scholarly journals The Need of Non-traditional Techniques to Screen for the Virus

2020 ◽  
Vol 8 (T1) ◽  
pp. 1-2
Author(s):  
Davide Borroni ◽  
Kunal Gadhvi

BACKGROUND: At the present moment, the etiological diagnosis of SARS-CoV-2 is based on the polymerase chain reaction (PCR). False negative cases are increasingly reported in several studies using reverse transcription-PCR (RT-PCR). For example, the positive rate of RT-PCR for throat swabs was reported to be about 60% in early stage of COVID-19. AIM: We aimed to present metagenomic next-generation sequencing (mNGS) as a potential tool to detect pathogens. METHODS: In the recent year, mNGS is shown the potential to detect pathogens without the need of hypothesis guided approach and is proven to be highly effective. RESULTS: A recent prospective study in the United States compared the diagnostic performance of routine diagnostic tests with mNGS and showed that mNGS detected a bacteria or virus in the CSF of 13 of 58 patients presenting with meningoencephalitis who were negative for or not assessed with routine diagnostic test including PCR. NGS also has the advantage to cover entire viral genomes. CONCLUSION: As viral metagenomics has significantly improved in recent years and become more cost effective, we think that a change in the approach toward a shot-gun metagenomic testing should be explored and could potentially aid the diagnosis of COVID-19 cases and the management of this pandemic.

1995 ◽  
Vol 31 (5-6) ◽  
pp. 323-328 ◽  
Author(s):  
K. A. Reynolds ◽  
C. P. Gerba ◽  
I. L. Pepper

Sewage outfalls and storm water runoff introduces pathogenic human enteric viruses into marine coastal waters, which may pose a potential public health risk. Although members of the enterovirus group have been suggested as possible indicators of sewage pollution in marine waters, the lack of rapid, sensitive and cost effective methods have prevented routine monitoring in the United States. This study compared traditional cell culture and direct RT-PCR (reverse transcriptase-polymerase chain reaction) amplification for detection of an enterovirus. Poliovirus could be recovered from 100 L of artificial seawater with an average efficiency of 77%, using adsorption and elution from electronegative filters. Viruses were eluted from the filters with 1.5% beef extract for viruses (BEV) adjusted to pH 9.5 and reconcentrated by organic flocculation to a volume of 30 mL. Substances which interfered with detection by RT-PCR were removed by treatment of the concentrates with sephadex and chelex resins. Direct RT-PCR could detect 2.5 and 0.025 PFU (plaque forming units) for single (25 cycles) and double PCR (2 × 25 cycles) in 10 μL of pure culture poliovirus samples, respectively. These methods are currently being applied to assess the occurrence of enteroviruses at marine bathing beaches influenced by sewage discharges.


2020 ◽  
Vol 222 (10) ◽  
pp. 1612-1619 ◽  
Author(s):  
Christopher K C Lai ◽  
Zigui Chen ◽  
Grace Lui ◽  
Lowell Ling ◽  
Timothy Li ◽  
...  

Abstract Background Self-collected specimens have been advocated to avoid infectious exposure to healthcare workers. Self-induced sputum in those with a productive cough and saliva in those without a productive cough have been proposed, but sensitivity remains uncertain. Methods We performed a prospective study in 2 regional hospitals in Hong Kong. Results We prospectively examined 563 serial samples collected during the virus shedding periods of 50 patients: 150 deep throat saliva (DTS), 309 pooled-nasopharyngeal (NP) and throat swabs, and 104 sputum. Deep throat saliva had the lowest overall reverse-transcriptase polymerase chain reaction (RT-PCR)-positive rate (68.7% vs 89.4% [sputum] and 80.9% [pooled NP and throat swabs]) and the lowest viral ribonucleic acid (RNA) concentration (mean log copy/mL 3.54 vs 5.03 [sputum] and 4.63 [pooled NP and throat swabs]). Analyses with respect to time from symptom onset and severity also revealed similar results. Virus yields of DTS correlated with that of sputum (Pearson correlation index 0.76; 95% confidence interval, 0.62–0.86). We estimated that the overall false-negative rate of DTS could be as high as 31.3% and increased 2.7 times among patients without sputum. Conclusions Deep throat saliva produced the lowest viral RNA concentration and RT-PCR-positive rate compared with conventional respiratory specimens in all phases of illness. Self-collected sputum should be the choice for patients with sputum.


