Rapid detection of Salmonella typhimurium by photonic PCR-LFIS dual mode visualization

Salmonella spp., as one of the foodborne pathogens, is a severe threat to global public health. Rapid screening of salmonella spp. in contaminated food with low infective doses is the key to preventing food poisoning. In this study, a fast visualization method for detecting Salmonella typhimurium (S. typhimurium) was developed based on photonic PCR and AuNPs lateral-flow immunochromatography strip (LFIS). In addition, quantitative detection of target bacteria could be achieved by utilizing the photothermal effect of AuNPs, and the sensitivity could be improved by amplifying the photothermal signal. On the optimized conditions, the developed photonic PCR-LFIS assay was highly sensitive, with a detection limit as low as 19 cfu mL-1 of bacteria in pure culture after laser irradiation, and highly specific, exhibiting no cross-reaction with Salmonella enteritidis, Listeria monocytogenes, Escherichia coli, and Staphylococcus aureus. Notably, S. typhimurium could be detected in pork, egg white, and milk without pre-treatment, with the recovery rates of the three samples between 81 % and 109 %. In conclusion, the photonic PCR-LFIS assay realizes sensitive, simple, and rapid detection of S. typhimurium.

Clinical evaluation of a modified SARS-CoV-2 rapid molecular assay, ID NOW ™ COVID-19 2.0

In the diagnosis of coronavirus disease 2019 (COVID-19), several types of instruments and reagents for SARS-CoV-2 nucleic acid testing have been introduced to meet clinical needs. We evaluated the clinical performances of ID NOW™ COVID-19 2.0 (ID NOW™ 2.0), which is capable of detecting SARS-CoV-2 within 12 min as part of point-of-care testing (POCT). Patients who displayed COVID-19 related symptoms, and who were tested for screening purposes, were recruited to this study. Two nasopharyngeal swabs were collected and tested using the ID NOW™ 2.0 test. Reference testing was performed using the cobas 8800 or 6800 (reagents: cobas SARS-CoV-2 and Flu A/B). A total of 38 samples and 46 samples were tested positive and negative, respectively, by the reference test. The ID NOW™ 2.0 showed a sensitivity of 94.7% (95% CI: 82.3-99.4) and a specificity of 100% (95% CI: 92.3-100). Samples that were positive by reference testing had cycle threshold (Ct) values ranging from 11.90 to 35.41. Among these reference positive samples, two samples were negative by ID NOW™ 2.0 with Ct values of 35.25 and 35.41. For samples with Ct values < 35, the sensitivity of ID NOW™ 2.0 was 100%. In Japan, the restrictions related to COVID-19 have been relaxed, however the COVID-19 epidemic still continues. ID NOW™ 2.0 is expected to be used as a rapid and reliable alternative to laboratory-based RT-PCR methods.

What contributes to the re-positive nucleic acid test results for the omicron variant of SARS-CoV-2 in the shelter cabin hospital in Shanghai, China?

Background

Despite the increasing reports of re-positive SARS-CoV-2 cases after recovery and discharge from hospitals, our knowledge remains very limited regarding the contributing factors of re-positivity and its roles in the transmission and epidemiology of the Omicron variant.

Methods

In this retrospective study, re-positivity is defined as the positive nucleic acid result (Ct < 35) following two consecutive negative results during hospitalization. A total of 751 patients from Shanghai Shelter Cabin Hospital were enrolled and divided with a ratio of about 1:2 into the re-positivity group and the non-re-positivity group. Patients required three consecutive negative results daily as the de-isolation criterion. The follow-up time of discharged patients lasted five weeks. Univariate regression analysis was used to compare variables between the re-positivity and non-re-positivity groups, and the single re-positivity and multiple re-positivity groups, with P < 0.05 defined as the statistical significance of differences. Subsequently, variables with P < 0.2 were subjected to multivariate logistic regression analysis to investigate the odds ratio (OR) of re-positivity and the influencing factors of re-positivity of the Omicron variant.

Results

The re-positivity group had a higher proportion of males (68.1% vs 58.1%, p = 0.000), a higher education level (31.9% vs 12.7%, p = 0.007), a longer hospitalization duration (13 days vs 8 days, p = 0.000), and a higher Convidecia vaccination rate (6.0% vs 2.4%, p = 0.011). Further multivariable analysis showed male (OR = 2.168, p = 0.000), Convidecia vaccination (OR = 2.634, p = 0.014), hospitalization duration (OR = 2.146, p = 0.000) and education level (OR = 1.595, p = 0.007) were associated with re-positivity. The average rate of re-positivity was 25% during hospitalization and decreased to 0.4% among discharged patients. Re-positivity was more common in the period with a larger number of hospitalized patients and in larger wards with a larger number of patients.

Conclusion

A large number of hospitalized patients, large-sized wards, and gender are significant contributing factors to re-positivity. Division of the shelter cabin hospital into small independent wards and requirement of three consecutive results daily as the de-isolation criterion might be more beneficial to the control and prevention of the spread of the Omicron variant.

