scholarly journals 520. Longitudinal Analysis of SARS-CoV-2 Viruses in Hospitalized Adults

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S325-S326
Author(s):  
Lacy Simons ◽  
Ramon Lorenzo-Redondo ◽  
Hannah Nam ◽  
Scott C Roberts ◽  
Michael G Ison ◽  
...  
Keyword(s):  
Viral Load ◽  
Genome Sequencing ◽  
Viral Genome ◽  
Temporal Dynamics ◽  
Population Level ◽  
Hospital Staff ◽  
Therapeutic Interventions ◽  
Viral Loads ◽  
Qrt Pcr ◽  
Over Time

Abstract Background The rapid spread of SARS-CoV-2, the causative agent of Coronavirus disease 2019 (COVID-19), has been accompanied by the emergence of viral mutations, some of which may have distinct virological and clinical consequences. While whole genome sequencing efforts have worked to map this viral diversity at the population level, little is known about how SARS-CoV-2 may diversify within a host over time. This is particularly important for understanding the emergence of viral resistance to therapeutic interventions and immune pressure. The goal of this study was to assess the change in viral load and viral genome sequence within patients over time and determine if these changes correlate with clinical and/or demographic parameters. Methods Hospitalized patients admitted to Northwestern Memorial Hospital with a positive SARS-CoV-2 test were enrolled in a longitudinal study for the serial collection of nasopharyngeal specimens. Swabs were administered to patients by hospital staff every 4 ± 1 days for up to 32 days or until the patients were discharged. RNA was extracted from each specimen and viral loads were calculated by quantitative reverse transcriptase PCR (qRT-PCR). Specimens with qRT-PCR cycle threshold values less than or equal to 30 were subject to whole viral genome sequencing by reverse transcription, multiplex PCR, and deep sequencing. Variant populations sizes were estimated and subject to phylogenetic analysis relative to publicly available SARS-CoV-2 sequences. Sequence and viral load data were subsequently correlated to available demographic and clinical data. Results 60 patients were enrolled from March 26th to June 20th, 2020. We observed an overall decrease in nasopharyngeal viral load over time across all patients. However, the temporal dynamics of viral load differed on a patient-by-patient basis. Several mutations were also observed to have emerged within patients over time. Distribution of SARS-CoV-2 viral loads in serially collected nasopharyngeal swabs in hospitalized adults as determined by qRT-PCR. Samples were collected every 4 ± 1 days (T#1–8) and viral load is displayed by log(copy number). Conclusion These data indicate that SARS-CoV-2 viral loads in the nasopharynx decrease over time and that the virus can accumulate mutations during replication within individual patients. Future studies will examine if some of these mutations may provide fitness advantages in the presence of therapeutic and/or immune selective pressures. Disclosures Michael G. Ison, MD MS, AlloVir (Consultant)

scholarly journals Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality

2021 ◽  
Author(s):  
Julio Silva ◽  
Carolina Lucas ◽  
Maria Sundaram ◽  
Benjamin Israelow ◽  
Patrick Wong ◽  
...  
Keyword(s):  
Viral Load ◽  
Disease Severity ◽  
T Cell Subsets ◽  
Temporal Association ◽  
Strongly Correlated ◽  
Immunological Parameters ◽  
Viral Loads ◽  
Patient Demographics ◽  
Over Time

