Ultrastructural analysis of nasopharyngeal epithelial cells from patients with SARS-CoV-2 infection

The nasal epithelium is an initial site for SARS-CoV-2 infection, responsible for the ongoing COVID-19 pandemic. However, the pathogenicity and morphological impact of SARS-CoV-2 on the nasopharynx cells from symptomatic patients with different viral loads remain poorly understood. Here, we investigated the ultrastructure of nasal cells obtained from individuals at distinct disease days and with high and low SARS-CoV-2 loads. Squamous and ciliated cells were the main cells observed in SARS-CoV-2 negative samples. We identified virus-like particles (VLPs) and replication organelles (RO)-like structures in the squamous cells from high viral load samples after 3- and 4-days of symptoms. Ultrastructural changes were found in those cells, such as the loss of microvilli and primary cilium, the increase of multivesicular bodies and autophagosomes, and signs of cell death. No ciliated cells were found in those samples. Squamous cells from low viral load sample after 5 days of symptoms showed few microvilli and no primary cilium. VLPs and RO-like structures were found in the ciliated cells only. No ultrastructural alterations were seen in the cells from low viral load individuals after 10- and 14-days of symptoms. Our results shed light on the ultrastructural effects of SARS-CoV-2 infection on the human nasopharyngeal cells.

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Performance of the Innova SARS-CoV-2 antigen rapid lateral flow test in the Liverpool asymptomatic testing pilot: population based cohort study

BMJ ◽

10.1136/bmj.n1637 ◽

2021 ◽

pp. n1637 ◽

Cited By ~ 1

Author(s):

Marta García-Fiñana ◽

David M Hughes ◽

Christopher P Cheyne ◽

Girvan Burnside ◽

Mark Stockbridge ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Viral Load ◽

Predictive Value ◽

High Viral Load ◽

Test Results ◽

Chain Reaction ◽

Viral Loads ◽

Flow Test ◽

Polymerase Chain ◽

Lateral Flow Test

Abstract Objective To assess the performance of the SARS-CoV-2 antigen rapid lateral flow test (LFT) versus polymerase chain reaction testing in the asymptomatic general population attending testing centres. Design Observational cohort study. Setting Community LFT pilot at covid-19 testing sites in Liverpool, UK. Participants 5869 asymptomatic adults (≥18 years) voluntarily attending one of 48 testing sites during 6-29 November 2020. Interventions Participants were tested using both an Innova LFT and a quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) test based on supervised self-administered swabbing at testing sites. Main outcome measures Sensitivity, specificity, and predictive values of LFT compared with RT-qPCR in an epidemic steady state of covid-19 among adults with no classic symptoms of the disease. Results Of 5869 test results, 22 (0.4%) LFT results and 343 (5.8%) RT-qPCR results were void (that is, when the control line fails to appear within 30 minutes). Excluding the void results, the LFT versus RT-qPCR showed a sensitivity of 40.0% (95% confidence interval 28.5% to 52.4%; 28/70), specificity of 99.9% (99.8% to 99.99%; 5431/5434), positive predictive value of 90.3% (74.2% to 98.0%; 28/31), and negative predictive value of 99.2% (99.0% to 99.4%; 5431/5473). When the void samples were assumed to be negative, a sensitivity was observed for LFT of 37.8% (26.8% to 49.9%; 28/74), specificity of 99.6% (99.4% to 99.8%; 5431/5452), positive predictive value of 84.8% (68.1% to 94.9%; 28/33), and negative predictive value of 93.4% (92.7% to 94.0%; 5431/5814). The sensitivity in participants with an RT-qPCR cycle threshold (Ct) of <18.3 (approximate viral loads >10 6 RNA copies/mL) was 90.9% (58.7% to 99.8%; 10/11), a Ct of <24.4 (>10 4 RNA copies/mL) was 69.4% (51.9% to 83.7%; 25/36), and a Ct of >24.4 (<10 4 RNA copies/mL) was 9.7% (1.9% to 23.7%; 3/34). LFT is likely to detect at least three fifths and at most 998 in every 1000 people with a positive RT-qPCR test result with high viral load. Conclusions The Innova LFT can be useful for identifying infections among adults who report no symptoms of covid-19, particularly those with high viral load who are more likely to infect others. The number of asymptomatic adults with lower Ct (indicating higher viral load) missed by LFT, although small, should be considered when using single LFT in high consequence settings. Clear and accurate communication with the public about how to interpret test results is important, given the chance of missing some cases, even at high viral loads. Further research is needed to understand how infectiousness is reflected in the viral antigen shedding detected by LFT versus the viral loads approximated by RT-qPCR.