Wearable nucleic acid testing platform - A perspective on rapid self-diagnosis and surveillance of infectious diseases

Wearable biosensors (WB) are currently attracting considerable interest for rapid detection and monitoring of biomarkers including metabolites, protein, and pathogen in bodily fluids (e.g., sweat, saliva, tears, and interstitial fluid). Another branch of WB termed wearable nucleic acid testing (NAT) is blossoming thanks to the development of microfluidic technology and isothermal nucleic acid amplification technique (iNAAT); however, there are only few reports on this. The wearable NAT is an emerging field of point-of-care (POC) diagnostics, and holds the promise for time-saving self-diagnosis, and evidence-based surveillance of infectious diseases in remote or low-resource settings. The use of wearable NAT can also be advanced to include molecular diagnosis, the identification of cancer biomarkers, genetic abnormalities, and other aspects. The wearable NAT provides the potential for evidence-based surveillance of infectious diseases when combined with internet connectivity and App software. To make the wearable NAT accessible to the end users, however, improvements must be made to the fabrication, cost, speed, sensitivity, specificity, sampling, iNAAT, analyzer, and a few other features. So, in this paper, we looked at the wearable NAT's most recent development, identified its difficulties, and defined its potential for managing infectious diseases quickly in the future. This is the wearable NAT review's first effort. We expect that this article will provide the concise resources needed to develop and deploy an efficient wearable NAT system.

Economic Evaluation of Nucleic Acid Testing for Screening of Blood Donations for Thalassemia Patients (ECONAT) in Western India

Background

Transfusion Transmitted infections(TTI) are of significant concern for blood safety. The thalassemia patients who receive multiple transfusions are at an increased risk of TTIs and the Nucleic Acid Test (NAT ) has been advocated for safe blood. Though NAT can reduce the window period compared to serology, cost is a constraint.

Methods

The thalassemia patient and NAT yield data from the centralized NAT lab in AIIMS Jodhpur was evaluated for cost-effectiveness using the Markov model. The incremental cost-effectiveness ratio (ICER) was calculated by dividing the difference between the cost for NAT and the cost of medical management of TTI-related complications by the product of the difference in utility value of a TTI health state with time and Gross National Income(GNI) per capita.

Results

Out of the 48,762 samples tested by NAT, 43 samples were discriminated NAT yield all of which were reactive for Hepatitis B (NAT yield of 1:1134). There was no HCV and HIV NAT yield despite HCV being the most prevalent TTI in this population. The cost of this intervention was INR 5,85,14,400. The number of lifetime QALY saved was 1.38 years. The cost of medical management is INR 82,19,114. Therefore the ICER for intervention is INR 3,64,45,860 per QALY saved which is 274 times the GNI per capita of India.

Conclusions

The provision of IDNAT-tested blood for thalassemia patients in Rajasthan state was not found to be cost-effective. Measures to bring down the cost or alternative options to increase blood safety should be explored.

Fluorescence-based simultaneous dual oligo sensing of HCV genotypes 1 and 3 using magnetite nanoparticles

Nucleic acid tests (NATs) have gained an important position in biosensing in the context of the increasing need to meet the stringent requirements for accurate diagnosis of infectious diseases with high sensitivity and selectivity. Recently, the development of new strategies towards multiplex detection of analytes in a single assay is gaining impetus since such an approach would lead to high throughput analysis, leading to substantial benefits in terms of time, infrastructure, labor, and cost. In this work, we demonstrate a facile fluorescence-based simultaneous dual oligo sensing of genotypes 1 and 3 by employing two target sequences (36-mers each) derived from the NS4B and NS5A regions of HCV genome, respectively. A set of 18-mer amine-tagged probes and another set of 18-mer fluorescently-labeled probes that were complementary to each half of the 36-mer target sequences were designed. The amine-tagged probes were immobilized over aldehyde-derivatized magnetite nanoparticles (NPs) via imine bond formation, which was characterized using X-ray photoelectron spectroscopy (XPS) and energy dispersive spectroscopy (EDS) mapping techniques. The successful hybridization between the two probes with their target followed by magnetic removal of the NPs from the solution enabled quantitative analysis of the target by measuring the fluorescence intensity of the residual concentration of the fluorescently-tagged probe. In this manner, the targets corresponding to genotypes 1 and 3 were simultaneously detected with the detection limit in the range of 10-15 nM. The current strategy can potentially be amalgamated with existing nanotechnology-based techniques towards multiplex oligo sensing of several pathogens.

Cost-effectiveness analysis on COVID-19 surveillance strategy of large-scale sports competition

Background

Nucleic acid test (NAT) could effectively control the spread of COVID-19 caused by large-scale sports competitions. However, quantitative analysis on the appropriate frequency of NAT is scarce, and the cost-effectiveness and necessity of high-frequency NAT remain to be fully explored and validated. This study aims to optimize the COVID-19 surveillance strategies through cost-effectiveness analysis for the Tokyo 2020 Olympic Games and the upcoming Beijing 2022 Olympic Winter Games.

Methods

A total of 18 scenarios were designed regarding the NAT frequency, symptom monitoring, and strengthening close-contact control. An agent-based stochastic dynamic model was used to compare the cost-effectiveness of different NAT scenarios and optimize the surveillance strategies. The dynamics of the proposed model included the arrival and departure of agents, transmission of the disease according to Poisson processes, and quarantine of agents based on regular NATs and symptom onset. Accumulative infections, cost, and incremental cost-effectiveness ratio (ICER) were simulated in the frame of the model. ICER was used to compare the cost-effectiveness of different scenarios. Univariate sensitivity analysis was performed to test the robustness of the results.

Results

In Scenario 16, where the competition-related personnel (CRP) received NAT daily and national sports delegation (NSD) with quarantined infections accepted an additional NAT daily, accumulative infection was 320.90 (90 initial infections), the total cost was (United States Dollar) USD 8 920 000, and the cost of detecting out each infection was USD 27 800. Scenario 16 would reduce the total cost by USD 22 570 000 (avoid 569.61 infections), USD 1 420 000 (avoid 47.2 infections) compared with Scenario 10 (weekly NAT, strengthened close contact control) and Scenario 7 (daily NAT, no strengthened close contact control), respectively. Sensitivity analysis showed that the result was most sensitive to the change in basic reproductive number.