2003 ◽  
Vol 69 (6) ◽  
pp. 3158-3164 ◽  
Author(s):  
G. Shay Fout ◽  
Beth C. Martinson ◽  
Michael W. N. Moyer ◽  
Daniel R. Dahling

ABSTRACT Untreated groundwater is responsible for about half of the waterborne disease outbreaks in the United States. Human enteric viruses are thought to be leading etiological agents of many of these outbreaks, but there is relatively little information on the types and levels of viruses found in groundwater. To address this problem, monthly samples from 29 groundwater sites were analyzed for 1 year for enteroviruses, hepatitis A virus, Norwalk virus, reoviruses, and rotaviruses by multiplex reverse transcription-PCR (RT-PCR). A procedure with which to remove environmental RT-PCR inhibitors from groundwater samples was developed. The procedure allowed an average of 71 liters of the original groundwater to be assayed per RT-PCR, with an average virus recovery rate of 74%, based on seeded samples. Human enteric viruses were detected in 16% of the groundwater samples analyzed, with reoviruses being the most frequently detected virus group.


2017 ◽  
Vol 83 (6) ◽  
Author(s):  
Chao Liao ◽  
Yong Zhao ◽  
Luxin Wang

ABSTRACT This study developed RNA-based predictive models describing the survival of Vibrio parahaemolyticus in Eastern oysters (Crassostrea virginica) during storage at 0, 4, and 10°C. Postharvested oysters were inoculated with a cocktail of five V. parahaemolyticus strains and were then stored at 0, 4, and 10°C for 21 or 11 days. A real-time reverse transcription-PCR (RT-PCR) assay targeting expression of the tlh gene was used to evaluate the number of surviving V. parahaemolyticus cells, which was then used to establish primary molecular models (MMs). Before construction of the MMs, consistent expression levels of the tlh gene at 0, 4, and 10°C were confirmed, and this gene was used to monitor the survival of the total V. parahaemolyticus cells. In addition, the tdh and trh genes were used for monitoring the survival of virulent V. parahaemolyticus. Traditional models (TMs) were built based on data collected using a plate counting method. From the MMs, V. parahaemolyticus populations had decreased 0.493, 0.362, and 0.238 log10 CFU/g by the end of storage at 0, 4, and 10°C, respectively. Rates of reduction of V. parahaemolyticus shown in the TMs were 2.109, 1.579, and 0.894 log10 CFU/g for storage at 0, 4, and 10°C, respectively. Bacterial inactivation rates (IRs) estimated with the TMs (−0.245, −0.152, and −0.121 log10 CFU/day, respectively) were higher than those estimated with the MMs (−0.134, −0.0887, and −0.0732 log10 CFU/day, respectively) for storage at 0, 4, and 10°C. Higher viable V. parahaemolyticus numbers were predicted using the MMs than using the TMs. On the basis of this study, RNA-based predictive MMs are the more accurate and reliable models and can prevent false-negative results compared to TMs. IMPORTANCE One important method for validating postharvest techniques and for monitoring the behavior of V. parahaemolyticus is to establish predictive models. Unfortunately, previous predictive models established based on plate counting methods or on DNA-based PCR can underestimate or overestimate the number of surviving cells. This study developed and validated RNA-based molecular predictive models to describe the survival of V. parahaemolyticus in oysters during low-temperature storage (0, 4, and 10°C). The RNA-based predictive models show the advantage of being able to count all of the culturable, nonculturable, and stressed cells. By using primers targeting the tlh gene and pathogenesis-associated genes (tdh and trh), real-time RT-PCR can evaluate the total surviving V. parahaemolyticus population as well as differentiate the pathogenic ones from the total population. Reliable and accurate predictive models are very important for conducting risk assessment and management of pathogens in food.


2009 ◽  
Vol 84 (4) ◽  
pp. 1674-1682 ◽  
Author(s):  
Linlin Li ◽  
Amit Kapoor ◽  
Beth Slikas ◽  
Oderinde Soji Bamidele ◽  
Chunlin Wang ◽  
...  

