather/season conditions, estimated average viral shedding rate per head, size of infected herd, and size of exposed herd. In the baseline Kansas scenario (KS/103/W), the median of the maximum daily risk of infecting a 1000-head exposed herd ranged from 58.16 % at 1 km to 0.78 % at 10 km (Table 4). In the baseline Iowa scenario (IA/103/W), the median of the maximum daily risk of infecting a 1000-head exposed herd ranged from 21.78 % at 1 km to 0.05 % at 10 km (Table 4).The minimum control area recommended by the United States Department of Agriculture (USDA) in an FMD outbreak is 10 km from the infected premise. Our results indicate that significant risk of windborne spread may extend beyond 10 km in certain situations. This is particularly a concern in areas where there are large feedlots in relatively close proximity, such as in southwestern Kansas. Our model may be useful as a research tool in the absence of an outbreak and may help direct surveillance and response efforts in the event of an outbreak.

Protective Efficacy Evaluation of Four Inactivated Commercial Vaccines Against Low Pathogenic Avian Influenza H9N2 Virus Under Experimental Conditions in Broiler Chickens.

Avian influenza vaccines are commonly used in the poultry industry. The objective of this study was to compare, under experimental conditions, the protective efficacy of four imported commercial inactivated H9N2 vaccines (A, B, C, and D) in broiler chickens. A total of 150 one-day-old chicks were divided into six groups: four experimental groups, each containing 30 chicks, received one of the vaccines (A, B, C, or D) delivered in a 0.3-ml dose subcutaneously at 1 day of age, whereas the control, Group T, was not vaccinated but challenged and Group E was kept unvaccinated and unchallenged. At 21 days postvaccination, Groups A, B, C, D, and T were challenged with 107 embryo infective dose 50% of A/Chicken/Morocco/01/2016 (H9N2). All chicks were observed daily for clinical signs during the 12 days postchallenge (dpc). At 5 and 12 dpc, chicks were euthanatized for necropsy examination. Blood samples were collected weekly for serologic analysis and oropharyngeal swabs were collected for virus detection by real-time RT-PCR. Respiratory signs started at 48 hr pc and maximum severity was observed on 9 dpc. Chiefly, the birds vaccinated with vaccine B showed significantly more respiratory signs than did their counterparts. Serologic analysis revealed that the sera of Groups A and D birds showed a decrease in antibody (Ab) levels up to day 26; then a slight increase of Ab level was observed until day 31, while Group B and C birds showed a stabilization of the titers from day 21 until the end of the experiment. The viral shedding rate was significantly lower in Groups C and A (40%-50% of the birds shed virus for <7 days) compared with other challenged groups (60%-75% of the birds shed virus for ≥9 days). This experiment illustrated that vaccination applied on the first day in the hatchery with the four vaccines tested did not provide an acceptable protection against H9N2 in comparison with the controls that did not receive any vaccine. However, at first glance, we might favor vaccines A and C for their ability to reduce and shorten viral shedding as compared with vaccines B and D.

Coronavirus disease 2019 severity in obesity: Metabolic dysfunction-associated fatty liver disease in the spotlight.

The coronavirus disease 2019 (COVID-19) outbreak has drawn the scientific community's attention to pre-existing metabolic conditions that could aggravate the infection, causing extended viral shedding, prolonged hospitalization, and high death rates. Metabolic dysfunction-associated fatty liver disease (MAFLD) emerges as a surrogate for COVID-19 severity due to the constellation of metabolic alterations it entails. This review outlines the impact MAFLD exerts on COVID-19 severity in obese subjects, besides the possible mechanistic links to the poor outcomes. The data collected showed that MAFLD patients had poorer COVID-19 outcomes than non-MAFLD obese subjects. MAFLD is generally accompanied by impaired glycemic control and systemic arterial hypertension, both of which can decompensate during the COVID-19 clinical course. Also, MAFLD subjects had higher plasma inflammatory marker concentrations than non-MAFLD subjects, which might be related to an intensified cytokine storm syndrome frequently associated with the need for mechanical ventilation and death. In conclusion, MAFLD represents a higher risk than obesity for COVID-19 severity, resulting in poor outcomes and even progression to non-alcoholic steatohepatitis. Hepatologists should include MAFLD subjects in the high-risk group, intensify preventive measurements, and prioritize their vaccination.

578 Urine cytomegalovirus shedding among seropositive pregnant women

Globally, the majority of congenital cytomegalovirus(CMV) infection is thought to occur following maternal re-infection or re-activation. We seek to characterize the rates of viral shedding during pregnancy among HIV-negative, CMV-seropositive women. Prospective cohort study of CMV-seropositive women throughout gestation at one tertiary care hospital between 9/1/2018 and 9/1/2020. Subjects eligible if positive for CMV Immunoglobulin G(IgG) during early pregnancy screening. Subjects excluded for HIV positivity. Urine samples collected at three timepoints during pregnancy. Using Immediate early 1 (IE-1) gene as indicative of the presence of CMV, DNA isolated and quantified from samples for viral load(VL) calculation: No VL detected, VL 1-2000 copies/mL (low-shedders), VL >2000 copies/mL (high-shedders). Of the 244 subjects enrolled, 54% were White, mean (standard deviation) age was 31 (5.5) years, and 61% had children living at home. More than a third also worked in healthcare or had a household member who worked in healthcare(Table 1). Of 583 urine samples tested, 307 (52.7%) had no virus detected, and 276 (47.3%) qualitatively showed evidence of CMV. Of positive samples, 252 (91.3%) were low-shedders, and 24 (8.7%) were high-shedders. The distribution was relatively evenly spread across trimesters, including delivery samples(Figure 1). Approximately half of urine samples from known CMV-seropositive women in our cohort had evidence of viral shedding, and occurred in all trimesters. Further study is needed to better understand risk factors associated with viral shedding and the clinical implications of shedding in seropositive women.View Large Image Figure ViewerDownload Hi-res image Download (PPT)