Tracking community infection dynamics of COVID-19 by monitoring SARS-CoV-2 RNA in wastewater, counting positive reactions by qPCR

Wastewater-based epidemiology has proved useful for monitoring the COVID-19 infection dynamics in communities. However, in some countries, low concentrations of SARS-CoV-2 RNA in wastewater make this difficult. Getting meaningful information from wastewater-based epidemiology in regions of low prevalence remains a key challenge. Here we used real-time reverse-transcription PCR (RT-qPCR) to monitor SARS-CoV-2 RNA in wastewater from October 2020 to February 2021 during the third wave of the COVID-19 outbreak in Japan. Viral RNA was below the limit of quantification in all samples. However, by counting the positive reactions in repeated qPCR of each sample, we found that the ratio of positive reactions to all tests in wastewater was significantly correlated with the number of clinically confirmed cases by the date of symptom onset during periods of both increasing and decreasing infection. Time-step analysis indicated that COVID-19 patients excreted large amounts of virus in their feces 2 days either side of symptom onset, which wastewater surveillance could detect. The positive count method is thus useful for tracing COVID-19 dynamics in regions of low prevalence.

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Method for analysis of ClO2 and Cl2 air emissions from pulp mill

Nordic Pulp & Paper Research Journal ◽

10.1515/npprj-2018-0012 ◽

2019 ◽

Vol 34 (1) ◽

pp. 19-27

Author(s):

Kimona Häggström ◽

Magnus Gunnarsson ◽

Katarina Bremert-Jirholm ◽

Nina Simic

Keyword(s):

Chlorine Dioxide ◽

Analytical Method ◽

Kraft Pulp ◽

Pulp Mill ◽

Air Emissions ◽

Pulp Mills ◽

Limit Of Quantification ◽

Regulatory Standards ◽

Low Concentrations ◽

Kraft Pulp Mills

Abstract Chlorine dioxide is commonly used as a bleaching agent in kraft pulp mills. Scrubbers are required to remove any remaining ClO2 from the plant tail gases. To control the air emissions of chlorine compounds, chlorine dioxide and chlorine contents must be monitored to ensure that the strict regulatory standards are met. However, the currently used analytical method is not suitable for detection of low concentrations of chlorine and chlorine dioxide. A new method for measuring chlorine dioxide and chlorine emissions was developed, which ensures compliance with the stringent requirements imposed by the authorities. The two species could be measured separately with a limit of quantification of 3 ppm. The method was robust and easy to use in the pulp mill environment and it was validated both in the laboratory and the field. The specificity of the method was demonstrated, Cl2 analysis was not sensitive to the presence of ClO2 and vice versa. The uncertainty (±2×RSD) of the analytical method in the field was estimated from duplicate measurements performed in the range of 3–500 ppm for ClO2 and 3–300 ppm for Cl2, and was found to be ±20 % and ±10 %, respectively. Possible interferences in the analytical method are also discussed.

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Stability-Indicating Photochemical Method for the Assay of Thiamine by Spectrophotometry

Journal of Spectroscopy ◽

10.1155/2018/3178518 ◽

2018 ◽

Vol 2018 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Iqbal Ahmad ◽

Syed Haider Abbas ◽

Zubair Anwar ◽

Muhammad Ali Sheraz ◽

Sofia Ahmed ◽

...

Keyword(s):

Limit Of Detection ◽

The United States ◽

Limit Of Quantification ◽

Chromatography Method ◽

Stability Indicating ◽

Low Concentrations ◽

Photochemical Method ◽

Significant Difference ◽

Liquid Chromatography Method ◽

States Pharmacopeia

A stability-indicating photochemical method has been developed for the assay of thiamine (TH) salts in aqueous solution and in fresh and aged vitamin preparations. It is based on the photooxidation of TH by UV irradiation to form thiochrome (TC) in alkaline solution. The TC : TH ratio under controlled conditions of light intensity, temperature, pH, exposure time, and irradiation distance is constant and can be used to determine the concentration of UV irradiated TH solutions. TC, on extraction with isobutanol from the photodegraded solution of TH, has been determined by the UV spectrophotometric method at 370 nm. It exhibits a high intensity of absorption in the UV region that can be used for the assay of even low concentrations of TH. Under optimum conditions, Beer’s law is obeyed in the concentration range of 0.20–2.00 mg/100 ml (R2 = 09998). The limit of detection (LOD) and limit of quantification (LOQ) are 0.0076 and 0.0231 mg/100 ml, respectively. The method has been validated and applied to aqueous solutions and vitamin preparations. The results have statistically been compared with the United States Pharmacopeia liquid chromatography method. It has been found that there is no significant difference between the two methods at 95% confidence level.