Conclusions

High-frequency NATs such as bidaily, daily, and twice a day were cost-effective. NAT daily for CRP with strengthening close-contact control could be prioritized in defense against COVID-19 at large-scale sports competitions. This study could assist policymakers by assessing the cost-effectiveness of NAT scenarios and provide the host country with an optimal COVID-19 surveillance strategy.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s40249-022-00955-3.

Rapid point-of-care testing for SARS-CoV-2 virus nucleic acid detection by an isothermal and nonenzymatic Signal amplification system coupled with a lateral flow immunoassay strip

An outbreak of a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), began in December 2019. Accurate, rapid, convenient, and relatively inexpensive diagnostic methods for SARS-CoV-2 infection are important for public health and optimal clinical care. The current gold standard for diagnosing SARS-CoV-2 infection is reverse transcription-polymerase chain reaction (RT-PCR). However, RTPCR assays are designed for use in well-equipped laboratories with sophisticated laboratory infrastructure and highly trained technicians, and are unsuitable for use in under-equipped laboratories and in the field. In this study, we report the development of an accurate, rapid, and easy-to-implement isothermal and nonenzymatic signal amplification system (a catalytic hairpin assembly (CHA) reaction) coupled with a lateral flow immunoassay (LFIA) strip-based detection method that can detect SARSCoV-2 in oropharyngeal swab samples. Our method avoids RNA isolation, PCR amplification, and elaborate result analysis, which typically takes 6-8 h. The entire CHA-LFIA detection method, from nasopharyngeal sampling to obtaining test results, takes less than 90 min. Such methods are simple and require no expensive equipment, only a simple thermostatically controlled water bath and a fluorescence reader device. We validated our method using synthetic oligonucleotides and clinical samples from 15 patients with SARS-CoV-2 infection and 15 healthy individuals. Our detection method provides a fast, simple, and sensitive (with a limit of detection (LoD) of 2000 copies/mL) alternative to the SARS-CoV-2 RT-PCR assay, with 100 % positive and negative predictive agreements.

[Application of anti-HCV and HCV RNA detection in intravenous drug users]

Objective: To explore the diagnostic value of anti-HCV and HCV RNA so as to provide an accurate and efficient detection strategy for the diagnosis of HCV in intravenous drug users. Methods: 527 plasma samples from intravenous drug users were collected, and preliminary anti-HCV ELISA screening test was performed. A recombinant immunoblot assay (RIBA) was used as confirmatory assay for reactive antibody samples. All samples were tested for HCV RNA, followed by analysis of anti-HCV screening test, RIBA and HCV nucleic acid test results. Results: Anti-HCV ELISA results were reactive in 386 out of 527 intravenous drug users and non-reactive in 141. Among the 386 reactive antibody samples detected by RIBA, 370 cases were anti-HCV positive, 6 cases were anti-HCV indeterminate and 10 cases were anti-HCV negative. Anti-HCV ELISA and RIBA positive coincidence detection rate was 95.85% (370/386), and 70.21% (370/527) among intravenous drug users. HCV RNA was negative in all 10 anti-HCV RIBA non-reactive samples. 376 anti-HCV RIBA-positive and indeterminate samples were tested for HCV RNA, of which 56.93% (300/527) were current HCV infection, and 14.42% (76/527) were past HCV infection. Among 141 anti-HCV ELISA negative samples, the residual risk by anti-HCV ELISA screening for HCV RNA was 1.52% (8/527). HCV viral load distribution among intravenous drug users showed that the high viral load value (>10(7) IU/ml) and low viral load values (< 10(2) IU/ml) accounted for 1.95% and 2.27%, respectively, while the samples with viral load value of 1×10(2) ~ 1×10(7) IU/ mL accounted for 95.78% (295/308), and were mainly distributed in 1×10(5) ~ 1×10(6) IU/ml (37.99%). ELISA + RIBA + NAT assay detection strategies had differentiated 300 cases of current HCV infection, 76 cases of past HCV infection and 10 cases of false positive anti-HCV results, while ELISA+NAT assay detection strategies had only detected 300 cases of current HCV infection. However, of the 386 positive subjects screened for antibodies, 10 (2.59%) were undifferentiated false positives. Conclusion: Intravenous drug users are the high-risk population of HCV infection with high prevalence and high viral load. Anti-HCV screening for intravenous drug users will have a certain degree of residual risk. Therefore, anti-HCV ELISA screening and nucleic acid detection strategy can accurately diagnose the current infected patients; however, it cannot distinguish the false positive results of antibody screening.

Novel automated sample-to-result SARS-CoV-2 laboratory-developed RT-PCR assay for high-throughput testing using LabTurbo AIO 48 system

•

LabTurbo AIO 48 can accurately identify SARS-CoV-2 infection.

•

LabTurbo AIO 48 can reduce by ~ 47.9% the sample-to-result time.

•

LabTurbo AIO 48 is more sensitive than the reference detection assay.

•

LabTurbo AIO 48 can provide high-throughput and reliable SARS-CoV-2 diagnostic results.

