Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR

Viral Co-Infection in Bats: A Systematic Review

Co-infection is an underappreciated phenomenon in contemporary disease ecology despite its ubiquity and importance in nature. Viruses, and other co-infecting agents, can interact in ways that shape host and agent communities, influence infection dynamics, and drive evolutionary selective pressures. Bats are host to many viruses of zoonotic potential and have drawn increasing attention in their role as wildlife reservoirs for human spillover. However, the role of co-infection in driving viral transmission dynamics within bats is unknown. Here, we systematically review peer-reviewed literature reporting viral co-infections in bats. We show that viral co-infection is common in bats but is often only reported as an incidental finding. Biases identified in our study database related to virus and host species were pre-existing in virus studies of bats generally. Studies largely speculated on the role co-infection plays in viral recombination and few investigated potential drivers or impacts of co-infection. Our results demonstrate that current knowledge of co-infection in bats is an ad hoc by-product of viral discovery efforts, and that future targeted co-infection studies will improve our understanding of the role it plays. Adding to the broader context of co-infection studies in other wildlife species, we anticipate our review will inform future co-infection study design and reporting in bats. Consideration of detection strategy, including potential viral targets, and appropriate analysis methodology will provide more robust results and facilitate further investigation of the role of viral co-infection in bat reservoirs.

Experimental Infection and Transmission of SARS-CoV-2 Delta and Omicron Variants among Beagle Dogs

We assessed susceptibility of dogs to SARS-COV-2 Delta and Omicron variants by experimentally inoculating beagle dogs. Moreover, we investigated transmissibility of the variants from infected to naive dogs. The dogs were susceptible to infection without clinical signs and transmitted both strains to other dogs through direct contact.

Susceptibility to SARS-CoV-2 and MERS-CoV in Beagle Dogs

The coronavirus disease 19 (COVID-19) pandemic, caused by the severe acute respiratory syndrome, coronavirus 2 (SARS-CoV-2), has resulted in unprecedented challenges to healthcare worldwide. In particular, the anthroponotic transmission of human coronaviruses has become a common concern among pet owners. Here, we experimentally inoculated beagle dogs with SARS-CoV-2 or Middle East respiratory syndrome (MERS-CoV) to compare their susceptibility to and the pathogenicity of these viruses. The dogs in this study exhibited weight loss and increased body temperatures and shed the viruses in their nasal secretions, feces, and urine. Pathologic changes were observed in the lungs of the dogs inoculated with SARS-CoV-2 or MERS-CoV. Additionally, clinical characteristics of SARS-CoV-2, such as increased lactate dehydrogenase levels, were identified in the current study.

COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) pandemic has prompted a lot of questions globally regarding the range of information about the virus's possible routes of transmission, diagnostics, and therapeutic tools. Worldwide studies have pointed out the importance of monitoring and early surveillance techniques based on the identification of viral RNA in wastewater. These studies indicated the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in human feces, which is shed via excreta including mucus, feces, saliva, and sputum. Subsequently, they get dumped into wastewater, and their presence in wastewater provides a possibility of using it as a tool to help prevent and eradicate the virus. Its monitoring is still done in many regions worldwide and serves as an early "warning signal"; however, a lot of limitations of wastewater surveillance have also been identified.

A Retrospective Population Study of 385 191 Positive Real-Time Reverse Transcription-Polymerase Chain Reaction Tests For SARS-CoV-2 from a Single Laboratory in Katowice, Poland from April 2020 to July 2022

