scholarly journals Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies

PLoS Biology ◽  
2021 ◽  
Vol 19 (7) ◽  
pp. e3001333
Author(s):  
Stephen M. Kissler ◽  
Joseph R. Fauver ◽  
Christina Mack ◽  
Scott W. Olesen ◽  
Caroline Tai ◽  
...  
Keyword(s):  
Credible Interval ◽  
Threshold Value ◽  
Turnaround Time ◽  
Viral Rna ◽  
Reverse Transcription Pcr ◽  
Viral Proliferation ◽  
Asymptomatic Individuals ◽  
Clinical Measures ◽  
Public Health Strategies ◽  
Prospective Longitudinal

SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform clinical measures and interventions such as test-based screening. We used prospective longitudinal quantitative reverse transcription PCR testing to measure the viral RNA trajectories for 68 individuals during the resumption of the 2019–2020 National Basketball Association season. For 46 individuals with acute infections, we inferred the peak viral concentration and the duration of the viral proliferation and clearance phases. According to our mathematical model, we found that viral RNA concentrations peaked an average of 3.3 days (95% credible interval [CI] 2.5, 4.2) after first possible detectability at a cycle threshold value of 22.3 (95% CI 20.5, 23.9). The viral clearance phase lasted longer for symptomatic individuals (10.9 days [95% CI 7.9, 14.4]) than for asymptomatic individuals (7.8 days [95% CI 6.1, 9.7]). A second test within 2 days after an initial positive PCR test substantially improves certainty about a patient’s infection stage. The effective sensitivity of a test intended to identify infectious individuals declines substantially with test turnaround time. These findings indicate that SARS-CoV-2 viral concentrations peak rapidly regardless of symptoms. Sequential tests can help reveal a patient’s progress through infection stages. Frequent, rapid-turnaround testing is needed to effectively screen individuals before they become infectious.

scholarly journals SARS-CoV-2 viral dynamics in acute infections

2020 ◽  
Author(s):  
Stephen M. Kissler ◽  
Joseph R. Fauver ◽  
Christina Mack ◽  
Scott W. Olesen ◽  
Caroline Tai ◽  
...  
Keyword(s):  
Public Health ◽  
National Basketball Association ◽  
Viral Rna ◽  
Rapid Progression ◽  
Viral Dynamics ◽  
Acute Infections ◽  
Viral Proliferation ◽  
Asymptomatic Individuals ◽  
Prospective Longitudinal ◽  
Viral Titers

AbstractBackgroundSARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform clinical measures and interventions such as test-based screening.MethodsWe used prospective longitudinal RT-qPCR testing to measure the viral RNA trajectories for 68 individuals during the resumption of the 2019-20 National Basketball Association season. For 46 individuals with acute infections, we inferred the peak viral concentration and the duration of the viral proliferation and clearance phases.FindingsOn average, viral RNA concentrations peaked 2.7 days (95% credible interval [1.2, 3.8]) after first detection at a cycle threshold value of 22.4 [20.6, 24.1]. The viral clearance phase lasted longer for symptomatic individuals (10.5 days [6.5, 14.0]) than for asymptomatic individuals (6.7 days [3.2, 9.2]). A second test within 2 days after an initial positive PCR substantially improves certainty about a patient’s infection phase. The effective sensitivity of a test intended to identify infectious individuals declines substantially with test turnaround time.InterpretationSARS-CoV-2 viral concentrations peak rapidly regardless of symptoms. Sequential tests can help reveal a patient’s progress through infection stages. Frequent rapid-turnaround testing is needed to effectively screen individuals before they become infectious.FundingNWO Rubicon 019.181EN.004 (CBFV); clinical research agreement with the NBA and NBPA (NDG); Huffman Family Donor Advised Fund (NDG); Fast Grant funding from the Emergent Ventures at the Mercatus Center; George Mason University (NDG); the Morris-Singer Fund for the Center for Communicable Disease Dynamics at the Harvard T.H. Chan School of Public Health (YHG).Research in ContextEvidence before this studySARS-CoV-2 viral dynamics affect clinical and public health measures, informing patient care, testing algorithms, contact tracing protocols, and clinical trial design. We searched Web of Science using the search terms “ALL = ((SARS-CoV-2 OR COVID-19) AND (viral OR RNA) AND (load OR concentration OR shedding) AND (dynamic* OR kinetic* OR trajector*))” which returned 83 references. Of these, 22 were not pertinent to within-host SARS-CoV-2 viral dynamics. The remaining 61 studies tracked SARS-CoV-2 viral trajectories in a variety of geographic locations and patient populations. Together, these studies report that viral titers normally peak at or before the onset of symptoms and that a long tail of intermittent positive tests can follow a period of acute infection. Plasma but not nasopharyngeal viral concentration is associated with increased disease severity. Most studies tracked hospitalized patients after the onset of symptoms. Two of the studies tracked pre-symptomatic and/or asymptomatic patients, but these were too sparsely sampled to clearly discern viral dynamics during the earliest stage of infection.Added value of this studyWe implemented prospective longitudinal real time quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) testing for SARS-CoV-2 in a cohort of individuals during the resumption of the 2019-20 National Basketball Association season. This allowed us to explicitly measure viral titers during the full course of 46 acute infections. Consistent with other studies, we find that peak viral concentrations do not differ substantially between symptomatic and asymptomatic individuals but that symptomatic individuals take longer to clear the virus than asymptomatic individuals. For both symptomatic and asymptomatic individuals, viral titers normally peak within 3 days of the first positive test. This study is the first to describe the time course of viral concentrations during the earliest stage of infection when individuals are most likely to be infectious.Implications of all the available evidenceSymptomatic and asymptomatic individuals follow similar SARS-CoV-2 viral trajectories. Due to the rapid progression from first possible detection to peak viral concentration, frequent rapid-turnaround testing is needed to screen individuals prior to them becoming infectious.