Background and aims

Immediate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for preventing the spread of coronavirus disease 2019 (COVID-19). The LabTurbo AIO 48 system is an automated platform that allows nucleic acid extraction and sample analysis on the same instrument, producing faster results without affecting their accuracy. We aimed to independently evaluate the LabTurbo AIO 48 (all-in-one system) for SARS-CoV-2 detection.

Materials and methods

Comparative limit of detection (LOD) was assessed on both the LabTurbo AIO 48 and current standard detection system based on real-time reverse transcriptase polymerase chain reaction (RT-PCR), using SARS-CoV-2 RNA control. Additional 125 primary clinical samples were assessed using both the protocols in parallel.

Results

The turnaround time from sample to results for 48 samples analyzed on LabTurbo AIO 48 was approximately 2.5 h, whereas that analyzed using the in-house RT-PCR protocol was 4.8 h. LabTurbo AIO 48 also demonstrated higher sensitivity than our reference RT-PCR assay, with a LOD of 9.4 copies/reaction. The overall percentage agreement between both the methods for 125 samples was 100%.

Conclusion

LabTurbo AIO 48 is a robust detection option for SARS-CoV-2, allowing faster results and, consequently, aiding in better control and prevention of COVID-19.

Suspected SARS-CoV-2 infection with fever and coronary heart disease: A case report

BACKGROUND

The coronavirus disease 2019 (COVID-19) is an emerging infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Suspected cases accounted for a large proportion in the early stage of the COVID-19 outbreak. The deviation of the nucleic acid test by throat swab (the current gold standard of COVID-19) caused by variation in sampling techniques and reagent kits and coupled with nonspecific clinical manifestations make confirmation of the suspected cases difficult. Proper management of the suspected cases of COVID-19 is crucial for disease control.

CASE SUMMARY

A 65-year-old male presented with fever, lymphopenia, and chest computed tomography (CT) images similar to COVID-19 after percutaneous coronary intervention. The patient was diagnosed as having bacterial pneumonia with cardiogenic pulmonary edema instead of COVID-19. This was based on four negative results for throat swab detection of SARS-CoV-2 nucleic acid using reverse transcriptase-polymerase chain reaction assay and one negative result for serological antibody of SARS-CoV-2 with the serological assay. Additionally, the distribution of ground-glass opacities and thickened blood vessels from the CT images differed from COVID-19 features, which further supported the exclusion of COVID-19.

CONCLUSION

Distinguishing COVID-19 patients from those with bacterial pneumonia with cardiogenic pulmonary edema can be difficult. Therefore, it requires serious identification.

Recurrence of SARS-CoV-2 nucleic acid positive test in patients with COVID-19: a report of two cases

BACKGROUND

The recurrence of positive SARS-CoV-2 nucleic acid test results in patients with COVID-19 is becoming more important and warrants more attention.

CASE PRESENTATION

This study reports 2 cases, a child with mild COVID-19 and an adult female with moderate COVID-19, who were discharged after three consecutive negative nucleic acid tests and were later readmitted to the hospital for recurrence of SARS-CoV-2 nucleic acid positivity. By tracking the patients' symptoms, serum antibodies, and imaging manifestations after readmission, we found that they showed a trend of gradual improvement and recovery throughout treatment. They were cured without additional treatment, with the appearance of antibodies and the recovery of immune functions.

CONCLUSIONS

It is deemed extremely necessary to improve the discharge standard of care. At the same time, nucleic acid detection is recommended to increase the dynamic monitoring of serum antibodies and imaging, strengthen the management of discharged patients, and appropriately extend the home or centralized isolation time.

The impact of the COVID-19 pandemic on pediatric operations: a retrospective study of Chinese children

BACKGROUND

The aim of this study was to quantify the impact of coronavirus disease 2019 (COVID-19) on pediatric operations, and establish preoperative, intraoperative, and postoperative protocols to improve the pediatric operations.

METHODS

We here compare the number of patients who underwent surgery in Chongqing Medical University Affiliated Children's Hospital during the pandemic (January 23-March 11), after the pandemic (March 12-April 30), after our measures were put in place (May 1-May 21), and the equivalent period in 2019.

RESULT

During the COVID-19 pandemic, 62.68% fewer patients underwent surgery than during the homologous period of time 1 year earlier (P < 0.01). After the COVID-19 pandemic, the number of orchidopexy cases increased significantly from 175.14 to 504.57 per week (P < 0.01). The large number of patients that accrued in our hospital may have increased the risk of COVID-19 transmission. In response, hospitals and clinics have made protocols and reorganized healthcare facilities (e.g., performing nucleic acid tests (NAT), adding adequate personal protective equipment (PPE)) from May 1, 2020. After the measures were implemented, the number of operations performed remained stable and comparable to the pre-pandemic period. COVID-19 RNA detection was performed in 5104 cases and there were no new confirmed cases in our hospital.

CONCLUSION

This outbreak of COVID-19 has affected not only individuals with COVID-19 but also patients seeking surgical operations. Understanding the present situation helps clinicians provide a high level of treatment to all children.