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SARS-CoV-2 Persistence in Immunocompromised Children

10.22541/au.162448803.31733691/v1 ◽

2021 ◽

Author(s):

Susan Dolan ◽

Jean Mulcahy Levy ◽

Angla Moss ◽

Kelly Pearce ◽

Samuel Dominguez ◽

...

Keyword(s):

Viral Load ◽

Median Time ◽

Immunosuppressive Treatment ◽

Viral Persistence ◽

High Viral Load ◽

Viral Loads ◽

Mild Disease ◽

Kaplan Meier ◽

Diagnostic Panel ◽

Event Times

Introduction/Objectives: We evaluated the length of time immunocompromised children (ICC) remain positive for SARS-CoV-2, identified factors associated with viral persistence and determined cycle threshold (CT) values of children with viral persistence as a surrogate of viral load. Methods: We conducted a retrospective cohort study of ICC at a pediatric hospital from March 2020-2021. Immunocompromised status was defined as primary, secondary or acquired due to medical comorbidities/immunosuppressive treatment. The primary outcome was time to first-of-two consecutive negative SARS-CoV-2 Polymerase chain reaction (PCR) tests at least 24 hours apart. Testing of sequential clinical specimens from the same subject was conducted using the Centers for Disease Control (CDC) 2019-nCoV Real-Time RT-PCR Diagnostic Panel assay. Descriptive statistics, Kaplan-Meier curve median event times and log-rank-sum tests were used to compare outcomes between groups. Results: Ninety-one children met inclusion criteria. Median age was 15.5 years (IQR 8-18 yrs), 64% were male, 58% were white, and 43% were Hispanic/Latinx. Most (67%) were tested in outpatient settings and 58% were asymptomatic. The median time to two negative tests was 42 days (IQR 25.0,55.0), with no differences in median time by illness presentation or level of immunosuppression. Seven children had >1 sample available for repeat testing, and 5/7 (71%) children had initial CT values of <30, (moderate to high viral load); 4 children had CT values of <30 3-4 weeks later, suggesting persistent moderate to high viral loads. Conclusions: Most ICC with SARS-CoV-2 infection had mild disease, with prolonged viral persistence >6 weeks and moderate to high viral load.

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Evaluation of saliva sampling procedures for SARS-CoV-2 diagnostics reveals differential sensitivity and association with viral load

10.1101/2020.10.06.20207902 ◽

2020 ◽

Author(s):

Pieter Mestdagh ◽

Michel Gillard ◽

Marc Arbyn ◽

Jean-Paul Pirnay ◽

Jeroen Poels ◽

...

Keyword(s):

Viral Load ◽

High Risk ◽

Health Professionals ◽

High Viral Load ◽

Sampling Procedure ◽

Differential Sensitivity ◽

Collection Method ◽

Viral Loads ◽

Saliva Collection ◽

Sampling Procedures

AbstractNasopharyngeal sampling has been the preferential collection method for SARS-CoV-2 diagnostics. Alternative sampling procedures that are less invasive and do not require a healthcare professional would be more preferable for patients and health professionals. Saliva collection has been proposed as such a possible alternative sampling procedure. We evaluated the sensitivity of SARS-CoV-2 testing on two different saliva collection devices (spitting versus swabbing) compared to nasopharyngeal swabs in over 2500 individuals that were either symptomatic or had high-risk contacts with infected individuals. We observed an overall poor sensitivity in saliva for SARS-CoV-2 detection (30.8% and 22.4% for spitting and swabbing, respectively). However, when focusing on individuals with medium to high viral load, sensitivity increased substantially (97.0% and 76.7% for spitting and swabbing, respectively), irrespective of symptomatic status. Our results suggest that saliva cannot readily replace nasopharyngeal sampling for SARS-CoV-2 diagnostics but may enable identification of cases with medium to high viral loads.

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High Resolution Analysis of Respiratory Syncytial Virus Infection In Vivo

Viruses ◽

10.3390/v11100926 ◽

2019 ◽

Vol 11 (10) ◽

pp. 926 ◽

Cited By ~ 4

Author(s):

Waleed Aljabr ◽

Stuart Armstrong ◽

Natasha Y. Rickett ◽

Georgios Pollakis ◽

Olivier Touzelet ◽

...