scholarly journals Ocular manifestations of a hospitalised patient with confirmed 2019 novel coronavirus disease

2020 ◽  
Vol 104 (6) ◽  
pp. 748-751 ◽  
Author(s):  
Lu Chen ◽  
Meizhou Liu ◽  
Zheng Zhang ◽  
Kun Qiao ◽  
Ting Huang ◽  
...  
Keyword(s):  
Threshold Value ◽  
Viral Rna ◽  
Rt Pcr ◽  
Illness Onset ◽  
Reverse Transcription Pcr ◽  
Ocular Manifestations ◽  
Conjunctival Swab ◽  
Precautionary Measures ◽  
Novel Coronavirus ◽  
Hospitalised Patient

PurposeTo report the ocular characteristics and the presence of viral RNA of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in conjunctival swab specimens in a patient with confirmed 2019 novel coronavirus disease (COVID-19).Participant and methodsA 30-year-old man with confirmed COVID-19 and bilateral acute conjunctivitis which occurred 13 days after illness onset. Based on detailed ophthalmic examination, reverse transcription PCR (RT-PCR) was performed to detect SARS-CoV-2 virus in conjunctival swabs. The ocular characteristics, presence of viral RNA and viral dynamics of SARS-CoV-2 in the conjunctival specimens were evaluated.ResultsSlit lamp examination showed bilateral acute follicular conjunctivitis. RT-PCR assay demonstrated the presence of viral RNA in conjunctival specimen 13 days after onset (cycle threshold value: 31). The conjunctival swab specimens remained positive for SARS-CoV-2 on 14 and 17 days after onset. On day 19, RT-PCR result was negative for SARS-CoV-2.ConclusionSARS-CoV-2 is capable of causing ocular complications such as viral conjunctivitis in the middle phase of illness. Precautionary measures are recommended when examining infected patients throughout the clinical course of the infection. However, conjunctival sampling might not be useful for early diagnosis because the virus may not appear initially in the conjunctiva.

scholarly journals Selective and Nonselective Packaging of Cellular RNAs in Retrovirus Particles

2007 ◽  
Vol 81 (12) ◽  
pp. 6623-6631 ◽  
Author(s):  
Samuel J. Rulli ◽  
Catherine S. Hibbert ◽  
Jane Mirro ◽  
Thoru Pederson ◽  
Shyam Biswal ◽  
...  
Keyword(s):  
Leukemia Virus ◽  
Signal Recognition Particle ◽  
Viral Rna ◽  
Genomic Rna ◽  
Gag Protein ◽  
Mrna Species ◽  
Reverse Transcription Pcr ◽  
Cellular Mrnas ◽  
A Minor ◽  
Hiv 1

