scholarly journals Estimating epidemiologic dynamics from cross-sectional viral load distributions

Science ◽  
2021 ◽  
pp. eabh0635
Author(s):  
James A. Hay ◽  
Lee Kennedy-Shaffer ◽  
Sanjat Kanjilal ◽  
Niall J. Lennon ◽  
Stacey B. Gabriel ◽  
...  
Keyword(s):  
Population Distribution ◽  
Quantitative Polymerase Chain Reaction ◽  
Cross Sectional ◽  
Outbreak Management ◽  
Viral Loads ◽  
Time Estimates ◽  
Load Distributions ◽  
Random Samples ◽  
Combining Data ◽  
Polymerase Chain

Estimating an epidemic’s trajectory is crucial for developing public health responses to infectious diseases, but case data used for such estimation are confounded by variable testing practices. We show that the population distribution of viral loads observed under random or symptom-based surveillance, in the form of cycle threshold (Ct) values obtained from reverse-transcription quantitative polymerase chain reaction testing, changes during an epidemic. Thus, Ct values from even limited numbers of random samples can provide improved estimates of an epidemic’s trajectory. Combining data from multiple such samples improves the precision and robustness of such estimation. We apply our methods to Ct values from surveillance conducted during the SARS-CoV-2 pandemic in a variety of settings and offer alternative approaches for real-time estimates of epidemic trajectories for outbreak management and response.

scholarly journals Epidemiological profile of SARS-CoV-2 among selected regions in Ghana: A cross-sectional retrospective study

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243711
Author(s):  
Michael Owusu ◽  
Augustina Angelina Sylverken ◽  
Sampson Twumasi Ankrah ◽  
Philip El-Duah ◽  
Nana Kwame Ayisi-Boateng ◽  
...  
Keyword(s):  
Retrospective Study ◽  
Reproductive Number ◽  
Cross Sectional ◽  
Viral Loads ◽  
Review Period ◽  
Clinical Presentations ◽  
Study Population ◽  
Polymerase Chain ◽  
Epidemiological Profile ◽  
Asymptomatic Subjects

Background Global cases of COVID-19 continue to rise, causing havoc to several economies. So far, Ghana has recorded 48,643 confirmed cases with 320 associated deaths. Although summaries of data are usually provided by the Ministry of Health, detailed epidemiological profile of cases are limited. This study sought to describe the socio-demographic features, pattern of COVID-19 spread and the viral load dynamics among subjects residing in northern, middle and part of the southern belt of Ghana. Methods This was a cross-sectional retrospective study that reviewed records of samples collected from February to July, 2020. Respiratory specimens such as sputum, deep-cough saliva and nasopharyngeal swabs were collected from suspected COVID-19 subjects in 12 regions of Ghana for laboratory analysis and confirmation by real-time reverse transcription polymerase chain reaction (RT-PCR). Results A total of 72,434 samples were collected during the review period, with majority of the sampled individuals being females (37,464; 51.9%). The prevalence of SARS-CoV-2 identified in the study population was 13.2% [95%CI: 12.9, 13.4). Males were mostly infected (4,897; 51.5%) compared to females. Individuals between the ages 21–30 years recorded the highest number of infections (3,144, 33.4%). Symptomatic subjects had higher viral loads (1479.7 copies/μl; IQR = 40.6–178919) than asymptomatic subjects (49.9; IQR = 5.5–3641.6). There was significant association between gender or age and infection with SARS-CoV-2 (p<0.05). Among all the suspected clinical presentations, anosmia was the strongest predictor of SARS-CoV-2 infection (Adj. OR (95%CI): 24.39 (20.18, 29.49). We observed an average reproductive number of 1.36 with a minimum of 1.28 and maximum of 1.43. The virus trajectory shows a gradual reduction of the virus reproductive number. Conclusion This study has described the epidemiological profile of COVID-19 cases in northern, middle and part of the southern belt of Ghana, with males and younger individuals at greater risk of contracting the disease. Health professionals should be conscious of individuals presenting with anosmia since this was seen as the strongest predictor of virus infection.