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Evaluation of Serological Tests for SARS-CoV-2: Implications for Serology Testing in a Low-Prevalence Setting

The Journal of Infectious Diseases ◽

10.1093/infdis/jiaa467 ◽

2020 ◽

Vol 222 (8) ◽

pp. 1280-1288 ◽

Cited By ~ 9

Author(s):

Katherine Bond ◽

Suellen Nicholson ◽

Seok Ming Lim ◽

Theo Karapanagiotidis ◽

Eloise Williams ◽

...

Keyword(s):

Symptom Onset ◽

Optimal Algorithm ◽

Point Of Care ◽

Performance Characteristics ◽

Serological Tests ◽

Specimen Collection ◽

Commercial Enzyme Immunoassay ◽

Low Prevalence ◽

Flow Devices

Abstract Background Robust serological assays are essential for long-term control of the COVID-19 pandemic. Many recently released point-of-care (PoCT) serological assays have been distributed with little premarket validation. Methods Performance characteristics for 5 PoCT lateral flow devices approved for use in Australia were compared to a commercial enzyme immunoassay (ELISA) and a recently described novel surrogate virus neutralization test (sVNT). Results Sensitivities for PoCT ranged from 51.8% (95% confidence interval [CI], 43.1%–60.4%) to 67.9% (95% CI, 59.4%–75.6%), and specificities from 95.6% (95% CI, 89.2%–98.8%) to 100.0% (95% CI, 96.1%–100.0%). ELISA sensitivity for IgA or IgG detection was 67.9% (95% CI, 59.4%–75.6%), increasing to 93.8% (95% CI, 85.0%–98.3%) for samples >14 days post symptom onset. sVNT sensitivity was 60.9% (95% CI, 53.2%–68.4%), rising to 91.2% (95% CI, 81.8%–96.7%) for samples >14 days post symptom onset, with specificity 94.4% (95% CI, 89.2%–97.5%). Conclusions Performance characteristics for COVID-19 serological assays were generally lower than those reported by manufacturers. Timing of specimen collection relative to onset of illness or infection is crucial in reporting of performance characteristics for COVID-19 serological assays. The optimal algorithm for implementing serological testing for COVID-19 remains to be determined, particularly in low-prevalence settings.

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Sources of Low Concentrations of Bisphenol A in Canned Beverage Products

Journal of Food Protection ◽

10.4315/0362-028x-73.8.1548 ◽

2010 ◽

Vol 73 (8) ◽

pp. 1548-1551 ◽

Cited By ~ 34

Author(s):

XU-LIANG CAO ◽

JEANNETTE CORRIVEAU ◽

SVETLANA POPOVIC

Keyword(s):

Bisphenol A ◽

Exposure Assessment ◽

Soft Drink ◽

Management Plan ◽

Limit Of Quantification ◽

Chemicals Management ◽

Low Concentrations ◽

Glass Bottles ◽

The Government

Although migration from can coatings is likely the source of bisphenol A (BPA) for the canned soft drink products with relatively high BPA concentrations, questions have been raised concerning the exact sources of BPA for those canned soft drink products with low BPA concentrations. Information is also needed for BPA concentrations in canned beer products to conduct proper exposure assessment for BPA under the Government of Canada's Chemicals Management Plan. In this work, 22 soft drink samples and 16 beer samples in both cans and plastic and/or glass bottles were analyzed for BPA. BPA was not detected in any of the soft drink samples in either plastic or glass bottles except for one product with a BPA concentration (0.018 μg/liter) close to the limit of quantification (0.015 μg/liter). BPA was detected in all of the corresponding soft drink products in cans, indicating that migration from can coatings is the likely source for BPA in canned products. Because considerable interference with ions m/z 213 and m/z 228 from sample matrices was observed for all beer samples, BPA concentrations in beer samples were measured using the ion m/z 270 instead. BPA was detected in only one of the seven beer products in glass bottles (0.054 μg/liter) but was detected in all corresponding beer samples in cans at low concentrations ranging from 0.081 to 0.54 μg/liter, indicating that migration from can coatings is likely the source of BPA in canned beer products.