ABSTRACT Assembly of retrovirus particles normally entails the selective encapsidation of viral genomic RNA. However, in the absence of packageable viral RNA, assembly is still efficient, and the released virus-like particles (termed “Ψ−” particles) still contain roughly normal amounts of RNA. We have proposed that cellular mRNAs replace the genome in Ψ− particles. We have now analyzed the mRNA content of Ψ− and Ψ+ murine leukemia virus (MLV) particles using both microarray analysis and real-time reverse transcription-PCR. The majority of mRNA species present in the virus-producing cells were also detected in Ψ− particles. Remarkably, nearly all of them were packaged nonselectively; that is, their representation in the particles was simply proportional to their representation in the cells. However, a small number of low-abundance mRNAs were greatly enriched in the particles. In fact, one mRNA species was enriched to the same degree as Ψ+ genomic RNA. Similar results were obtained with particles formed from the human immunodeficiency virus type 1 (HIV-1) Gag protein, and the same mRNAs were enriched in MLV and HIV-1 particles. The levels of individual cellular mRNAs were ∼5- to 10-fold higher in Ψ− than in Ψ+ MLV particles, in agreement with the idea that they are replacing viral RNA in the former. In contrast, signal recognition particle RNA was present at the same level in Ψ− and Ψ+ particles; a minor fraction of this RNA was weakly associated with genomic RNA in Ψ+ MLV particles.

Abstract W P371: Periodontal Disease is Associated with Aortic Arch Atheroma a Marker of Recurrent Vascular Events in Stroke/TIA Patients

Stroke ◽  
2015 ◽  
Vol 46 (suppl_1) ◽  
Author(s):  
Matthew Chung ◽  
Alan Hinderliter ◽  
Steven Offenbacher ◽  
James Beck ◽  
Souvik Sen
Keyword(s):  
Risk Factor ◽  
Periodontal Disease ◽  
Aortic Arch ◽  
Vascular Event ◽  
Stroke Work ◽  
Transesophageal Echocardiogram ◽  
Vascular Events ◽  
Clinical Measures ◽  
Prospective Longitudinal ◽  
Work Up

Background: Periodontal disease (PD) is independently associated with recurrent vascular events in Stroke/TIA. Aortic arch atheroma (AA) is an independent risk factor for stroke. The association between PD and AA has not been described. Objective: To test the association between: 1) significant AA and recurrent vascular event in stroke/TIA 2) PD and AA (plaque severity and characteristics) Methods: In this prospective longitudinal hospital-based cohort study, PD was assessed in Stroke/TIA patients. Based on clinical measures patients were classified to have high (HPD) versus low periodontal disease (LPD). As part of their stroke work-up, AA was assessed using transesophageal echocardiogram (TEE). Based on plaque thickness the AA was graded as mild (0-0.99 mm), moderate (1-3.99 mm) or severe (≥4 mm), as well as plaque characteristics, namely mobility, ulceration and calcification. The patients were followed up for recurrent vascular events, namely stroke, TIA, myocardial infarction and vascular death. Results: In an eighteen-month period, 106 patients were evaluated, 40(38%) showed HPD and 27 (26%) had recurrent vascular events over a median of 24 months (range 12-24 months). AA assessed by TEE revealed 16 with mild, 73 with moderate, and 17 with severe plaque. Those with severe AA had a higher rate of recurrent vascular event compared to those without (Figure). Severe AA was associated with recurrent vascular events (HR 2.3, 95% CI, 1.02-5.32). HPD patients had higher (p = 0.004) AA plaque thickness (Mean±SD 2.0±2.4 mm) compared with LPD (1.6±1.2 mm). HPD was associated with moderate AA (OR 10.5, 95% CI, 1.3-84) and severe AA (OR 16.9, 95% CI, 1.8-158). Among plaque characteristics HPD was associated (p=0.02) with calcification. Conclusion: In stroke/TIA patients severe AA is associated with recurrent vascular events. HPD is associated with an increased AA plaque thickness and calcification. The results suggest that PD may be a risk factor for AA.

scholarly journals Bioluminescent Enzyme Immunoassay for the Detection of Norovirus Capsid Antigen

2012 ◽  
Vol 19 (12) ◽  
pp. 1949-1954 ◽  
Author(s):  
Nozomi Sakamaki ◽  
Yoshiyuki Ohiro ◽  
Mitsuki Ito ◽  
Mitsuru Makinodan ◽  
Tsubasa Ohta ◽  
...  
Keyword(s):  
Enzyme Immunoassay ◽  
Fecal Sample ◽  
Recombinant Virus ◽  
Turnaround Time ◽  
Rapid Diagnosis ◽  
Analytical Sensitivity ◽  
Good Reproducibility ◽  
Reverse Transcription Pcr ◽  
Response Range ◽  
Coefficients Of Variation