Keyword(s):

Viral Load ◽

Respiratory Syncytial Virus ◽

The Elderly ◽

High Viral Load ◽

Label Free ◽

Respiratory Problems ◽

Viral Loads ◽

High Resolution Analysis ◽

Syncytial Virus

Human respiratory syncytial virus (HRSV) is a major cause of pediatric infection and also causes disease in the elderly and those with underlying respiratory problems. There is no vaccine for HRSV and anti-viral therapeutics are not broadly applicable. To investigate the effect of HRSV biology in children, nasopharyngeal aspirates were taken from children with different viral loads and a combined high throughput RNAseq and label free quantitative proteomics approach was used to characterize the nucleic acid and proteins in these samples. HRSV proteins were identified in the nasopharyngeal aspirates from infected children, and their abundance correlated with viral load (Ct value), confirming HRSV infection. Analysis of the HRSV genome indicated that the children were infected with sub-group A virus and that minor variants in nucleotide frequency occurred in discrete clusters along the HRSV genome, and within a patient clustered distinctly within the glycoprotein gene. Data from the samples were binned into four groups; no-HRSV infection (control), high viral load (Ct < 20), medium viral load (Ct = 20–25), and low viral load (Ct > 25). Cellular proteins associated with the anti-viral response (e.g., ISG15) were identified in the nasopharyngeal aspirates and their abundance was correlated with viral load. These combined approaches have not been used before to study HRSV biology in vivo and can be readily applied to the study the variation of virus host interactions.

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Feasibility and Effectiveness Assessment of SARS-CoV-2 Antigenic Tests in Mass Screening of a Pediatric Population and Correlation with the Kinetics of Viral Loads

Viruses ◽

10.3390/v13102071 ◽

2021 ◽

Vol 13 (10) ◽

pp. 2071

Author(s):

Marcello Lanari ◽

Giovanni Battista Biserni ◽

Matteo Pavoni ◽

Eva Caterina Borgatti ◽

Marta Leone ◽

...

Keyword(s):

Viral Load ◽

Mass Screening ◽

Point Of Care ◽

Pediatric Population ◽

Late Phase ◽

High Viral Load ◽

Pediatric Emergency ◽

Nucleic Acid Amplification ◽

Baseline Sensitivity ◽

Viral Loads

The gold standard for diagnosis of SARS-CoV-2 infection has been nucleic acid amplification tests (NAAT). However, rapid antigen detection kits (Ag-RDTs), may offer advantages over NAAT in mass screening, generating results in minutes, both as laboratory-based test or point-of-care (POC) use for clinicians, at a lower cost. We assessed two different POC Ag-RDTs in mass screening versus NAAT for SARS-CoV-2 in a cohort of pediatric patients admitted to the Pediatric Emergency Unit of IRCCS—Polyclinic of Sant’Orsola, Bologna (from November 2020 to April 2021). All patients were screened with nasopharyngeal swabs for the detection of SARS-CoV-2-RNA and for antigen tests. Results were obtained from 1146 patients. The COVID-19 Ag FIA kit showed a baseline sensitivity of 53.8% (CI 35.4–71.4%), baseline specificity 99.7% (CI 98.4–100%) and overall accuracy of 80% (95% CI 0.68–0.91); the AFIAS COVID-19 Ag kit, baseline sensitivity of 86.4% (CI 75.0–93.9%), baseline specificity 98.3% (CI 97.1–99.1%) and overall accuracy of 95.3% (95% CI 0.92–0.99). In both tests, some samples showed very low viral load and negative Ag-RDT. This disagreement may reflect the positive inability of Ag-RDTs of detecting antigen in late phase of infection. Among all cases with positive molecular test and negative antigen test, none showed viral loads > 106 copies/mL. Finally, we found one false Ag-RDTs negative result (low cycle thresholds; 9 × 105 copies/mL). Our results suggest that both Ag-RDTs showed good performances in detection of high viral load samples, making it a feasible and effective tool for mass screening in actively infected children.