Evaluation of the exposure risk of SARS-CoV-2 in different hospital environment

The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has imposed a significant impact on social and economic activities. As a high infectious pathogen, the existence of SARS-CoV-2 in public space is very important for its transmission. During the COVID-19 pandemic, hospitals are the main places to deal with the diseases. In this work, we evaluated the exposure risk of SARS-CoV-2 in hospital environment in order to protect healthcare workers (HCWs). Briefly, air and surface samples from 6 different sites of 3 hospitals with different protection levels were collected and tested for the SARS-CoV-2 nucleic acid by reverse transcription real-time fluorescence PCR method during the COVID-19 epidemic. We found that the positive rate of SARS-CoV-2 nucleic acid was 7.7 % in a COVID-19 respiratory investigation wards and 82.6 % in a ICUs with confirmed COVID-19 patients. These results indicated that in some wards of the hospital, such as ICUs occupied by COVID-19 patients, the nucleic acid of SARS-CoV-2 existed in the air and surface, which indicates the potential occupational exposure risk of HCWs. This study has clarified retention of SARS-CoV-2 in different sites of hospital, suggesting that it is necessary to monitor and disinfect the SARS-CoV-2 in hospital environment during COVID-19 pandemic, and will help to prevent the iatrogenic infection and nosocomial transmission of SARS-CoV-2 and to better protect the HCWs.

Biosafety threats of the rapidly established labs for SARS-CoV-2 tests in China

To increase the capacity of identifying coronavirus disease 2019 (COVID-19) infection, many Biosafety Level 2 (BSL-2) labs have been established in a short period of time for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid tests all over the world. However, their biosafety has not been evaluated, which could have been the first gateway to SARS-CoV-2 transmission. During 9-11 March 2020, the first comprehensive evaluation of the biosafety in all 89 labs qualified for conducting SARS-CoV-2 tests in Sichuan Province of China was conducted. The degree of compliance with 39 criteria in five categories was evaluated: biosafety requirements for lab activities (14 criteria), sample transfer, acceptance and management (6 criteria), waste management (9 criteria), personnel training and protection (4 criteria), and lab environmental disinfection, emergency plans and accident handling (6 criteria). Our results revealed that, although an overall median compliance rate of 94.6% for 39 criteria, only four of 89 labs met all of them. Criteria in personnel training and protection have been most satisfactorily met, followed by lab environmental disinfection, emergency plans and accident handling. The most severe risk was the lack of automatic doors at the main entrance or in core operation areas, especially among labs in CDC and hospitals. This risk, together with failure for keeping pressure in the core operation areas 25 ± 5 Pa (mainly among labs in the third-party testing agencies), may cause accidental exposure to biological agents from lab activities. Other severe risk included failure for standard labeling of SARS-CoV-2 wastes and lacking regular monitoring of sterilization effects. Our findings would provide experiences and lessons for strengthening lab biosafety in other Chinese provinces, and also serve as an important reference for many other countries where such labs are being or will be quickly built for fighting the COVID-19. The information of lab safety should be considered to be internally linked to the national intelligent syndromic surveillance system (NISSS), for better improving the safety of the labs at the greatest need and facilitating more comprehensive surveillance of risk for disease outbreak.

Analysis of adjunctive serological detection to nucleic acid test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection diagnosis

BACKGROUND

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused coronavirus disease 2019 (COVID-19) epidemic in China, December 2019. The clinical features and treatment of COVID-19 patients remain largely elusive. However, accurate detection is required for SARS-CoV-2 infection diagnosis. We aimed to evaluate the antibodies-based test and nucleic acid-based test for SARS-CoV-2-infected patients.

METHODS

We retrospectively studied 133 patients diagnosed with SARS-CoV-2 and admitted to Renmin Hospital of Wuhan University, China, from January 23 to March 1, 2020. Demographic data, clinical records, laboratory tests, and outcomes were collected. Data were accessed by SARS-CoV-2 IgM-IgG antibody test and real-time reverse transcriptase PCR (RT-PCR) detection for SARS-CoV-2 nucleic acid in COVID-19 patients.

RESULTS

Of 133 COVID-19 patients, there were 44 moderate cases, 52 severe cases, and 37 critical cases with no differences in gender and age among three subgroups. In RT-PCR detection, the positive rate was 65.9%, 71.2%, and 67.6% in moderate, severe, and critical cases, respectively. Whereas the positive rate of IgM/IgG antibody detection in patients was 79.5%/93.2%, 82.7%/100%, and 73.0%/97.3% in moderate, severe, and critical cases, respectively. Moreover, the IgM and IgG antibodies concentrations were also examined with no differences among three subgroups.

CONCLUSION

The IgM-IgG antibody test exhibited a useful adjunct to RT-PCR detection, and improved the accuracy in COVID-19 diagnosis regardless of the severity of illness, which provides an effective complement to the false-negative results from a nucleic acid test for SARS-CoV-2 infection diagnosis after onsets.

Positive rate of RT-PCR detection of SARS-CoV-2 infection in 4880 cases from one hospital in Wuhan, China, from Jan to Feb 2020

BACKGROUND

There's an outbreak of a novel coronavirus (SARS-CoV-2) infection since December 2019, first in China, and currently with more than 80 thousand confirmed infection globally in 29 countries till March 2, 2020. Identification, isolation and caring for patients early are essential to limit human-to-human transmission including reducing secondary infections among close contacts and health care workers, preventing transmission amplification events. The RT-PCR detection of viral nucleic acid test (NAT) was one of the most quickly established laboratory diagnosis method in a novel viral pandemic, just as in this COVID-19 outbreak.

METHODS

4880 cases that had respiratory infection symptoms or close contact with COVID-19 patients in hospital in Wuhan, China, were tested for SARS-CoV-2 infection by use of quantitative RT-PCR (qRT-PCR) on samples from the respiratory tract. Positive rates were calculated in groups divided by genders or ages.