BACKGROUND This retrospective population study identified 385 191 positive real-time reverse transcription-polymerase chain reaction (RT-PCR) tests for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a single laboratory in Katowice, Poland, from April 2020 to July 2022. MATERIAL AND METHODS The material was nasopharyngeal, nasopharyngeal swab or bronchial lavage, and bronchoalveolar lavage (BAL) to confirm or exclude SARS-CoV-2 infection with the RT-PCR technique. Personal data are use according to the Provisions on the Protection of Personal Data by the Gyn-Centrum laboratory. RESULTS In 9 months of 2020, the number of SARS-CoV-2 results was 88 986; in 2021, it was 168 439, and in the first 7 months of 2022, it was 12 786. In 2020, the highest number of positive results was recorded in the third quarter (83 094 cases); 2021, in the 1st, 2nd, and 4th quarters (58 712; 37 720; and 71 753 cases, respectively), and in 2022, in the 1st quarter (127 613 cases) of the year. A positive result was observed more often in women and people aged 30-39, followed by those 40-49 years. Patients aged 10-19 years comprised the smallest population of SARS-CoV-2-positive cases. CONCLUSIONS In the Polish population studied, from April 2020 to July 2022, the detection rates of SARS-CoV-2 positivity were significantly higher for women than for men and in the 30-49 age group for both sexes. Also, the infection detection rate of 385 191 out of 1 332 659 patient samples, or 28.9%, supports that the Polish society adhered to public health recommendations for infection control during the COVID-19 pandemic.

Nanotechnology-based diagnostic methods for coronavirus: From nucleic acid extraction to amplification

The recent emergence of human coronaviruses (CoVs) causing severe acute respiratory syndrome (SARS) is posing a great threat to global public health. Therefore, the rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people's lives and preventing epidemics. Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Applications of nucleic acid detection range from genotyping and genetic prognostics, to expression profiling and detection of infectious disease. The nucleic acid detection for infectious diseases is widely used, as evidenced by the widespread use of COVID-19 tests for the containment of the pandemic. Nanotechnology influences all medical disciplines and has been considered as an essential tool for novel diagnostics, nanotherapeutics, vaccines, medical imaging, and the utilization of biomaterials for regenerative medicine. In this review, the recent advances in the development of nanotechnology-based diagnostic methods for coronavirus, and their applications in nucleic acid detection are discussed in detail. The techniques for the amplification of nucleic acids are summarized, as well as the use of magnetic nanoparticles for nucleic acid extraction. Besides, current challenges and future prospects are proposed, along with the great potential of nanotechnology for the effective diagnosis of coronavirus.

Evaluation of Laboratory Results with Data from Bio-Speedy Respiratory Panel 2 in Nasopharyngeal Swab Specimens of COVID-19-Suspected Patients Having PCR(-) Results

Objective: The distinction between COVID-19 and other respiratory infections can be difficult during the flu and winter seasons. The aim of this study is to detect bacterial/viral microorganisms in nasopharyngeal swab samples and to evaluate routine laboratory results of patients with PCR (-) but suspected covid 19. Methods: Between 1 July 2021 and 31 December 2021, 78 patients who were hospitalized and followed up in the suspected Covid service were included in the study. The patients were divided into two groups as those with and without growth on the respiratory panel. Laboratory, demographic and radiological data were compared between groups. Results: C-reactive protein (CRP) and ferritin levels were found to be statistically significantly higher in the group with growth on the respiratory panel compared to the group without growth (p= .05, p= .041, respectively). Reproduction was detected in nasopharyngeal swab samples taken in 56.4% of the patients. More than half of the patients were radiologically defined as CO-RADS 3. Conclusion: It should not be forgotten that other respiratory viral and bacterial infections that mimic the COVID-19 clinic are also commonly observed during this period.

Acquired insights from the long-term surveillance of SARS-CoV-2 RNA for COVID-19 monitoring: The case of Monterrey Metropolitan Area (Mexico)

Wastewater-based epidemiology offers a time- and cost-effective way to monitor SARS-CoV-2 spread in communities and therefore represents a complement to clinical testing. WBE applicability has been demonstrated in a number of cases over short-term periods as a method for tracking the prevalence of SARS-CoV-2 and an early-warning tool for predicting outbreaks in the population. This study reports SARS-CoV-2 viral loads from wastewater treatment plants (WWTPs) and hospitals over a 6-month period (June to December 2020). Results show that the overall range of viral load in positive tested samples was between 1.2 × 10³ and 3.5 × 10⁶ gene copies/l, unveiling that secondary-treated wastewaters mirrored the viral load of influents. The interpretation suggests that the viral titers found in three out of four WWTPs were associated to clinical COVID-19 surveillance indicators preceding 2-7 days the rise of reported clinical cases. The median wastewater detection rate of SARS-CoV-2 was one out of 14,300 reported new cases. Preliminary model estimates of prevalence ranged from 0.02 to 4.6% for the studied period. This comprehensive statistical and epidemiological analysis demonstrates that the applied wastewater-based approach to COVID-19 surveillance is in general consistent and feasible, although there is room for improvements.