ABSTRACT Circoviruses are known to infect birds and pigs and can cause a wide range of severe symptoms with significant economic impact. Using viral metagenomics, we identified circovirus-like DNA sequences and characterized 15 circular viral DNA genomes in stool samples from humans in Pakistan, Nigeria, Tunisia, and the United States and from wild chimpanzees. Distinct genomic features and phylogenetic analysis indicate that some viral genomes were part of a previously unrecognized genus in the Circoviridae family we tentatively named “Cyclovirus” whose genetic diversity is comparable to that of all the known species in the Circovirus genus. Circoviridae detection in the stools of U.S. adults was limited to porcine circoviruses which were also found in most U.S. pork products. To determine whether the divergent cycloviruses found in non-U.S. human stools were of dietary origin, we genetically compared them to the cycloviruses in muscle tissue samples of commonly eaten farm animals in Pakistan and Nigeria. Limited genetic overlap between cycloviruses in human stool samples and local cow, goat, sheep, camel, and chicken meat samples indicated that the majority of the 25 Cyclovirus species identified might be human viruses. We show that the genetic diversity of small circular DNA viral genomes in various mammals, including humans, is significantly larger than previously recognized, and frequent exposure through meat consumption and contact with animal or human feces provides ample opportunities for cyclovirus transmission. Determining the role of cycloviruses, found in 7 to 17% of non-U.S. human stools and 3 to 55% of non-U.S. meat samples tested, in both human and animal diseases is now facilitated by knowledge of their genomes.


2014 ◽  
Vol 24 (8) ◽  
pp. 1480-1485 ◽  
Author(s):  
Britt K. Erickson ◽  
Laura M. Divine ◽  
Charles A. Leath ◽  
J. Michael Straughn

ObjectiveThe objective of this study was to determine the costs and outcomes of inguinal-femoral lymph node dissection (IF-LND) versus sentinel lymph node biopsy (SLNB) for the management of early-stage vulvar cancer.MethodsA cost-effectiveness model compared 2 different strategies for the management of early-stage vulvar cancer: (1) vulvectomy and SLNB and (2) vulvectomy and IF-LND. Probabilities of inguinal-femoral node metastases and recurrence rates associated with each strategy were estimated from published data. Actual payer costs of surgery and radiation therapy were obtained using 2012 CPT codes and Medicare payment information. Rates and costs of postoperative complications including lymphedema, lymphocyst formation, and infection were estimated and included in a separate model. Cost-effectiveness ratios were determined for each strategy. Sensitivity analyses were performed to evaluate pertinent uncertainties in the models.ResultsFor the estimated 3000 women diagnosed annually with early-stage vulvar cancer in the United States, the annual cost of the SLNB strategy is $65.2 million compared with $76.8 million for the IF-LND strategy. Three-year inguinal-femoral recurrence-free survival was similar between groups (96.9% vs 97.3%). This translates into a lower cost-effectiveness ratio for the SLNB strategy ($22,416), compared with the IF-LND strategy ($26,344). When adding complication costs to the model, cost-effectiveness ratios further favor the SLNB strategy ($23,711 vs $31,198). Sensitivity analysis revealed that the SLNB strategy remained cost-effective until the recurrence rate after a negative sentinel lymph node approaches 9%.ConclusionsSentinel lymph node biopsy is the most cost-effective strategy for the management of patients with early-stage vulvar cancer due to lower treatment costs and lower costs due to complications.


Author(s):  
Lingjie Song ◽  
Guibao Xiao ◽  
Xianqin Zhang ◽  
Zhan Gao ◽  
Shixia Sun ◽  
...  