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The Comparison of Honeybee Viral Loads for Six Honeybee Viruses (ABPV, BQCV, CBPV, DWV, LSV3 and SBV) in Healthy and Clinically Affected Honeybees with TaqMan Quantitative Real-Time RT-PCR Assays

Viruses ◽

10.3390/v13071340 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1340

Author(s):

Laura Šimenc ◽

Tanja Knific ◽

Ivan Toplak

Keyword(s):

Viral Load ◽

Real Time ◽

Viral Infections ◽

Clinical Signs ◽

High Viral Load ◽

Deformed Wing Virus ◽

Viral Loads ◽

Additional Information ◽

Queen Cell ◽

Paralysis Virus

The viral loads of acute bee paralysis virus (ABPV), black queen cell virus (BQCV), chronic bee paralysis virus (CBPV), deformed wing virus (DWV), Lake Sinai virus 3 (LSV3), and sacbrood bee virus (SBV) were determined in samples with the use of quantitative TaqMan real-time reverse transcription and polymerase chain reaction (RT-qPCR). A total of 108 samples of healthy adult honeybees from four differently located apiaries and samples of honeybees showing different clinical signs of viral infections from 89 apiaries were collected throughout Slovenia. The aim of this study was to discover correlations between viral loads and clinical signs in adult honeybees and confirm previously set threshold viral load levels between healthy and clinically affected honeybees. Within this study, two new RT-qPCR assays for quantification of LSV3 and SBV were developed. Statistically significant differences in viral loads of positive samples were identified between healthy and clinically affected honeybees for ABPV, CBPV, DWV, and SBV, while for BQCV and LSV3, no statistical differences were observed between both groups. Despite high detected LSV3 prevalence and viral loads around 6.00 log10 viral copies/bee, this lineage probably has a limited impact on the health status of honeybee colonies. The determined viral loads between 3.94 log10 and 13.17 log10 in positive samples for six viruses, collected over 10 consecutive months, including winter, present additional information of high viral load variations in healthy honeybee colonies.

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Size and duration of COVID-19 clusters go along with a high SARS-CoV-2 viral load : a spatio-temporal investigation in Vaud state, Switzerland

10.1101/2021.02.16.21251641 ◽

2021 ◽

Author(s):

Anaïs Ladoy ◽

Onya Opota ◽

Pierre-Nicolas Carron ◽

Idris Guessous ◽

Séverine Vuilleumier ◽

...

Keyword(s):

Viral Load ◽

Relative Risk ◽

Urban Areas ◽

High Viral Load ◽

Space Time ◽

Public Health Decision ◽

Viral Loads ◽

Health Decision ◽

Spatio Temporal ◽

Number Of Individuals

AbstractTo understand the geographical and temporal spread of SARS-CoV-2 during the first wave of infection documented in the canton of Vaud, Switzerland, we analysed clusters of positive cases using the precise place of residence of 33’651 individuals tested (RT-PCR) between January 10 and June 30, 2020. We identified both space-time (SaTScan) and transmission (MST-DBSCAN) clusters; we estimated their duration, their transmission behavior (emergence, growth, reduction, etc.) and relative risk. For each cluster, we computed the within number of individuals, their median age and viral load.Among 1’684 space-time clusters identified, 457 (27.1%) were significant (p ≤ 0.05), i.e. harboring a higher relative risk of infection, as compared to other regions. They lasted a median of 11 days (IQR 7-13) and included a median of 12 individuals per cluster (IQR 5-20). The majority of significant clusters (n=260; 56.9 %) had at least one person with an extremely high viral load (above 1 billion copies/ml). Those clusters were considerably larger (median of 17 infected individuals, p < 0.001) than clusters with subjects showing a viral load lower than 1 million copies/ml (median of 3 infected individuals). The highest viral loads were found in clusters with the lowest average age, while clusters with the highest average age had low to middle viral load. Interestingly, in 20 significant clusters the viral load of three first cases were all below 100’000 copies/ml suggesting that subjects with less than 100’000 copies/ml may still have been contagious. Noteworthy, the dynamics of transmission clusters made it possible to identify three diffusion zones, which mainly differentiated rural from urban areas, the latter being more prone to last and spread in a new nearby clusters.The use of geographic information is key for public health decision makers to mitigate the spread of the virus. This study suggests that early localization of clusters help implementing targeted protective measures limiting the spread of the SARS-CoV-2 virus.

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Viral load and antibody levels in patients with COVID-19

GSC Advanced Research and Reviews ◽

10.30574/gscarr.2021.8.3.0180 ◽

2021 ◽

Vol 8 (3) ◽

pp. 010-018

Author(s):

Iva Christova ◽

Iva Trifonova ◽

Teodora Gladnishka ◽

Elena Dragusheva ◽

Georgi Popov ◽

...