Surface plasmon resonance biosensor with laser heterodyne feedback for highly-sensitive and rapid detection of COVID-19 spike antigen

The ongoing outbreak of the COVID-19 has highlighted the importance of the pandemic prevention and control. A rapid and sensitive antigen assay is crucial in diagnosing and curbing pandemic. Here, we report a novel surface plasmon resonance biosensor based on laser heterodyne feedback interferometry for the detection of SARS-CoV-2 spike antigen, which is achieved by detecting the tiny difference in refractive index between different antigen concentrations. The biosensor converts the refractive index changes at the sensing unit into the intensity changes of light through surface plasmon resonance, achieving label-free and real-time detection of biological samples. Moreover, the gain amplification effect of the laser heterodyne feedback interferometry further improved the sensitivity of this biosensor. The biosensor can rapidly respond to continuous and periodic changes in the refractive index with a high resolution of 3.75 × 10-8 RIU, demonstrating the repeatability of the biosensor. Afterwards, the biosensor is immobilized by the anti-SARS-CoV-2 spike monoclonal antibodies, thus realizing the specific recognition of the antigen. The biosensor exhibited a high sensitivity towards the concentration of the antigen with a linear dynamic range of five orders of magnitude and a resolution of 0.08 pg/mL. These results indicate that this principle can be used as a rapid diagnostic method for COVID-19 antigens without sample labelling.

Risk factors of COVID-19 vertical transmission among pregnant and non-pregnant Filipinos in Metro Manila: a multicentre cohort study protocol

INTRODUCTION

The novel (COVID-19 was first reported to have originated in Wuhan, China, in December 2019. This new strain, SARS-CoV-2, has spread rapidly worldwide, prompting the WHO to declare the COVID-19 outbreak a global pandemic. The main objective of this cohort study is to determine the risk factors of COVID-19, the modes of COVID-19 vertical transmission, and the maternal and fetal outcomes among non-pregnant and pregnant women and their fetuses.

METHODS AND ANALYSIS

This is a multicentre epidemiological study that will involve a prospective cohort. COVID-19 status among consulting non-pregnant and pregnant women in public hospitals in Manila, Philippines, will be determined and monitored for 6-12 months. Swab specimens from the nasopharynx, cervix, rectum, amniotic fluid, placenta, cord blood and breastmilk will be collected during consult and admission for reverse transcription-PCR (RT-PCR) testing. Blood will be collected during the postdelivery period to monitor the women and their neonates for any undue development and determine the antibody development to indicate an infective or non-infective state. Evidence of vertical transmission will be explored with the presence or absence of the virus using the maternal and fetal neonatal RT-PCR and lateral flow antibody status. Descriptive and inferential statistics will be done, including the associations between exposures and risk factors, description of clinical characteristics, and the COVID-19 status of the participants.

ETHICS AND DISSEMINATION

The Single Joint Research Ethics Board of the Department of Health has approved this protocol (SJREB 2020-30). The study results will be disseminated through conference presentations, peer-reviewed articles, and various stakeholder public forums and activities.

Diagnostic performance and clinical feasibility of a novel one-step RT-qPCR assay for simultaneous detection of multiple severe acute respiratory syndrome coronaviruses

Coronavirus disease 2019 (COVID-19) is an acute respiratory infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Other coronaviruses (CoVs) can also infect humans, although the majority cause only mild respiratory symptoms. Because early diagnosis of SARS-CoV-2 is critical for preventing further transmission events and improving clinical outcomes, it is important to be able to distinguish SARS-CoV-2 from other SARS-related CoVs in respiratory samples. Therefore, we developed and evaluated a novel reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay targeting the genes encoding the spike (S) and membrane (M) proteins to enable the rapid identification of SARS-CoV-2, including several new circulating variants and other emerging SARS-like CoVs. By analysis of in vitro-transcribed mRNA, we established multiplex RT-qPCR assays capable of detecting 5 × 10° copies/reaction. Using RNA extracted from cell culture supernatants, our multiple simultaneous SARS-CoV-2 assays had a limit of detection of 1 × 10° TCID₅₀/mL and showed no cross-reaction with human CoVs or other respiratory viruses. We also validated our method using human clinical samples from patients with COVID-19 and healthy individuals, including nasal swab and sputum samples. This novel one-step multiplex RT-qPCR assay can be used to improve the laboratory diagnosis of human-pathogenic CoVs, including SARS-CoV-2, and may be useful for the identification of other SARS-like CoVs of zoonotic origin.