AbstractIn 2019, a novel coronavirus (SARS-CoV-2) was first discovered in Wuhan, Hubei, China, causing severe respiratory disease in humans, and has been identified as a public health emergency of international concern. With the spread of the virus, there are more and more false negative cases of RT-PCR nucleic acid detection in the early stage of potential infection. In this paper, we collected the epidemiological history, clinical manifestations, outcomes, laboratory results and images of a SARS-CoV-2 carrier with no significant past medical history. The patient was quarantined because of her colleague had been diagnosed. After the onset of clinical symptoms, chest CT results showed patchy ground-glass opacity (GGO) in her lungs, but it took a total of nine nucleic acid tests to confirm the diagnosis, among which the first eight RT-PCR results were negative or single-target positive. In addition to coughing up phlegm during her stay in the hospital, she did not develop chills, fever, abdominal pain, diarrhea and other clinical symptoms. Since initial antiviral treatment, the lung lesions were absorbed. But the sputum nucleic acid test was still positive. In combination with antiviral and immune therapy, the patient tested negative for the virus. Notably, SARS-CoV-2 was detected only in the lower respiratory tract samples (sputum) throughout the diagnosis and treatment period. This is a confirmed case of SARS-CoV-2 infection with common symptoms, and her diagnosis has undergone multiple false negatives, suggesting that it is difficult to identify certain carriers of the virus and that such patients may also increase the spread of the SARS-CoV-2.


Author(s):  
Karrie K. K. Ko ◽  
Nurdyana Binte Abdul Rahman ◽  
Shireen Yan Ling Tan ◽  
Kenneth X. L. Chan ◽  
Sui Sin Goh ◽  
...  

Accurate diagnostic detection of SARS-CoV-2 currently depends on the large-scale deployment of RT-PCR assays. SARS-CoV-2 RT-PCR assays target predetermined regions in the viral genomes by complementary binding of primers and probes to nucleic acid sequences in the clinical samples.


Author(s):  
Aso Faeq Salih ◽  
Adnan Mohammed Hamawand ◽  
Riyadh Abd Aljabbar Sattar

Most ofnewborns with Congenital Heart Defects (CHDs) can be detected by using echocardiography. However, if such defects are not diagnosed in earlier time, therefore a severe hypoxemia, shock, acidosis and death are considered of some potential sequelae. A prospective study from January 2012 to the end of 2013 was performed and 2181 neonates were enrolled in the study. The pulse oximetry screening (POS) for both hands and one foot were obtained within the first 3-6 hours of life, when post ductal saturation was below 90%, it was considered as a positive screening, while when the saturation is between 90-95% and the difference between pre-and post-ductal saturation was more than 3%, the baby was provisionally considered to be screening as a positive then echocardiography is planned. Among 100 positive POS babies, 45 (45%) of them were detected with CHS, 12 (12%) was with a major CHS and 33 (33%) was with a minor CHS. Out of 12 patients with a major CHD 6 of them (50%) were asymptomatic at the time of POS.POS result was a true negative in 2078 patients, a true positive in 45 patients, false negative in 3 patients, and false positive in 55 and 28/55 of the false positive rate with POS had other pathology. The false positive rate with pulse oximetry screening is (55/2081) = 0.26%. Sensitivity, specificity, positive and negative predictive value for POS in detection of major CHD were 80%, 97.29%, 17.9% and 99.80%, respectively. Pulse oximetry screening is significantly improving the detection of life threatening congenital heart disease at an early stage.


Author(s):  
Yunbao Pan ◽  
Xinran Li ◽  
Gui Yang ◽  
Junli Fan ◽  
Yueting Tang ◽  
...  

AbstractAn outbreak of new coronavirus SARS-CoV-2 was occurred in Wuhan, China and rapidly spread to other cities and nations. The standard diagnostic approach that widely adopted in the clinic is nuclear acid detection by real-time RT-PCR. However, the false-negative rate of the technique is unneglectable and serological methods are urgently warranted. Here, we presented the colloidal gold-based immunochromatographic (ICG) strip targeting viral IgM or IgG antibody and compared it with real-time RT-PCR. The sensitivity of ICG assay with IgM and IgG combinatorial detection in nuclear acid confirmed cases were 11.1%, 92.9% and 96.8% at the early stage (1-7 days after onset), intermediate stage (8-14 days after onset), and late stage (more than 15 days), respectively. The ICG detection capacity in nuclear acid-negative suspected cases was 43.6%. In addition, the consistencies of whole blood samples with plasma were 100% and 97.1% in IgM and IgG strips, respectively. In conclusion, serological ICG strip assay in detecting SARS-CoV-2 infection is both sensitive and consistent, which is considered as an excellent supplementary approach in clinical application.


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