ABSTRACTAn ultrasensitive and fully automated bioluminescent enzyme immunoassay (BLEIA) was developed for the detection of norovirus (NV) capsid antigen. In the evaluation tests with recombinant virus-like particles, the BLEIA demonstrated broad reactivity against several NV genotypes (genotypes 1, 3, 4, 7, 8, and 12 in genogroup I [GI] and genotypes 1, 2, 3, 4, 5, 6, 12, and 13 in GII), a wide dose-response range from 0.25 pg/ml to 10,000 pg/ml, and good reproducibility with low coefficients of variation (CVs) (within-run CVs of <2.8%, between-day CVs of <3.7%). In the evaluation tests with NV-positive fecal samples, a good correlation (y= 0.66x −3.21,r= 0.84) between the BLEIA and real-time quantitative reverse transcription-PCR was obtained. Furthermore, in the dilution test with NV specimens, the analytical sensitivity of NV was estimated to be 105to 106copies/g of fecal sample, indicating that the analytical sensitivity of the BLEIA is comparable to that of commercially available molecular methods. All assay steps are fully automated, the turnaround time is 46 min, and the throughput of the assay is 120 tests/h. These results indicate that the BLEIA is potentially useful for the rapid diagnosis of NV in epidemic and sporadic gastroenteritis.

scholarly journals A Novel Method for the Capture-based Purification of Whole Viral Native RNA Genomes

2018 ◽  
Author(s):  
Cedric Chih Shen Tan ◽  
Sebastian Maurer-Stroh ◽  
Yue Wan ◽  
October Michael Sessions ◽  
Paola Florez de Sessions
Keyword(s):  
Rna Sequencing ◽  
Turnaround Time ◽  
Viral Rna ◽  
Nucleic Acid Hybridization ◽  
Proof Of Concept ◽  
Purification Method ◽  
Viral Genomes ◽  
Viral Particles ◽  
Sequencing Strategy ◽  
Enrichment Protocol

ABSTRACTCurrent technologies for targeted characterization and manipulation of viral RNA primarily involve amplification or ultracentrifugation with isopycnic gradients of viral particles to decrease host RNA background. The former strategy is non-compatible for characterizing properties innate to RNA strands such as secondary structure, RNA-RNA interactions, and also for nanopore direct RNA sequencing involving the sequencing of native RNA strands. The latter strategy, ultracentrifugation, causes loss in genomic information due to its inability to retrieve unassembled viral RNA. To address this, we developed a novel application of current nucleic acid hybridization technologies for direct characterization of RNA. In particular, we modified a current enrichment protocol to capture whole viral native RNA genomes for downstream RNA assays to circumvent the abovementioned problems. This technique involves hybridization of biotinylated baits at 500 nucleotides (nt) intervals, stringent washes and release of free native RNA strands using DNase I treatment, with a turnaround time of about 6 h 15 min. RT-qPCR was used as the primary proof of concept that capture-based purification indeed removes host background. Subsequently, capture-based purification was applied to direct RNA sequencing as proof of concept that capture-based purification can be coupled with downstream RNA assays. We report that this protocol was able to successfully purify viral RNA by 561-791 fold. We also report that application of this protocol to direct RNA sequencing yielded a reduction in human host RNA background by 1580 fold, a 99.91% recovery of viral genome with at least 15x coverage, and a mean coverage across the genome of 120x. This report is, to the best of our knowledge, the first description of a capture-based purification method for assays that involve direct manipulation or characterisation of native RNA. This report also describes a successful application of capture-based purification as a direct RNA sequencing strategy that addresses certain limitations of current strategies in sequencing RNA viral genomes.

scholarly journals 393. Characteristics of SARS-CoV-2 RNA Viral Loads among Nursing Home Residents and Staff with Repeat Positive Tests ≥ 90 Days After Initial Infection: 5 US Jurisdictions, July 2020–March 2021

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S298-S299
Author(s):  
W Wyatt Wilson ◽  
Kelly M Hatfield ◽  
Stacy Tressler ◽  
Cara Bicking Kinsey ◽  
Renee Zell ◽  
...  
Keyword(s):  
Viral Load ◽  
Nursing Home Residents ◽  
Viral Rna ◽  
Continuous Variables ◽  
Test Results ◽  
Convenience Sample ◽  
Initial Infection ◽  
Viral Loads ◽  
Chi Squared ◽  
Asymptomatic Individuals