Highly sensitive, scalable, and rapid SARS-CoV-2 biosensor based on In2O3 nanoribbon transistors and phosphatase

Developing convenient and accurate SARS-CoV-2 antigen test and serology test is crucial in curbing the global COVID-19 pandemic. In this work, we report an improved indium oxide (In₂O₃) nanoribbon field-effect transistor (FET) biosensor platform detecting both SARS-CoV-2 antigen and antibody. Our FET biosensors, which were fabricated using a scalable and cost-efficient lithography-free process utilizing shadow masks, consist of an In₂O₃ channel and a newly developed stable enzyme reporter. During the biosensing process, the phosphatase enzymatic reaction generated pH change of the solution, which was then detected and converted to electrical signal by our In₂O₃ FETs. The biosensors applied phosphatase as enzyme reporter, which has a much better stability than the widely used urease in FET based biosensors. As proof-of-principle studies, we demonstrate the detection of SARS-CoV-2 spike protein in both phosphate-buffered saline (PBS) buffer and universal transport medium (UTM) (limit of detection [LoD]: 100 fg/mL). Following the SARS-CoV-2 antigen tests, we developed and characterized additional sensors aimed at SARS-CoV-2 IgG antibodies, which is important to trace past infection and vaccination. Our spike protein IgG antibody tests exhibit excellent detection limits in both PBS and human whole blood ((LoD): 1 pg/mL). Our biosensors display similar detection performance in different mediums, demonstrating that our biosensor approach is not limited by Debye screening from salts and can selectively detect biomarkers in physiological fluids. The newly selected enzyme for our platform performs much better performance and longer shelf life which will lead our biosensor platform to be capable for real clinical diagnosis usage.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material (materials and methods for device fabrication, functionalization of In₂O₃ devices, photographs of the liquid gate measurement setup, mobilities of the nine devices labeled in Fig. 1(b), family curves of I _DS-V _DS with the liquid gate setup and current change after bubbling the substrate solution (current vs. time curve for S1 antigen detection)) is available in the online version of this article at 10.1007/s12274-022-4190-0.

Testing and diagnosis of SARS-CoV-2 infection

The recent outbreak of the coronavirus disease 2019 (COVID-19) has rapidly spread around the world since its discovery in China, in December 2019. The current standard method for determining whether a patient is infected with the SARS-CoV-2 virus involves taking a nasal or throat swab sample, which is then sent to laboratories for testing. The laboratories then use polymerase chain reaction (PCR)-based technology on respiratory specimens remain the gold standard to determine if the genetic material of the virus is present in the sample and use this information to diagnose the patient. However, serologic immunoassays and point-of-care technologies are rapidly emerging with high specificity and sensitivity as well. Even if there are excellent techniques for diagnosing symptomatic patients with COVID-19 in equipped laboratories, critical gaps still exist in the screening of asymptomatic individuals who are in the incubation phase of the virus, as well as in the accurate determination of live virus shedding during convalescence to inform decisions for ending isolation.