RESULTS

The positive rate was about 38% for the total 4880 specimens. Male and older population had a significant higher positive rates. However, 57% was positive among the specimens from the Fever Clinics. Binary logistic regression analysis showed that age, not gender, was the risk factor for SARS-CoV-2 infection in fever clinics.

CONCLUSIONS

Therefore, we concluded that viral NAT played an important role in identifying SARS-CoV-2 infection.

A preliminary study on serological assay for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 238 admitted hospital patients

In this study, we aimed to evaluate the diagnostic value of serological assay for SARS-CoV-2. A newly-developed ELISA assay for IgM and IgG antibodies against N protein of SARS-CoV-2 was used to screen the serums of 238 admitted hospital patients between February 6 and February 14, 2020 with confirmed or suspected SARS-CoV-2. SARS-CoV-2 RNA was detected on pharyngeal swab specimens using real time RT-PCR. 194 (81.5%) of the serums were detected to be antibody (IgM and/or IgG) positive, significantly higher than the positive rate of viral RNA (64.3%). There was no difference in the positive rate of antibodies between the confirmed patients (83.0%, 127/153) and the suspected patients (78.8%, 67/85), whose nucleic acid tests were negative. The antibody positive rates were very low in the first five days after initial onset of symptoms, and then rapidly increased as the disease progressed. After 10 days, the antibody positive rates jumped from below 50% to over 80%. However, the positive rates of viral RNA maintained above 60% in the first 11 days after initial onset of symptoms, and then rapidly decreased. Overall, the suspected patients were most likely infected by SARS-CoV-2. Before the 11th day after initial onset of symptoms, nucleic acid test is key for confirmation of viral infection. The combination of serological assay can greatly improve the diagnostic efficacy. After the 11th day post-disease onset, the diagnosis for viral infection should be majorly dependent on serological assay.

[WITHDRAWN: Potential false-positive rate among the 'asymptomatic infected individuals' in close contacts of COVID-19 patients]

Editor office’s response for Ahead of Print article withdrawn The article “Potential false-positive rate among the ‘asymptomatic infected individuals’ in close contacts of COVID-19 patients” was under strong discussion after pre-published. Questions from the readers mainly focused on the article’s results and conclusions were depended on theoretical deduction, but not the field epidemiology data and further researches were needed to prove the current theory. Based on previous discussions, the article was decided to be offline by the editorial board from the pre-publish lists. Objective: As the prevention and control of COVID-19continues to advance, the active nucleic acid test screening in the close contacts of the patients has been carrying out in many parts of China. However, the false-positive rate of positive results in the screening has not been reported up to now. But to clearify the false-positive rate during screening is important in COVID-19 control and prevention. Methods: Point values and reasonable ranges of the indicators which impact the false-positive rate of positive results were estimated based on the information available to us at present. The false-positive rate of positive results in the active screening was deduced, and univariate and multivariate-probabilistic sensitivity analyses were performed to understand the robustness of the findings. Results: When the infection rate of the close contacts and the sensitivity and specificity of reported results were taken as the point estimates, the positive predictive value of the active screening was only 19.67%, in contrast, the false-positive rate of positive results was 80.33%. The multivariate-probabilistic sensitivity analysis results supported the base-case findings, with a 75% probability for the false-positive rate of positive results over 47%. Conclusions: In the close contacts of COVID-19 patients, nearly half or even more of the 'asymptomatic infected individuals' reported in the active nucleic acid test screening might be false positives.

Evaluation of the performance of the Cepheid Xpert HIV-1 Viral Load Assay for quantitative and diagnostic uses

BACKGROUND

Cepheid's Xpert HIV-1 Viral Load (Xpert VL), a simplified, automated, single-use quantitative assay used with the GeneXpert System, is not FDA approved.

OBJECTIVES

Using stored plasma, we conducted a study to assess the ability of Xpert VL to quantify viral load relative to the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 (Cobas VL) and to examine the use of the Xpert VL as a qualitative diagnostic test.

STUDY DESIGN

Following HIV-1 viral stock dilutions, we conducted a probit analysis to identify the concentration where 95 % of specimens had quantified VLs. We also examined Xpert and Cobas log VL correlation in linearity panels; compared the proportion of 220 seroconverter specimens with virus detected using McNemar's test; and tested specimens from persons with untreated, established HIV-1 infection (n=149) and uninfected persons (n=497). Furthermore, we examined Xpert VL as a qualitative test in seroconverter specimens with early (n=20) and later (n=68) acute infections.

RESULTS

At 1.80 log10 copies/mL, 95 % of specimens had quantifiable virus using Xpert VL. Xpert and Cobas VLs were highly correlated (R²=0.994). The proportion of seroconverter specimens with virus detected using Cobas and with Xpert VL was not statistically different (p=0.0578). Xpert VL detected 97.9 % of established infections, and specificity was 99.80 % (95 % CI 98.87%-99.99%). Xpert VL detected 90 % and 98.5 % of early and later acute infections, respectively.

CONCLUSIONS

If approved, Xpert VL could allow U.S. laboratories that cannot bring on large, complex testing platforms to conduct HIV monitoring. An approval for diagnostic use may provide timely identification of HIV infections.

Safe-Testing Algorithm for Individual-Donation Nucleic Acid Testing: 10 Years of Experience in a Low-Prevalence Country

Introduction

A highly sensitive and specific nucleic acid test (NAT) for the blood-borne viruses human immunodeficiency virus (HIV), hepatitis C (HCV), and hepatitis B (HBV) is essential for the safety of blood components. Since more than 2 decades, NAT screening of blood donations has become standard in developed countries that have implemented the individual-donation (ID-NAT) and mini-pool NAT (MP-NAT) approaches. With this powerful technique, confirmation of initial reactive (IR) NAT samples becomes a challenge. Different algorithms are currently in use to eliminate false reactive results. To show that the algorithm implemented in 2007, that uses repeat testing of IR samples in duplicate runs, is a safe strategy, especially in low endemic countries, data from a 10-year experience of ID-NAT were extensively analyzed when follow-up data were available.