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SARS-CoV-2 Infection in One Cat and Three Dogs Living in COVID-19-Positive Households in Madrid, Spain

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.779341 ◽

2021 ◽

Vol 8 ◽

Author(s):

Guadalupe Miró ◽

Javier Regidor-Cerrillo ◽

Rocio Checa ◽

Carlos Diezma-Díaz ◽

Ana Montoya ◽

...

Keyword(s):

Clinical Signs ◽

Nasal Discharge ◽

Virus Shedding ◽

Clinical Exam ◽

Reverse Transcription Pcr ◽

Infection Dynamics ◽

Variant Lineage ◽

Biochemical Profiles ◽

Alpha Variant ◽

Complete Blood Counts

In this study, we describe SARS-CoV-2 infection dynamics in one cat and three dogs from households with confirmed human cases of COVID-19 living in the Madrid Community (Spain) at the time of expansion (December 2020 through June 2021) of the alpha variant (lineage B.1.1.7). A thorough physical exam and nasopharyngeal, oropharyngeal, and rectal swabs were collected for real-time reverse-transcription PCR (RT-qPCR) SARS-CoV-2 testing on day 0 and in successive samplings on days 7, 14, 21, and 47 during monitoring. Blood was also drawn to determine complete blood counts, biochemical profiles, and serology of the IgG response against SARS-CoV-2. On day 0, the cat case 1 presented with dyspnea and fever associated with a mild bronchoalveolar pattern. The dog cases 2, 3, and 4 were healthy, but case 2 presented with coughing, dyspnea, and weakness, and case 4 exhibited coughing and bilateral nasal discharge 3 and 6 days before the clinical exam. Case 3 (from the same household as case 2) remained asymptomatic. SARS-CoV-2 detection by RT-qPCR showed that the cat case 1 and the dog case 2 exhibited the lowest cycle threshold (Ct) (Ct < 30) when they presented clinical signs. Viral detection failed in successive samplings. Serological analyses revealed a positive IgG response in cat case 1 and dog cases 3 and 4 shortly after or simultaneously to virus shedding. Dog case 2 was seronegative, but seroconverted 21 days after SARS-CoV-2 detection. SARS-CoV-2 genome sequencing was attempted, and genomes were classified as belonging to the B.1.1.7 lineage.

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Factors associated with prolonged viral shedding and impact of lopinavir/ritonavir treatment in hospitalised non-critically ill patients with SARS-CoV-2 infection

European Respiratory Journal ◽

10.1183/13993003.00799-2020 ◽

2020 ◽

Vol 56 (1) ◽

pp. 2000799 ◽

Cited By ~ 36

Author(s):

Dan Yan ◽

Xiao-Yan Liu ◽

Ya-nan Zhu ◽

Li Huang ◽

Bi-tang Dan ◽

...

Keyword(s):