Midturbinate Swabs Are Comparable to Nasopharyngeal Swabs for Quantitative Detection of Respiratory Syncytial Virus in Infants

2018 ◽  
Vol 8 (6) ◽  
pp. 554-558 ◽  
Author(s):  
Anne J Blaschke ◽  
Matt McKevitt ◽  
Krow Ampofo ◽  
Tammi Lewis ◽  
Hao Chai ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Respiratory Syncytial Virus ◽  
Real Time ◽  
Reverse Transcription ◽  
Quantitative Polymerase Chain Reaction ◽  
Quantitative Detection ◽  
Chain Reaction ◽  
Viral Loads ◽  
Polymerase Chain ◽  
Syncytial Virus

Abstract Nasopharyngeal (NP) swabs are generally used to detect respiratory syncytial virus (RSV) in infants. However, midturbinate (MT) swabs may provide comparable results. In this study, we enrolled hospitalized infants aged &lt;24 months with RSV and collected NP and MT swabs. The resulting viral loads measured by real-time reverse-transcription quantitative polymerase chain reaction were similar. Most parents preferred MT swabs over NP swabs.

Comparison between Quantitative Polymerase Chain Reaction and Sodium Nitrate Flotation Microscopy in Diagnosing Soil-Transmitted Helminth Infections

2021 ◽  
Author(s):  
Adam W. Bartlett ◽  
Rebecca Traub ◽  
Salvador Amaral ◽  
Sze Fui Hii ◽  
Naomi E. Clarke ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Sodium Nitrate ◽  
Primary Schools ◽  
Quantitative Polymerase Chain Reaction ◽  
Infection Intensity ◽  
Diagnostic Technique ◽  
Chain Reaction ◽  
Cross Sectional Survey ◽  
Cross Sectional ◽  
Polymerase Chain

There is evolving interest in alternate microscopy techniques and quantitative polymerase chain reaction (qPCR) to evaluate soil-transmitted helminth (STH) burden. Using data from a cross-sectional survey of 540 schoolchildren across six primary schools in three municipalities of Timor-Leste, we compared the performance of microscopy using sodium nitrate flotation (SNF) and qPCR in determining STH prevalence and infection intensity. Prevalence by qPCR was higher than SNF for Ascaris lumbricoides (17.5% versus 11.2%), hookworm (8.3% versus 1.2%), and Trichuris trichiura (4.7% versus 1.6%). Agreement between SNF and qPCR was fair for hookworm (κ = 0.21) and moderate for A. lumbricoides (κ = 0.59) and T. trichiura (κ = 0.44). Nearly all infections were light intensity by SNF, whereas qPCR identified 36.1% as moderate or heavy infections using cycle threshold to eggs per gram conversion formulas. Quantitative polymerase chain reaction is a promising diagnostic technique, though further studies validating infection intensity correlates are required.

scholarly journals Evaluation of GBV-C / HVG viremia in HIV-infected women

2012 ◽  
Vol 54 (1) ◽  
pp. 31-35 ◽  
Author(s):  
Synara Araújo Silva ◽  
Célia Lima Rodrigues ◽  
Aléia Faustino Campos ◽  
José Eduardo Levi
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Quantitative Polymerase Chain Reaction ◽  
Polymerase Chain Reaction Method ◽  
Taqman Assay ◽  
Chain Reaction ◽  
Viral Loads ◽  
Additional Information ◽  
Factors Influencing ◽  
Polymerase Chain