Methods

From July 2007 to December 2014, the Procleix Ultrio assay on a Procleix Tigris system, and from January 2015 to December 2017, the cobas MPX on a cobas 8800 platform, were used for ID-NAT screening. All IR samples were subjected to repeat testing in duplicate independent runs. Only when both tests remained negative were the products released. Donor data from the last 10 years were investigated retrospectively, looking for the reoccurrence of a reactive result in a follow-up sample. Only those donors with at least an x + 1 donation result were included for the confirmation of a false reactive result.

Results

From the 1,830,657 donations tested, 2,450 samples were IR (0.13%); only 228 were repeat reactive ([RR], 18 HIV, 61 HCV, and 149 HBV samples), and 2,222 were non-RR (0.12%). Follow-up data were available from 1,267 donors (57%) for further analysis. All except one of these donors were ID-NAT-negative in all follow-up samples. The one exception was from a donor who acquired a fresh HBV infection 10 years after the IR donation (in the x + 28 donation) and subsequently seroconverted. Subsequent serological tests from all succeeding donations (x + 1, x + 2, etc.) were negative in all the other cases, proving that no seroconversion took place after the IR ID-NAT result.

Conclusions

The algorithm to deal with IR ID-NAT donations using duplicate repeat testing is very safe and cost-effective in low-prevalence countries. There is no unnecessary destruction of blood products, no counseling of false reactive donors, and also no need to add further complexity to the screening algorithm.

Prevalence of HIV Indeterminate Western Blot Tests and Follow-up of HIV Antibody Sero-Conversion in Southeastern China

HIV-indeterminate Western blotting (WB) results are typically obtained in WB confirmatory assays, and the number of indeterminate samples may increase with the detection of HIV infections, which will present considerable challenges for the management of HIV/AIDS. Nucleic acid detection has been used as a laboratory test for screening suspected or indeterminate samples. However, the effectiveness of these assays for the differential diagnosis of HIV-indeterminate WB samples remained undetermined. In this study, 210 subjects with HIV-indeterminate WB results were detected from 6360 positive HIV screening samples between 2015 and 2016 in southeastern China, in which HIV-indeterminate WB results accounted for 3.30%. The highest proportion of indeterminate results was observed in pregnant and lying-in women receiving physical examinations (16.67%), followed by that in voluntary blood donors (8.82%). The most common WB band patterns were p24, gp160 and p24, and gp160. The follow-up study revealed that the highest negative and positive conversion rates of HIV antibodies were in samples with a single p24 band (80.28%), and with gp160 and p24 bands (86.21%), respectively. Among the Env, Gag, and Pol antibodies, samples with a Gag band showed the highest negative conversion rate (81.25%), whereas the highest positive conversion rate was observed in samples with an Env band (56.76%). In addition, quantitative and qualitative HIV nucleic acid testing exhibited the highest sensitivity (96.3%) and specificity (97.85%), respectively. Our results indicate a lower proportion of HIV indeterminate WB results in southeastern China compared to previous reports, and the follow-up re-examination of patients with HIV indeterminate results should be performed. Nucleic acid testing facilitates the identification of HIV infections.

Prevalence of Hepatitis B Virus (HBV) Among Blood Donors in Eastern Saudi Arabia: Results From a Five-Year Retrospective Study of HBV Seromarkers

Background

Transfusion-transmissible hepatitis B virus (HBV) infection is a major problem worldwide. Recently, confirmatory nucleic acid tests (NATs) for HBV DNA have been employed in several countries. We assessed the prevalence and yearly trends of HBV infection in blood donors in the Eastern Province of Saudi Arabia, screening for HBV surface antigen (HBsAg), antibody against HBV core antigen (anti-HBc), and HBV DNA.

Methods

Between 2011 and 2015, a total of 22,842 donors were screenedfor HBsAg, anti-HBc, and HBV DNA using the HBsAg Qualitative II kit (Abbott, Ireland Diagnostics Division, Sligo, Ireland), ARCHITECT Anti-hepatitis B core antigen antibody (HBc) II Assay kit (Abbott GmbH & Co. KG, Wiesbaden, Germany), and NAT Procleix Ultrio Elite Assay kit (Grifols Diagnostic Solutions Inc., Los Angeles, CA, USA), respectively.

Results

A total of 739 (3.24%) donors were HbsAg(+), anti-HBc(+), or HBV DNA(+); 63 (0.28%) were HbsAg(+), anti-HBc(+), and HBV DNA(+). Twelve (0.05%) were anti-HBc(+) and HBV DNA(+) but HBsAg(−); they were considered to have occult infection. Further, 664 (2.91%) were HBsAg(−) but anti-HBc(+), indicating chronic or resolving infection. HBV prevalence increased significantly from 2011 to 2012, increased marginally till 2013, and showed a decreasing trend from 2013 (P>0.05).

Conclusions

The five-year prevalence of HBV infection among blood donors in the Eastern Province of Saudi Arabia (3.24%) is lower than that reported for other regions in the country. The occult HBV infection rate of 0.05% emphasizes the importance of NATs in isolating potential infectious blood units.