While several clinical and immunological parameters correlate with disease severity and mortality in SARS-CoV-2 infection, work remains in identifying unifying correlates of coronavirus disease 2019 (COVID-19) that can be used to guide clinical practice. Here, we examine saliva and nasopharyngeal (NP) viral load over time and correlate them with patient demographics, and cellular and immune profiling. We found that saliva viral load was significantly higher in those with COVID-19 risk factors; that it correlated with increasing levels of disease severity and showed a superior ability over nasopharyngeal viral load as a predictor of mortality over time (AUC=0.90). A comprehensive analysis of immune factors and cell subsets revealed strong predictors of high and low saliva viral load, which were associated with increased disease severity or better overall outcomes, respectively. Saliva viral load was positively associated with many known COVID-19 inflammatory markers such as IL-6, IL-18, IL-10, and CXCL10, as well as type 1 immune response cytokines. Higher saliva viral loads strongly correlated with the progressive depletion of platelets, lymphocytes, and effector T cell subsets including circulating follicular CD4 T cells (cTfh). Anti-spike (S) and anti-receptor binding domain (RBD) IgG levels were negatively correlated with saliva viral load showing a strong temporal association that could help distinguish severity and mortality in COVID-19. Finally, patients with fatal COVID-19 exhibited higher viral loads, which correlated with the depletion of cTfh cells, and lower production of anti-RBD and anti-S IgG levels. Together these results demonstrated that viral load – as measured by saliva but not nasopharyngeal — is a dynamic unifying correlate of disease presentation, severity, and mortality over time.

scholarly journals Spatial and temporal dynamics of SARS-CoV-2 in COVID-19 patients: A systematic review

2020 ◽  
Author(s):  
Anne Weiss ◽  
Mads Jellingsoe ◽  
Morten Otto Alexander Sommer
Keyword(s):  
Viral Load ◽  
Respiratory Tract ◽  
Symptom Onset ◽  
Temporal Dynamics ◽  
Adult Patients ◽  
Clinical Severity ◽  
Upper Respiratory Tract ◽  
Viral Detection ◽  
Spatial And Temporal Dynamics ◽  
Over Time

Background The spatial and temporal dynamics of SARS-CoV-2 have been mainly described in form of case series or retrospective studies. In this study, we aimed to provide a coherent overview from published studies of the duration of viral detection and viral load in COVID-19 patients, stratified by specimen type, clinical severity and age. Method We systematically searched PubMed/MEDLINE and Cochrane review database for studies published between 1. November 2019 and 23rd of April 2020. We included studies that reported individual viral data over time measuring negative conversion by two consecutive negative tests, individual clinical severity and age. We excluded studies that reported viral data as patient fraction, reported only baseline data, included solely asymptomatic patients or were interventional studies. Extracted data included author, title, design, sample size, thresholds and genes of RT-PCR, patient age, COVID-19 severity, clinical characteristics, treatment, location of viral sampling, duration of viral detection, and viral load. We pooled the data of selected studies to determine effect estimates of duration of viral detection. Combined viral load was visualized over time. Findings Out of 7226 titles screened, 37 studies met the inclusion criteria and were included in the qualitative analysis and 22 studies in the quantitative analysis comprising 650 COVID-19 patients. The pooled estimate of the duration of positive detection of the virus was in mild adult patients 12.1 days (CI: 10.12, 14.05) after symptom onset in the upper respiratory tract (URT), 24.1 days (CI: 10.02, 38.19) in lower respiratory tract (LRT), and 15.5 days (CI: 8.04, 22.88) in faeces. Further, in mild adult patients, the maximum viral load was ~ 6.61 x 108 viral copies/mL in the URT and ~ 2.69 x 108 viral copies/mL in the LRT, within the first week of symptom onset. The maximum viral load in faeces was reported as ~ 3.55 x 107 copies/mL on Day 9. In moderate-severe adult patients, the pooled estimate of mean duration of positive viral detection in the URT was 15.8 days (CI: 11.12, 20.56) after symptom onset, 23.2 days (CI: 21.49, 24.97) in the LRT, 20.8 days (CI: 16.40, 25.17) in faeces. The maximum viral load was 4.60 x 109 copies/mL on Day 8 in the URT, 3.45 x 108 copies/mL on Day 11 in the LRT, 2.76 x 106 copies/mL on Day 18 in faeces and 1 x 104 copies/mL on Day 3 in blood. In children with mild symptoms, the pooled estimate of the mean duration of positive SARS-CoV-2 viral detection was 11.1 days (CI: 7.14, 15.11) in the URT and 16.0 days (CI: 11.49, 20,47) in the faeces, without reporting quantitative viral data. Viral positivity was detected in the urine and eye in one patient. Interpretation Our analysis showed consistent viral detection from specimen from the URT, the LRT and faeces, irrespective of the clinical severity of COVID-19. Our analysis suggests that SARS-CoV-2 persists for a longer duration in the LRT compared to the URT, whereas the differences in the duration of viral detection between mild and moderate-severe patients is limited in the LRT, but an indication of longer duration of viral detection in feces and the URT for moderate-severe patients was shown. Further, viral load was demonstrated to peak in the URT within first weak of infection, whereas maximum viral load has been observed to occur later and within the second week of infection in the LRT. Funding This study was funded by Innovation Fund Denmark.