The present study aimed at standardizing a real-time quantitative polymerase chain reaction assay to evaluate the presence of GBV-C/HGV RNA. A "TaqMan" assay using primers and probe derived from the 5¢ NCR region was developed and validated. Two hundred and fifty-three plasma samples from HIV-infected women were tested for GBV-C viremia and antibody against the envelope protein 2. GBV-C RNA was detected in 22.5% of the patients whereas the antibody was identified in 25.3% of the cohort. Detection of viral RNA and of antibodies was mutually exclusive. Viral loads showed a mean of 1,777 arbitrary units / mL, being 1.1 and 13,625 arbitrary units / mL respectively the lowest and highest values measured. We conclude that the real-time quantitative polymerase chain reaction method developed is appropriate for the investigation of GBV-C RNA since it was shown to be highly specific and sensitive, as well as requiring few steps, preventing contamination and providing additional information as to the relative viremia of carriers, a parameter that must be included in studies evaluating the co-factors influencing the clinical outcome of HIV/AIDS.

scholarly journals LB-11. Comparison of Viral Loads in Individuals With or Without Symptoms At Time of COVID-19 Testing Among 32,480 Residents and Staff of Nursing Homes and Assisted Living Facilities in Massachusetts

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S848-S849
Author(s):  
Niall J Lennon ◽  
Michael Mina ◽  
Heidi L Rehm ◽  
Deborah T Hung ◽  
Sandra Smole ◽  
...  
Keyword(s):  
Viral Load ◽  
Nursing Homes ◽  
Assisted Living ◽  
Assisted Living Facilities ◽  
Cross Sectional ◽  
Viral Loads ◽  
Standard Curve ◽  
Load Distributions ◽  
Wide Range ◽  
Similar Range

Abstract Background Transmission of COVID-19 from people without symptoms confounds public health containment strategies. Comprehensive cross-sectional screening enables assessment of viral load independent of symptoms, informing transmission risks. We quantified SARS-CoV-2 burden by RT-qPCR from comprehensive screening of nursing homes and assisted living facilities in Massachusetts to inform our ability to detect SARS-CoV-2 in individuals with or without symptoms. Methods From 4/9/20 to 6/9/20, we tested nasopharyngeal (NP) swabs from 32,480 unique individuals comprising staff and residents of the majority of nursing homes and assisted living facilities in Massachusetts. Symptomatology at the time of sampling and demographic information were provided by each facility. NP swabs were collected, RNA extracted, and SARS-CoV-2 testing performed by RT-qPCR. We compared cycle thresholds (Ct) with a standard curve to quantify viral loads. Results The nursing home and assisted living facilities resident cohort (N = 16,966) was 65% female with mean age 82. The staff cohort (N = 15,514) was 76% female with mean age 45. In all, 2654 residents (15.5%) and 624 staff (4.1%) tested positive for SARS-CoV-2, including 12.7% of residents and 3.7% of staff without symptoms, compared to 53.1% of residents and 18.2% of staff with symptoms. The Ct distributions for viral probes were very similar between populations with and without symptoms (Fig 1), with a statistically but not meaningfully different mean (ΔCt 0.71 cycles, p = 0.006) and a similar range (12–38 cycles). This similarity persisted across all sub-categories examined (age, race, ethnicity, sex, resident/staff). Figure 1 Conclusion In a large cohort of individuals screened for SARS-CoV-2 by RT-qPCR, we found strikingly similar viral load distributions in patients with or without symptoms at the time of testing. The size of the study population, including both staff and residents spanning a wide range of ages, provides a comprehensive cross-sectional point prevalence measurement of viral burden. Because the distributions of viral loads are very similar regardless of symptoms, existing testing modalities validated for detection of SARS-CoV-2 RNA in symptomatic patients should perform similarly well in individuals without symptoms at the time of testing. Disclosures All Authors: No reported disclosures

scholarly journals Systematic Review of Normal Subjects Harbouring BCR-ABL1 Fusion Gene

2019 ◽  
Vol 143 (2) ◽  
pp. 96-111 ◽  
Author(s):  
Jew Win Kuan ◽  
Anselm Ting Su ◽  
Chooi Fun Leong ◽  
Motomi Osato ◽  
Goro Sashida
Keyword(s):  
Systematic Review ◽  
Fusion Gene ◽  
Normal Population ◽  
Quantitative Polymerase Chain Reaction ◽  
Normal Subjects ◽  
Poor Quality ◽  
Cross Sectional ◽  
Polymerase Chain