Risk Factors ◽

Symptom Onset ◽

Antiviral Treatment ◽

Older Age ◽

Rna Detection ◽

Factors Associated ◽

Viral Shedding ◽

Reverse Transcription Pcr ◽

Independent Risk Factors ◽

The Impact

BackgroundThe duration of viral shedding is central to the guidance of decisions about isolation precautions and antiviral treatment. However, studies regarding the risk factors associated with prolonged shedding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the impact of lopinavir/ritonavir (LPV/r) treatment on viral shedding remain scarce.MethodsData were collected from all SARS-CoV-2 infected patients who were admitted to isolation wards and had reverse transcription PCR conversion at the No. 3 People's Hospital of Hubei province, China, between 31 January and 9 March 2020. We compared clinical characteristics and SARS-CoV-2 RNA shedding between patients initiated with LPV/r treatment and those without. Logistic regression analysis was employed to evaluate the risk factors associated with prolonged viral shedding.ResultsOf 120 patients, the median age was 52 years, 54 (45%) were male and 78 (65%) received LPV/r treatment. The median duration of SARS-CoV-2 RNA detection from symptom onset was 23 days (interquartile range 18–32 days). Older age (OR 1.03, 95% CI 1.00–1.05; p=0.03) and the lack of LPV/r treatment (OR 2.42, 95% CI 1.10–5.36; p=0.029) were independent risk factors for prolonged SARS-CoV-2 RNA shedding. Patients who initiated LPV/r treatment within 10 days from symptom onset, but not initiated from day 11 onwards, had significantly shorter viral shedding duration compared with those without LPV/r treatment (median 19 days versus 28.5 days; log-rank p<0.001).ConclusionOlder age and the lack of LPV/r treatment were independently associated with prolonged SARS-CoV-2 RNA shedding in patients with coronavirus disease 2019 (COVID-19). Earlier administration of LPV/r treatment could shorten viral shedding duration.

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Analytical Performance of 4 Automated Assays for Measurement of Cystatin C

Clinical Chemistry ◽

10.1373/clinchem.2009.141531 ◽

2010 ◽

Vol 56 (8) ◽

pp. 1336-1339 ◽

Cited By ~ 19

Author(s):

Jinong Li ◽

Willard Dunn ◽

Autumn Breaud ◽

Debra Elliott ◽

Lori J Sokoll ◽

...

Keyword(s):

Cystatin C ◽

Limit Of Detection ◽

Reference Interval ◽

Comparison Method ◽

Analytical Performance ◽

Regression Equations ◽

Limit Of Quantification ◽

Serum Pool ◽

Low Concentrations ◽

Deming Regression

BACKGROUND We evaluated the analytical performance of 4 cystatin C assays (Siemens N Latex on BNII, Roche Tina-quant on Cobas c501, Genzyme on Cobas c501, and Tosoh ST AIA-PACK on Tosoh AIA-600II) according to guidelines published by the Clinical and Laboratory Standards Institute. METHODS We evaluated total imprecision, limit of detection, and limit of quantification for each assay using patient serum pools and linearity/recovery using serial dilutions of a patient serum pool with cystatin C–free serum. We compared patients (n = 102) using the Siemens assay as a comparison method. RESULTS All assays had limits of detection and quantification <0.08 and <0.39 mg/L, respectively. Total CVs were generally higher than the manufacturers' claims for all assays. The Roche assay overrecovered cystatin C, particularly at low concentrations (mean recovery 119%, 142% at 0.587 mg/L). Deming regression equations were y = 1.184x + 0.089, Sy|x = 0.246 for Genzyme; y = 0.937x + 0.231, Sy|x = 0.231 for Roche; and y = 1.010x + 0.216, Sy|x = 0.115 for Tosoh. The Genzyme assay appeared to report higher results than the Siemens assay, which is consistent with a higher reference interval specified by the manufacturer. CONCLUSIONS Although all assays were acceptable for clinical use, their diagnostic performances were not optimal. Limitations include imprecision greater than claimed, overrecovery for the Roche assay on low concentration samples, and differences in results for patient samples. The latter situation requires assay-specific cystatin C–based glomerular filtration rate prediction equations at least until calibration is standardized using the international cystatin C calibrator now being developed.

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Conflicting Effects of Climate and Vector Behavior on the Spread of a Plant Pathogen

Phytobiomes Journal ◽

10.1094/pbiomes-01-17-0004-r ◽

2017 ◽

Vol 1 (1) ◽

pp. 46-53 ◽

Cited By ~ 13

Author(s):

Matthew P. Daugherty ◽

Adam R. Zeilinger ◽

Rodrigo P. P. Almeida

Keyword(s):