scholarly journals Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmissibility

2021 ◽  
Author(s):  
Yun Lin ◽  
Bingyi Yang ◽  
Sarah Cobey ◽  
Eric Lau ◽  
Dillon Adam ◽  
...  
Keyword(s):  
Viral Load ◽  
Real Time ◽  
Temporal Distribution ◽  
Time Estimation ◽  
Population Level ◽  
Reproductive Number ◽  
Threshold Values ◽  
Illness Onset ◽  
Cycle Threshold ◽  
Viral Loads

Abstract Many locations around the world have used real-time estimates of the time-varying effective reproductive number (\({R}_{t}\)) of COVID-19 to provide evidence of transmission intensity to inform control strategies. Estimates of \({R}_{t}\) are typically based on statistical models applied to case counts and typically suffer lags of more than a week because of the incubation period and reporting delays. Noting that viral loads tend to decline over time since illness onset, analysis of the distribution of viral loads among confirmed cases can provide insights into epidemic trajectory. Here, we analyzed viral load data on confirmed cases during two local epidemics in Hong Kong, identifying a strong correlation between temporal changes in the distribution of viral loads (measured by cycle threshold values) and estimates of \({R}_{t}\) based on case counts. We demonstrate that cycle threshold values could be used to improve real-time \({R}_{t}\) estimation, enabling more timely tracking of epidemic dynamics.

scholarly journals Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
A Sarah Walker ◽  
Emma Pritchard ◽  
Thomas House ◽  
Julie V Robotham ◽  
Paul J Birrell ◽  
...  
Keyword(s):  
Viral Load ◽  
Single Gene ◽  
Population Level ◽  
National Institutes Of Health ◽  
Rt Pcr ◽  
Department Of Health ◽  
Health And Social Care ◽  
Antibody Tests ◽  
Nose And Throat ◽  
Over Time

Background: Information on SARS-CoV-2 in representative community surveillance is limited, particularly cycle threshold (Ct) values (a proxy for viral load).Methods: We included all positive nose and throat swabs 26-April-2020 to 13-March-2021 from the UK's national COVID-19 Infection Survey, tested by RT-PCR for the N, S and ORF1ab genes. We investigated predictors of median Ct value using quantile regression.Results: Of 3,312,159 nose and throat swabs, 27,902(0.83%) were RT-PCR-positive, 10,317(37%), 11,012(40%) and 6,550(23%) for 3, 2 or 1 of the N, S and ORF1ab genes respectively, with median Ct=29.2 (~215 copies/ml; IQR Ct=21.9-32.8, 14-56,400 copies/ml). Independent predictors of lower Cts (i.e. higher viral load) included self-reported symptoms and more genes detected, with at most small effects of sex, ethnicity and age. Single-gene positives almost invariably had Ct>30, but Cts varied widely in triple-gene positives, including without symptoms. Population-level Cts changed over time, with declining Ct preceding increasing SARS-CoV-2 positivity.Of 6,189 participants with IgG S-antibody tests post-first RT-PCR-positive, 4,808(78%) were ever antibody-positive; Cts were significantly higher in those remaining antibody-negative.Conclusions: Marked variation in community SARS-CoV-2 Ct values suggest that they could be a useful epidemiological early-warning indicator.Funding: Department of Health and Social Care, National Institutes of Health Research, Huo Family Foundation, Medical Research Council UK; Wellcome Trust.