Recombinase polymerase amplification combined with lateral flow dipstick for equipment-free detection of Salmonella in shellfish

Salmonella is a major pathogen that causes acute foodborne outbreaks worldwide. Seafood, particularly shellfish, is a proven source of Salmonella spp. infection because many people prefer to eat it raw or lightly cooked. However, traditional identification methods are too time-consuming and complex to detect contamination of bacteria in the food chain in a timely manner, and few studies have aimed to identify Salmonella in shellfish early in the supply chain. We herein developed a method for rapid detection of Salmonella in shellfish based on the method of recombinase polymerase amplification (RPA) combined with lateral flow dipstick (LFD), which targets the invasion gene A (invA). The RPA-LFD was able to function at 30-45 °C, and at the temperature of 40 °C, it only took 8 min of amplification to reach the test threshold of amplicons. The established method had both a good specificity and a sensitivity of 100 fg DNA per reaction (20 µL). Regarding practical performance, RPA-LFD performed better than real-time PCR. Another advantage of RPA-LFD is that it was capable of being performed without expensive equipments. Thus, RPA-LFD has potential for further development as a detection kit for Salmonella in shellfish and other foods under field conditions.

Detection and differentiation of HIV-2 using the point-of-care Alere q HIV-1/2 Detect nucleic acid test

BACKGROUND

The Alere q HIV-1/2 Detect test (Alere Detect) is a rapid point-of-care (POC) nucleic acid test (NAT) that can detect and differentiate HIV-1 and HIV-2 in 25-μL whole blood or plasma samples. The Alere Detect test has been validated for early infant diagnosis of HIV-1 infection, and it is the only POC NAT device currently known to detect HIV-2, which is endemic in West Africa.

OBJECTIVES

To evaluate the sensitivity detecting HIV-2 RNA and the differential performance of the Alere Detect.

STUDY DESIGN

Plasma samples from non-HIV (n=4), HIV-1 (n=22), HIV-2 (n=111; 29 Group A, 2 Group B) and HIV-1/HIV-2 dually-seropositive (n=8) participants in Senegal and the United States and HIV-2 reference strains (3 Group A, 1 Group B) were tested by Alere Detect, Abbott RealTime HIV-1 and the University of Washington HIV-2 RNA quantitative (UW HIV-2) assays.

RESULTS

The Alere Detect correctly differentiated between HIV-1 and HIV-2 in all 80 (100%) patient samples with detectable HIV RNA (n=20 HIV-1, 60 HIV-2). The overall HIV-2 detection concordance between Alere Detect and the UW HIV-2 assay was 68% (54/80); the concordance improved to 100% (30/30) for samples with HIV-2 RNA >300copies/mL. Neither assay detected HIV-2 RNA in 31 of 111 HIV-2 seropositive samples.

CONCLUSIONS

The Alere Detect test is a novel device detecting HIV RNA in clinical samples, and differentiating HIV-1 and HIV-2 with a high level of specificity. It has the potential for use as a rapid HIV-2 NAT-based diagnosis tool in resource-limited settings and to confirm HIV-2 infection for the CDC 4th generation HIV-1/2 diagnostic algorithm.

Low-cost, real-time, continuous flow PCR system for pathogen detection

In this paper, we present a portable and low cost point-of-care (POC) PCR system for quantitative detection of pathogens. Our system is based on continuous flow PCR which maintains fixed temperatures zones and pushes the PCR solution between two heated areas allowing for faster heat transfer and as a result, a faster PCR. The PCR system is built around a 46.0 mm × 30.9 mm × 0.4 mm disposable thermoplastic chip. In order to make the single-use chip economically viable, it was manufactured by hot embossing and was designed to be compatible with roll-to-roll embossing for large scale production. The prototype instrumentation surrounding the chip includes two heaters, thermal sensors, and an optical system. The optical system allows for pathogen detection via real time fluorescence measurements. FAM probes were used as fluorescent reporters of the amplicons generated during the PCR. To demonstrate the function of the chip, two infectious bacteria targets were selected: Chlamydia trachomatis and Escherichia coli O157:H7. For both bacteria, the limit of detection of the system was determined, PCR efficiencies were calculated, and different flow velocities were tested. We have demonstrated successful detection for these two bacterial pathogens highlighting the versatility and broad utility of our portable, low-cost, and rapid PCR diagnostic device.

Hepatitis C virus: Virology, diagnosis and treatment

More than twenty years of study has provided a better understanding of hepatitis C virus (HCV) life cycle, including the general properties of viral RNA and proteins. This effort facilitates the development of sensitive diagnostic tools and effective antiviral treatments. At present, serologic screening test is recommended to perform on individuals in the high risk groups and nucleic acid tests are recommended to confirm the active HCV infections. Quantization and genotyping of HCV RNAs are important to determine the optimal duration of anti-viral therapy and predict the likelihood of response. In the early 2000s, pegylated interferon plus ribavirin became the standard anti-HCV treatment. However, this therapy is not ideal. To 2014, boceprevir, telaprevir, simeprevir, sofosbuvir and Harvoni are approved by Food and Drug Administration for the treat of HCV infections. It is likely that the new all-oral, interferon-free, pan-genotyping anti-HCV therapy will be available within the next few years. Majority of HCV infections will be cured by these anti-viral treatments. However, not all patients are expected to be cured due to viral resistance and the high cost of antiviral treatments. Thus, an efficient prophylactic vaccine will be the next challenge in the fight against HCV infection.