Human Body Performance with COVID-19 Affectation According to Virus Specification Based on Biosensor Techniques

Life was once normal before the first announcement of COVID-19's first case in Wuhan, China, and what was slowly spreading became an overnight worldwide pandemic. Ever since the virus spread at the end of 2019, it has been morphing and rapidly adapting to human nature changes which cause difficult conundrums in the efforts of fighting it. Thus, researchers were steered to investigate the virus in order to contain the outbreak considering its novelty and there being no known cure. In contribution to that, this paper extensively reviewed, compared, and analyzed two main points; SARS-CoV-2 virus transmission in humans and detection methods of COVID-19 in the human body. SARS-CoV-2 human exchange transmission methods reviewed four modes of transmission which are Respiratory Transmission, Fecal-Oral Transmission, Ocular transmission, and Vertical Transmission. The latter point particularly sheds light on the latest discoveries and advancements in the aim of COVID-19 diagnosis and detection of SARS-CoV-2 virus associated with this disease in the human body. The methods in this review paper were classified into two categories which are RNA-based detection including RT-PCR, LAMP, CRISPR, and NGS and secondly, biosensors detection including, electrochemical biosensors, electronic biosensors, piezoelectric biosensors, and optical biosensors.

Recent advances in detection technologies for COVID-19

Corona Virus Disease 2019 (COVID-19) is a highly infectious respiratory illness that was caused by the SARS-CoV-2. It spread around the world in just a few months and became a worldwide pandemic. Quick and accurate diagnosis of infected patients is very important for controlling transmission. In addition to the commonly used Real-time reverse-transcription polymerase chain reaction (RT-PCR) detection techniques, other diagnostic techniques are also emerging endlessly. This article reviews the current diagnostic methods for COVID-19 and discusses their advantages and disadvantages. It provides an important reference for the diagnosis of COVID-19.

COVID-19 rhapsody: Rage towards advanced diagnostics and therapeutic strategy

The deadly global outbreak of coronavirus disease-2019 (COVID-19) has forged an unrivaled threat to human civilization. Contemplating its profuse impact, initial risk management and therapies are needed, as well as rapid detection strategies alongside treatments with existing drugs or traditional treatments to provide better clinical support for critical patients. Conventional detection techniques have been considered but do not sufficiently meet the current challenges of effective COVID-19 diagnosis. Therefore, several modern techniques including point-of-care diagnosis with a biosensor, clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins that function as nuclease (Cas) technology, next-generation sequencing, serological, digital, and imaging approaches have delivered improved and noteworthy success compared to that using traditional strategies. Conventional drug treatment, plasma therapy, and vaccine development are also ongoing. However, alternative medicines including Ayurveda, herbal drugs, homeopathy, and Unani have also been enlisted as prominent treatment strategies for developing herd immunity and physical defenses against COVID-19. All considered, this review can help develop rapid and simplified diagnostic strategies, as well as advanced evidence-based modern therapeutic approaches that will aid in combating the global pandemic.

Electrochemical investigations for COVID-19 detection-A comparison with other viral detection methods

Virus-induced infection such as SARS-CoV-2 is a serious threat to human health and the economic setback of the world. Continued advances in the development of technologies are required before the viruses undergo mutation. The low concentration of viruses in environmental samples makes the detection extremely challenging; simple, accurate and rapid detection methods are in urgent need. Of all the analytical techniques, electrochemical methods have the established capabilities to address the issues. Particularly, the integration of nanotechnology would allow miniature devices to be made available at the point-of-care. This review outlines the capabilities of electrochemical methods in conjunction with nanotechnology for the detection of SARS-CoV-2. Future directions and challenges of the electrochemical biosensors for pathogen detection are covered including wearable and conformal biosensors, detection of plant pathogens, multiplexed detection, and reusable biosensors for on-site monitoring, thereby providing low-cost and disposable biosensors.

Diagnosis for COVID-19: current status and future prospects

Introduction: Coronavirus disease 2019 (COVID-19), a respiratory illness caused by novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), had its first detection in December 2019 in Wuhan (China) and spread across the world. In March 2020, the World Health Organization (WHO) declared COVID-19 a pandemic disease. The utilization of prompt and accurate molecular diagnosis of SARS-CoV-2 virus, isolating the infected patients, and treating them are the keys to managing this unprecedented pandemic. International travel acted as a catalyst for the widespread transmission of the virus.Areas covered: This review discusses phenotype, structural, and molecular evolution of recognition elements and primers, its detection in the laboratory, and at point of care. Further, market analysis of commercial products and their performance are also evaluated, providing new ways to confront the ongoing global public health emergency.Expert commentary: The outbreak for COVID-19 created mammoth chaos in the healthcare sector, and still, day by day, new epicenters for the outbreak are being reported. Emphasis should be placed on developing more effective, rapid, and early diagnostic devices. The testing laboratories should invest more in clinically relevant multiplexed and scalable detection tools to fight against a pandemic like this where massive demand for testing exists.