Abstract Background Background. Understanding the viral load and potential infectivity of individuals in nursing homes (NH) with repeat positive SARS-CoV-2 tests ≥ 90 days after initial infection has important implications for safety related to transmission in this high-risk setting. Methods Methods. We collected epidemiologic data by reviewing records of a convenience sample of NH residents and staff with respiratory specimens who had positive SARS-CoV-2 rRT-PCR test results from July 2020 through March 2021 and had a SARS-CoV-2 infection diagnosed ≥ 90 days prior. No fully vaccinated individuals were included. Each contributed one repeat positive specimen ≥ 90 days after initial, which was sent to CDC and retested using rRT-PCR. Specimens were assessed for replication-competent virus in cell culture if Cycle threshold (Ct) &lt; 34 and sequenced if Ct &lt; 30. Using Ct values as a proxy for viral RNA load, specimens were categorized as high (Ct &lt; 30) or low (if Ct ≥ 30 or rRT-PCR negative at retesting). Continuous variables were compared using Wilcoxon signed-rank tests. Proportions were compared using Chi-squared or Fisher’s exact tests. Results Results. Of 64 unvaccinated individuals with specimens from 61 unique NHs, 14 (22%) were sent for culture and sequencing. Ten of 64 (16%) had a high viral RNA load, of which four (6%) were culture positive and none were known variants of interest or concern (Figure 1). Median days to repeat positive test result were 122 (Interquartile range (IQR): 103–229) and 201 (IQR: 139–254), respectively, for high versus low viral load specimens (p=0.13). More individuals with high viral loads (5/10, 50%) reported COVID-19 symptoms than with a low viral load (1/27, 4%, p=0.003). Most individuals (46/58, 79%) were tested following known or suspected exposures, with no significant differences between high and low viral load (p=0.18). Conclusion In this study, nearly 1 in 6 NH residents and staff with repeat positive tests after 90 days demonstrated high viral RNA loads and viable virus, indicating possible infectivity. While individuals with high RNA viral load may be more likely to be symptomatic, distinguishing asymptomatic individuals who have high viral loads may be difficult with timing since initial infection, other test results, or exposure history alone. Disclosures John A. Jernigan, MD, MS, Nothing to disclose.

scholarly journals Rapid assessment of West Nile virus circulation in a German zoo based on honey-baited FTA cards in combination with box gravid traps

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Noelle Fynmore ◽  
Renke Lühken ◽  
Heike Maisch ◽  
Tina Risch ◽  
Sabine Merz ◽  
...  
Keyword(s):  
West Nile Virus ◽  
Rapid Assessment ◽  
Gravid Female ◽  
Virus Detection ◽  
Turnaround Time ◽  
Viral Rna ◽  
Mass Trapping ◽  
Vector Surveillance ◽  
West Nile ◽  
Fta Cards

Abstract Background For over a decade, monitoring of West Nile virus (WNV) in Germany has consisted of a bird monitoring programme as well as a mosquito-based surveillance programme employing CO2-baited encephalitis vector surveillance (EVS) traps for mass trapping and screening of mosquitoes. In contrast to the EVS traps, the Reiter/Cummings type box gravid trap collects gravid female mosquitoes, which have already taken a blood meal, increasing the likelihood of being infected with pathogens. The traps can be equipped with a honey-baited Flinders Technology Associates® (FTA) card to encourage sugar feeding by the trapped mosquitoes. FTA cards contain nucleic acid preserving substances, which prevent the degradation of viral RNA in the expectorated mosquito saliva and allows for testing the card for flavivirus RNA. This study aimed to assess the suitability of the method for WNV surveillance in Germany as an alternative to previous methods, which are expensive, time-consuming, and predominantly target host-seeking populations less likely to be infected with WNV. Methods In the Thüringer Zoopark Erfurt, snowy owls (Nyctea scandiaca) and greater flamingos (Phoenicopterus roseus) died of WNV infections in July and August 2020. In response, five Reiter/Cummings type box gravid traps were positioned during the daytime on the 10th, 13th, and 16th of September in five different locations. The FTA cards and mosquitoes in the chamber were collected, kept in a cool chain, and further processed for virus detection using a modified generic flavivirus reverse transcription PCR. Results A total of 15 trappings during September collected a total of 259 female mosquitoes, 97% of which were Culex pipiens sensu lato, as well as 14 honey-baited FTA cards. Eight mosquitoes tested PCR-positive for WNV. Four FTA cards tested PCR-positive for mosquito-borne flaviviruses, two of which were confirmed as WNV, and the remaining two confirmed as Usutu virus. Conclusion The suitability of the FTA cards in preserving viral RNA in the field and rapid turnaround time from collection to result is combined with a simple, cost-effective, and highly specific trapping method to create an arbovirus surveillance system, which circumvents many of the difficulties of previous surveillance programmes that required the analysis of mosquitoes in the laboratory. Graphical Abstract

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