Keyword(s):

Viral Load ◽

High Viral Load ◽

Igg Antibodies ◽

Rt Pcr ◽

Serum Samples ◽

Weekly Basis ◽

Specific Antibody Response ◽

Viral Loads ◽

Antibody Levels ◽

Kinetics Of

Relations between viral load, antibody levels and COVID-19 severity are not well studied and results from such investigations are controversial. In this study, we investigated kinetics of viral load and antibody responses to SARS-CoV-2 in 20 patients with COVID-19 and analysed the association with disease severity. The patients were followed on weekly basis within the first month after the onset and then once per month for the next 4 months. Serum samples were tested for IgA, IgM, and IgG antibodies against SARS-CoV-2 using ELISA tests. SARS-CoV-2 viral load in nasopharyngeal swabs was measured by quantitative Realtime RT-PCR. For vast majority of the patients, the viral loads were at their highest levels at presentation and then declined gradually. Despite development of specific antibody response 7-11 days after the onset of COVID-19, SARS-CoV-2 RNA was still detected in nasopharyngeal swabs of most of the patients. There was no direct link between viral load and severity of COVID-19: some of mild and some of severe cases started with a high viral load. There was a relationship between the time from the onset of the disease and the viral load: the highest viral load was in the first days. In more severe cases, there was a tendency for slower reduction in viral load and longer detection of SARS-CoV-2 virus. Levels of the specific antibodies increased earlier and to higher levels and were present for longer time in patients with more severe manifestations of COVID-19 than in those with milder disease.

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Evaluating the outcomes of enhanced adherence counselling intervention on clients with high viral loads in selected health facilities in Monze.

10.1101/2021.12.18.21267844 ◽

2021 ◽

Author(s):

Martha Kaira ◽

Tresford Sikazwe ◽

John Simwanza ◽

Mowa Zambwe ◽

Peter J. Chipimo

Keyword(s):

Viral Load ◽

High Viral Load ◽

Cross Sectional Study ◽

Health Facilities ◽

Sample Collection ◽

Viral Load Suppression ◽

Cross Sectional ◽

Viral Loads ◽

Adherence Counselling ◽

Counselling Intervention

To investigate the changes in Viral Load(VL) during Enhanced Adherence Counselling (EAC) sessions and its determinants among ART clients with unsuppressed VLs in Monze district. Method: A Cross-sectional study involving 616 HVL ART clients from 15 health facilities in Monze district which was conducted between October 1 2019 and March 30 2021. Results Out of 616 clients analysed, there was an improvement in viral load suppression following completion of EAC with a final outcome of 61% suppression. 28.7% remained unsuppressed. A total of 9.1% had no final viral load results documented and 0.2 % had been transferred out of their respective facilities and were not included in the study. Collection of repeat Viral loads was done on 84% of the clients with high viral load results while 16% had no record of sample collection. A total of 56 results were not received giving a result return of 89% from repeat samples collected. Females had a 40% likelihood of being unsuppressed at 95% CI (41% to 86%) compared to the males. Conclusion EAC improves the outcomes of HVLs and should be encouraged on all high viral clients. Programs should be developed to improve suppression in females on ART

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Case Report of COVID-19 after Full Vaccination: Viral Loads and Anti-SARS-CoV-2 Antibodies

Diagnostics ◽

10.3390/diagnostics11101815 ◽

2021 ◽

Vol 11 (10) ◽

pp. 1815

Author(s):

Magdalena Komiazyk ◽

Jaroslaw Walory ◽

Jan Gawor ◽

Iza Ksiazek ◽

Robert Gromadka ◽

...

Keyword(s):

Viral Load ◽

Immune Responses ◽

Coming Out ◽

High Viral Load ◽

Post Vaccination ◽

Viral Loads ◽

Sporadic Cases ◽

Alpha Variant ◽

The Uk ◽

Post Infectious

The introduction of effective vaccines against SARS-CoV-2 is expected to prevent COVID-19. However, sporadic cases of infection in vaccinated persons have been reported. We describe a case of a double-dose vaccinated woman with COVID-19. All stages of infection were observed, from no identification of virus, then the start of the infection, a high viral load, coming out of viraemia, and finally no detection of the virus. Despite the high viral load, the woman demonstrated mild COVID-19 symptoms, manifested only by a sore throat. The antibody results showed that she produced both post-infectious and post-vaccination immune responses. Phylogenetic analysis of the obtained viral genome sequence indicated that the virus belonged to the UK SARS-CoV-2 lineage B.1.1.7 (GR 501Y.V1; 20I/S:501Y.V1; Alpha variant).

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