Symptom Onset ◽

Plant Pathogen ◽

Climatic Conditions ◽

Interactive Effects ◽

Disease Dynamics ◽

Disease Symptoms ◽

Vector Population ◽

Infection Dynamics ◽

Higher Temperature ◽

Vector Behavior

Local climatic conditions are important determinants of disease dynamics through effects on vector population performance or distribution. Yet, climate may also be epidemiologically significant due to effects on host−pathogen infection dynamics. We developed a model to explore interactive effects between climate-mediated acceleration in disease phenology (i.e., faster incubation or symptom onset) and vector preference based on host symptom status. Higher incubation rates favored pathogen outbreaks, but more rapid symptom onset may constrain spread if vectors avoid symptomatic hosts. Next, we tested whether warmer conditions favored greater spread of the plant pathogen, Xylella fastidiosa, by its leafhopper vector, Graphocephala atropunctata. Inoculated and healthy plants were reared in two temperature-controlled greenhouses. At six times postinoculation, a healthy and inoculated plant were exposed to noninfective vectors, after which pathogen spread was evaluated. Incubation rate and symptom onset in infected hosts was significantly accelerated at higher temperature. Although there was a tendency for greater pathogen spread at higher temperature, the effect depended on time since inoculation. In later introductions, after disease symptoms manifest, vectors were more likely to be found on healthy hosts. Vector avoidance of symptoms, particularly for hosts reared at higher temperature, constrained pathogen spread at later introductions. These results indicate that climate and vector behavior may mediate interactively pathogen spread. Further consideration of such epidemiological complexities is needed to predict adequately the consequences of climate change for disease dynamics.

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Clinical illness with viable SARS-CoV-2 virus presenting 72 days after infection in an immunocompromised patient

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2021.120 ◽

2021 ◽

pp. 1-12

Author(s):

Carly M Hughes ◽

Gareth P Gregory ◽

Anna B Pierce ◽

Julian D Druce ◽

Mike Catton ◽

...

Keyword(s):

Public Health ◽

Symptom Onset ◽

Health Management ◽

Immunocompromised Patient ◽

Sputum Sample ◽

Initial Diagnosis ◽

Genomic Sequencing ◽

Clinical Illness ◽

Low Prevalence ◽

Management Issues

Abstract We present a case of late symptom onset of COVID-19 infection 72 days after initial diagnosis in an immunocompromised 53-year-old man. SARS-CoV-2 was cultured from his sputum sample at this time, and genomic sequencing suggested reinfection was unlikely. After receipt of convalescent plasma, SARS-CoV-2 became undetectable by PCR 111 days after diagnosis, although SARS-CoV-2 antibodies remained not detectable. This case posed difficult public health management issues in a low prevalence COVID-19 setting as the person required extended home isolation given his prolonged SARS-CoV-2 PCR detection.

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The Evaluation of the Detection of Cr(VI) in Leather

Analytica ◽

10.3390/analytica3010001 ◽

2021 ◽

Vol 3 (1) ◽

pp. 1-13

Author(s):

Stefan John Davis ◽

William Robert Wise ◽

Sandro Recchia ◽

Andrea Spinazzè ◽

Maurizio Masi

Keyword(s):

Supply Chain ◽

Hexavalent Chromium ◽

Marked Improvement ◽

Colorimetric Method ◽

Test Methods ◽

Standard Test ◽

Quantitative Detection ◽

Current Standard ◽

Limit Of Quantification ◽

Low Concentrations

The topic of hexavalent chromium (Cr(VI)) in leather has been debated throughout the whole supply chain for years. However, its significance has recently increased due to proposed changes in European legislation concerned with skin-sensitising substances suggesting that acceptable Cr(VI) concentrations in leather goods should be lowered from 3 mg kg−1 to 1 mg kg−1. The proposition of a stricter limit and current analytical difficulties created the need for a review of current standard test methods. The research presented in this paper investigates both the colorimetric (Part 1) and chromatographic (Part 2) methods under BS EN ISO 17075. The focus of the study was to identify possible sources of interference leading to large statistical variance in results and to define the limit of quantification with respect to the proposed new compliance limit. This study into the colorimetric method has shown that the presence of Cr(III), dyes, and proteins can be significant interferences, becoming critical at low Cr(VI) concentrations. Dilution factors worsen the problem of detecting low concentrations: a reliable quantitative detection of 0.01 mg kg−1 and 0.003 mg kg−1 Cr(VI) in solution are required at the 3 mg kg−1 and 1 mg kg−1 compliance limits in leather, respectively. BS EN ISO 17075 part 1 was shown to be incapable of reliably resolving to 3 mg kg−1 or below in leather. Part 2 shows a marked improvement in detection limits and reliability; however, data suggest that 1 mg kg−1 Cr(VI) is not reliably detectable in leather. Suggested improvements to the established test methods and a possible alternative are discussed.

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