The treatment of chronic myeloid leukaemia (CML) requires quantitative polymerase chain reaction (qPCR) to monitor BCR-ABL1 in International Scale (IS). Some normal subjects were found to harbour BCR-ABL1. We performed a systematic review on normal subjects harbouring BCR-ABL1. A literature search was done on July 16, 2017 using EBSCOhost Research Databases interface and Western Pacific Region Index Medicus. Two authors selected the studies, extracted the data, and evaluated the quality of studies using the modified Appraisal Tool for Cross-Sectional Studies independently. The outcomes were prevalence, level of BCR-ABL1IS, proportion, and time of progression to CML. The initial search returned 4,770 studies. Eleven studies, all having used convenient sampling, were included, with total of 1,360 subjects. Ten studies used qualitative PCR and one used qPCR (not IS). The mean prevalence of M-BCR was 5.9, 15.5, and 15.9% in cord blood/newborns/infants (CB/NB/I) (n = 170), children (n = 90), and adults (n = 454), respectively, while m-BCR was 15, 26.9, and 23.1% in CB/NB/I (n = 786), children (n = 67), and adults (n = 208), respectively. No study reported the proportion and time of progression to CML. Nine studies were graded as moderate quality, one study as poor quality, and one study as unacceptable. The result of the studies could neither be inferred to the general normal population nor compared. Follow-up data were scarce.

scholarly journals Usefulness of TrueNat: A Chip-based Real-time PCR Test for COVID-19

2021 ◽  
Author(s):  
Swarnim Swarn ◽  
Indu Prasad ◽  
Amit Kumar Anand ◽  
Binod Shankar Singh
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Quantitative Polymerase Chain Reaction ◽  
Reaction System ◽  
Kappa Coefficient ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Cross Sectional ◽  
Percent Agreement ◽  
Polymerase Chain

Introduction: For the containment of growing Coronavirus Disease (COVID-19) pandemic, rapid diagnostic facilities are need of today. Indigenously developed TrueNat assay is a point-of-care assay developed for early diagnosis of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). It is a portable, fully automated, chip-based, real-time quantitative polymerase chain reaction system with a turnaround time of 1.5-2 hours. Aim: To assess the practical utility and diagnostic accuracy of TrueNat testing for COVID-19 in a pandemic situation. Materials and Methods: A cohort selection cross-sectional study was conducted from July to September 2020 at Department of Biochemistry, Vardhaman Institute of Medical Sciences, Pawapuri, Bihar, India, after obtaining Institutional Ethics Committee (IEC) approval. A total of 296 cases with symptoms of COVID-19 were selected for the study. Assuming real-time Reverse Transcription- Polymerase Chain Reaction (rRT-PCR) to be the gold standard, we collected oropharyngeal swabs from symptomatic COVID-19 suspected cases and tested by both TrueNat and standard RT-PCR. Agreement between both the assays were assessed by overall, Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) and Cohen’s kappa coefficient using Epitools (Ausvet 2020). Results: Out of 296 oropharyngeal swabs taken from suspected COVID-19 patients, 19 were read as “invalid” and discarded; hence only 277 samples were tested by TrueNat and RT-PCR both. Assuming RT-PCR as standard, TrueNat assay demonstrated an overall percent agreement of 99.64%, PPA of 95.65%, NPA 99.81%. The kappa coefficient was 0.9546. Conclusion: TrueNat assay offers a rapid, accurate and affordable technique for COVID-19. It may be deployed for mass screening and confirmation of COVID-19 cases in hospitals and remote areas.

scholarly journals Desain Sekuen Primer Dan Probe Quantitative Polymerase Chain Reaction Gen Spesifik RLEP Mycobacterium Leprae

2020 ◽  
Vol 7 (1) ◽  
pp. 1
Author(s):  
Asryadin Adhin
Keyword(s):  
Polymerase Chain Reaction ◽  
Quantitative Polymerase Chain Reaction ◽  
Mycobacterium Leprae ◽  
Chain Reaction ◽  
Cross Sectional ◽  
Polymerase Chain