scholarly journals Sars-CoV-2 Genome Sequencing Methods Differ In Their Ability To Detect Variants From Low Viral Load Samples

2021 ◽  
Author(s):  
C. Lam ◽  
K. Gray ◽  
M. Gall ◽  
R. Sadsad ◽  
A. Arnott ◽  
...  
Keyword(s):  
Viral Load ◽  
Genome Sequencing ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Low Frequency ◽  
Variant Calling ◽  
High Sensitivity ◽  
Viral Escape ◽  
Viral Loads ◽  
Sensitivity Specificity

SARS-CoV-2 genomic surveillance has been vital in understanding the spread of COVID-19, the emergence of viral escape mutants and variants of concern. However, low viral loads in clinical specimens affect variant calling for phylogenetic analyses and detection of low frequency variants, important in uncovering infection transmission chains. We systematically evaluated three widely adopted SARS-CoV-2 whole genome sequencing methods for their sensitivity, specificity, and ability to reliably detect low frequency variants. Our analyses highlight that the ARTIC v3 protocol consistently displays high sensitivity for generating complete genomes at low viral loads compared with the probe-based Illumina respiratory viral oligo panel, and a pooled long-amplicon method. We show substantial variability in the number and location of low-frequency variants detected using the three methods, highlighting the importance of selecting appropriate methods to obtain high quality sequence data from low viral load samples for public health and genomic surveillance purposes.

scholarly journals 491. Persistence of SARS-CoV-2 Iinfection in Immunocompromised Children

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S346-S347
Author(s):  
Susan Dolan ◽  
Jean Mulcahy Levy ◽  
Angela Moss ◽  
Kelly Pearce ◽  
Molly Butler ◽  
...  
Keyword(s):  
Viral Load ◽  
Immunosuppressive Treatment ◽  
Viral Persistence ◽  
Research Support ◽  
Repeat Testing ◽  
Viral Loads ◽  
Negative Results ◽  
Significant Difference ◽  
Over Time ◽  
Research Grant

Abstract Background The temporal dynamics of SARS-CoV-2 infectivity in immunocompromised children (IC) are unknown but may have important infection control implications. We evaluated SARS-CoV-2 viral persistence and assessed factors associated with viral persistence and cycle threshold (CT) values as a surrogate of viral load for IC. Methods We conducted a retrospective cohort study of SARS-CoV-2-positive IC at a large quaternary pediatric hospital from March 2020-2021. Immunocompromised status was defined as primary or secondary/acquired immunodeficiencies due to comorbidities or immunosuppressive treatment. The primary outcome was time to first-of-two consecutively negative SARS-CoV-2 PCR tests ≥ 24 hours apart. Polymerase chain reaction (PCR) testing of sequential patient samples was conducted using the Centers for Disease Control 2019-nCoV Real-Time RT-PCR Diagnostic Panel (CDC assay). Chi-square, Fisher exact, and Wilcoxon tests were used to compare demographic and clinical characteristics. Kaplan-Meier curve median event times and log-rank tests were used to compare outcomes. Subjects without 2 consecutive negative tests censored at the last test. Analyses were conducted using SAS v 9.4. Results Ninety-one children met inclusion criteria, and 67 children had more than 1 test (Figure 1). Median age was 15.5 years (IQR 8-18 yrs), 64% were male, 58% of children were white, and 43% were Latinx. Most (67%) were tested in outpatient settings, and 58% of children were asymptomatic. The median time to two negative tests was 42 days (IQR 25.0,55.0), with no difference in duration of positivity with specific diagnoses, degree of lymphopenia, or symptomatic vs asymptomatic illness. Five of 7 (71%) children with samples available for repeat testing had initial CT values < 30, indicating a moderate to high viral load, and of these, 4 (57%) had repeat testing 21 to 30 days later with CT values < 30 (Figure 2), suggesting persistence of moderate to high viral loads. Figure 1. Plot of immunocompromised children in cohort with positive SARS CoV2 PCR and subsequent testing (n = 67). Timelines of immunocompromised children in cohort with positive SARS CoV2 PCR and subsequent testing, grouped by immunocompromising condition. Each line represents an individual patient. Positive results are shown in light grey, negative results are shown in black. Figure 2. Plot of CT values from SARS-CoV-2 PCR testing over time among children with sequential samples available for retesting (n = 7) Plot of CT values (y axis) from SARS-CoV-2 PCR testing on the CDC assay over time (x axis) in days from initial positive test. Repeated testing which yielded a negative result on the CDC assay or intermittent negative results on clinical testing represented as CT value of 40. Each line represents a unique patient. Conclusion The median duration of viral persistence among IC with SARS-CoV-2 infection was 6 weeks, with no significant difference in immunocompromised diagnoses or clinical presentation, with over half of children with testing on the same platform having moderate to high viral loads after 3 weeks, suggesting potential transmission risk. Disclosures Samuel R. Dominguez, MD, PhD, BioFire Diagnostics (Consultant, Research Grant or Support)DiaSorin Molecular (Consultant)Pfizer (Grant/Research Support) Samuel R. Dominguez, MD, PhD, BioFire (Individual(s) Involved: Self): Consultant, Research Grant or Support; DiaSorin Molecular (Individual(s) Involved: Self): Consultant; Pfizer (Individual(s) Involved: Self): Grant/Research Support Suchitra Rao, MBBS, MSCS, BioFire (Research Grant or Support)

scholarly journals Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses

2020 ◽  
Author(s):  
Damien Jacot ◽  
Gilbert Greub ◽  
Katia Jaton ◽  
Onya Opota
Keyword(s):  
Viral Load ◽  
Respiratory Viruses ◽  
Rt Pcr ◽  
Clinical Prognosis ◽  
Clinical Specimens ◽  
Viral Loads ◽  
Over Time

RT-PCR to detect SARS-CoV-2 RNA in clinical specimens was key to manage the COVID-19 pandemic. We monitored SARS-CoV-2 viral loads over time and across different patient populations. We analyzed RT-PCR results according to samples types, gender, age, and health units and compared SARS-CoV-2 viral load to other respiratory viruses, representing a total of 28,373 RT-PCR results including 22,323 SARS-CoV-2 RT-PCR. The importance of viral load to predict contagiousness and clinical prognosis is discussed.

scholarly journals Virological Breakthrough: A Risk Factor for Loss to Followup in a Large Community-Based Cohort on Antiretroviral Therapy

2011 ◽  
Vol 2011 ◽  
pp. 1-6 ◽  
Author(s):  
Catherine Orrell ◽  
Richard Kaplan ◽  
Robin Wood ◽  
Linda-Gail Bekker
Keyword(s):  
Viral Load ◽  
Antiretroviral Therapy ◽  
Viral Loads ◽  
First Line Therapy ◽  
Line Therapy ◽  
Resource Limited ◽  
Adherence Intervention ◽  
The Impact ◽  
Over Time ◽  
Virological Breakthrough

Background. We have previously shown that 75% of individuals on antiretroviral therapy (ART) in a resource-limited setting who experienced virological breakthrough to >1000 copies/mL were resuppressed after an intensive adherence intervention. This study examines the long-term outcomes of this group in order to understand the impact of the adherence intervention over time.Methods. ART-naïve adults commencing ART between September 2002 and December 2009 were reviewed. Those who achieved suppression (<50 copies/mL) were categorised by subsequent viral load: any >1000 copies/mL (virological breakthrough) or not. Those with breakthrough were sub-categorised by following viral load into failed (VL > 1000 copies/mL) or resuppressed (VL < 1000 copies/mL). Their outcome (lost-to follow-up, death, in care on first-line therapy or in care on second-line therapy) was determined as of the 13th April 2010.Findings. 4047 ART-naïve adults commenced ART. 3086 had >2 viral loads and were included in the analysis. 2959 achieved virological suppression (96%). Thereafter 2109 (71%) remained suppressed and 850 (29%) experienced breakthrough ( (33%) failed and (67%) resuppressed). Individuals with breakthrough were younger (), had lower CD4 counts (), and higher viral loads () than those who remained suppressed. By 7 years the risk of breakthrough was 42% and of failure 15%. Fewer adults with breakthrough remain in care over time (). Loss to care is similar whether the individuals failed or resuppressed.Interpretation. While 67% of those who experience initial virological breakthrough resuppress after an adherence intervention, these individuals are significantly less likely be retained in care than those who remain virologically suppressed throughout.