Kusta merupakan salah satu penyakit menular yang disebabkan oleh Mycobacterium leprae. Diagnosis infeksi penting untuk tujuan studi epidemiologis, penegakan diagnosa serta pemberian terapi pengobatan yang tepat pada pasien terinfeksi. Kusta tahap awal sulit didiagnosis hanya melalui kriteria klinis karena sensitivitas pewarnaan yang cukup rendah. Selain itu, tes serologis berdasarkan antigen M. leprae  spesifik tidak mendeteksi semua kasus klinis karena sebagian besar pasien pada tahap infeksi paucibacillary (PB) tidak memberikan tingkat respons antibodi yang signifikan. Pengembangan metode deteksi M. leprae  berbasis qPCR dengan target sekuen gen RLEP penting dilakukan sehingga dapat dijadikan alternatif metode deteksi yang lebih baik Dalam penelitian ini, desain sekuen pasangan primer dan probe menggunakan teknologi bioinformatika.Tujuan dari penelitian ini adalah untuk melakukan desain sekuen pasangan primer dan probe untuk pemeriksaan M. leprae  berbasis kuantitatif Polymerase Chain Reaction  menggunakan sekuen gen RLEP. Desain penelitian adalah deskriptif dengan jenis studi cross sectional. Data yang diperoleh dianalisis secara deskriptif.Hasil penelitian diperoleh : primer forward : 5’-GTGCGGCCACATTGACCA-3’ ’; primer reverse : 3’-GGCTGTGCTGAAGGCGATATC-5’ ’'dengan panjang amplikon 126 pasang basa, dan sekuen probe : 5’-CGCCGACACCTCAAGGCCA-3’. Sekuen pasangan primer dan probe memenuhi syarat untuk q-PCR.

scholarly journals Torque teno sus virus 1 and 2 viral loads in faeces of porcine circovirus 2-positive pigs

2015 ◽  
Vol 84 (2) ◽  
pp. 91-95 ◽  
Author(s):  
Alessandra M. M. G. de Castro ◽  
Cintia M. Baldin ◽  
Cintia M. Favero ◽  
Priscilla F. Gerber ◽  
Rafael I. Cipullo ◽  
...  
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Porcine Circovirus ◽  
Age Group ◽  
Nursery Pigs ◽  
Viral Loads ◽  
Faecal Samples ◽  
Disease Condition ◽  
Porcine Circovirus 2 ◽  
Polymerase Chain ◽  
Torque Teno Sus Virus

Recently, studies have suggested an association between the Torque teno sus virus (TTSuV) and the Porcine circovirus-2 (PCV2) in PCV2-associated disease cases. The aim of this study was to verify TTSuVs loads in pig faeces from PCV2-positive animals with and without diarrhea from PCVAD-affected and PCV2-unvaccinated herds. A total of 80 faecal samples were collected individually from nursery and grow-finish pigs with (n = 40) or without (n = 40) diarrhea. The samples were tested for PCV2 and TTSuVs by using DNA binding dye SYBR Green quantitative polymerase chain reaction (qPCR). Torque teno sus virus k2 (TTSuVk2) load in the faeces was significantly higher in the nursery pigs with diarrhea, and these pigs also exhibited significantly higher PCV2 (P < 0.01) faecal matter loads compared to the non-diarrheic animals from the same age group. Torque teno sus virus 1 (TTSuV1) viral loads were the same regardless of age group and disease condition. There were no correlations between PCV2 and TTSuV1 or TTSuVk2 and TTSuV1 viral loads; however, a weak correlation (r = 0.23, P = 0.03) was found between TTSuVk2 and PCV2 viral loads. In conclusion, TTSuVk2 viral loads were significantly higher in the diarrheic faeces from the nursery pigs. Additionally, the higher loads of PCV2 and TTSuVk2 in the nursery-diarrheic animals revealed that diarrhea might have an important role in the spread of both viruses in herds.

Sign in / Sign up

Export Citation Format

Share Document