scholarly journals The impact of SARS-CoV-2 vaccination on Alpha and Delta variant transmission

2021 ◽  
Author(s):  
David W Eyre ◽  
Donald Taylor ◽  
Mark Purver ◽  
David Chapman ◽  
Tom Fowler ◽  
...  
Keyword(s):  
Viral Load ◽  
Time Factors ◽  
Gene Detection ◽  
Viral Loads ◽  
Testing Data ◽  
Observational Cohort ◽  
Alpha Variant ◽  
The Impact ◽  
Index Cases ◽  
Over Time

Background Pre-Delta, vaccination reduced transmission of SARS-CoV-2 from individuals infected despite vaccination, potentially via reducing viral loads. While vaccination still lowers the risk of infection, similar viral loads in vaccinated and unvaccinated individuals infected with Delta question how much vaccination prevents onward transmission. Methods We performed a retrospective observational cohort study of contacts of SARS-CoV-2-infected index cases using contact testing data from England. We used multivariable logistic regression to investigate the impact of index case and contact vaccination on transmission, and how this varies with Alpha and Delta variants (classified using S-gene detection/calendar trends) and time since second vaccination. Results 51,798/139,164(37.2%) contacts tested were PCR-positive. Two doses of BNT162b2 or ChAdOx1 vaccines in Alpha variant index cases independently reduced PCR-positivity in contacts (aOR, adjusted odds ratio vs. unvaccinated=0.18[95%CI 0.12-0.29] and 0.37[0.22-0.63] respectively). The Delta variant attenuated vaccine-associated reductions in transmission: two BNT162b2 doses reduced Delta transmission (aOR=0.35[0.26-0.48]), more than ChAdOx1 (aOR=0.64[0.57-0.72]; heterogeneity p<0.001). Variation in viral load (Ct values) explained only a modest proportion of vaccine-associated transmission reductions. Transmission reductions declined over time since second vaccination, for Delta reaching similar levels to unvaccinated individuals by 12 weeks for ChAdOx1 and attenuating substantially for BNT162b2. Protection from vaccination in contacts also declined in the 3 months after second vaccination. Conclusions Vaccination reduces transmission of Delta, but by less than the Alpha variant. The impact of vaccination decreased over time. Factors other than PCR-measured viral load are important in vaccine-associated transmission reductions. Booster vaccinations may help control transmission together with preventing infections.

scholarly journals Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission

2020 ◽  
Author(s):  
Lucy Rivett ◽  
Sushmita Sridhar ◽  
Dominic Sparkes ◽  
Matthew Routledge ◽  
Nicholas K. Jones ◽  
...  
Keyword(s):  
Real Time ◽  
Healthcare Worker ◽  
Genome Sequencing ◽  
Viral Genome ◽  
Healthcare Workers ◽  
Hospital Staff ◽  
Rt Pcr ◽  
Household Contacts ◽  
Asymptomatic Carriage

Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 3-week period (April 2020), 1,032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-time RT-PCR was used to detect viral RNA from a throat+nose self-swab. 3% of HCWs in the asymptomatic screening group tested positive for SARS-CoV-2. 17/30 (57%) were truly asymptomatic/pauci-symptomatic. 12/30 (40%) had experienced symptoms compatible with coronavirus disease 2019 (COVID-19) >7 days prior to testing, most self-isolating, returning well. Clusters of HCW infection were discovered on two independent wards. Viral genome sequencing showed that the majority of HCWs had the dominant lineage B·1. Our data demonstrates the utility of comprehensive screening of HCWs with minimal or no symptoms. This approach will be critical for protecting patients and hospital staff.

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