Efficient Microfluidic-Based Air Sampling/Monitoring Platform for Detection of Aerosol SARS-CoV-2 On-site

Airborne pathogens have been considered as highly infectious and transmittable between humans. With the pandemic outbreak of the coronavirus disease 2019 (COVID-19), an on-site diagnostic system-integrated airborne pathogen-monitoring machine is recommended by experts for preventing and controlling the early stage β-coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread. In this work, a small-volume rotating microfluidic fluorescence chip-integrated aerosol SARS-CoV-2 sampling system was constructed to satisfy the demand for rapid on-site sample collection and detection of SARS-CoV-2. The rotating microfluidic fluorescence system with small volume has very high sensitivity in the detection of SARS-CoV-2 (detection limit of 10 copies/μL with the shortest Ct value of 15 min), which is comparable to reverse transcription polymerase chain reaction (RT-PCR). The precision variation coefficients within/between batches are very low [coefficient of variation (CV) % ≤ 5.0%]. Our work has passed the comprehensive inspection of the microfluidic chip performance by the Shanghai Medical Device Testing Institute [National Medical Inspection (Design) no. 4408] and successfully tested 115 clinical samples. The integrated system exhibits 100% specificity, high sensitivity (10 copies/μL), and good precision (CV % ≤ 5.0%) in the rapid detection of SARS-CoV-2, thus realizing rapid monitoring and diagnostics of SARS-CoV-2 nucleic acid on-site.

Laboratory detection methods for the human coronaviruses

Coronaviruses are a group of envelop viruses which lead to diseases in birds and mammals as well as human. Seven coronaviruses have been discovered in humans that can cause mild to lethal respiratory tract infections. HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1 are the low-risk members of this family and the reason for some common colds. Besides, SARS-CoV, MERS-CoV, and newly identified SARS-CoV-2, which is also known as 2019-nCoV, are the more dangerous viruses. Due to the rapid spread of this novel coronavirus and its related disease, COVID-19, a reliable, simple, fast, and low-cost detection method is necessary for patient diagnosis and tracking worldwide. Human coronaviruses detection methods were classified and presented in this article. The laboratory detection techniques include RT-PCR, RT-LAMP, electrochemical and optical biosensors for RNA detection, and whole virus or viral proteins detection assays.

Ravaging SARS-CoV-2: rudimentary diagnosis and puzzling immunological responses

INTRODUCTION

In December 2019, the first COVID-19 case, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was reported in Wuhan, China. The SARS-CoV-2 rapidly disseminated throughout the world via community spread, acquiring pandemic status with significant fatality.

OBSERVATIONS

Rapid SARS-CoV-2 diagnosis was soon perceived critical for arresting community spread and effective therapy development. Human SARS-CoV-2 infection can be diagnosed either by nucleic acid identification or specific antibody detection. Contrary to nucleic acid identification confirmed active SARS-CoV-2 infection; antibody detection confirms a past infection, even in asymptomatic subjects. SARS-CoV-2 specific antibodies augment the ability to effectively counter the virus. A crucial hurdle limiting the steadfast implementation of antibody detection is the time required for threshold B lymphocyte population generation. This process is dependent on precise antigen recognition and MHC class I molecules presentation.

CONCLUSIONS

Thus, nucleic acid and antibody dependent tests complement each other in identifying human SARS-CoV-2 infection and shaping up subsequent immunological responses. This article discusses the complimentary association of nucleic acid identification (corresponding to an active infection) and antibody testing (the yester CoV-2 infection vulnerability) as the diagnostic and screening measures of SARS-CoV-2 infection. Highlights Nucleic acid (RNA) identification and specific antibody detection against SARS-CoV-2 are the noted diagnostic mechanisms for screening human SARS-CoV-2 infection. While nucleic acid identification screens prevailing SARS-CoV-2 infection, detection of SARS-CoV-2 specific antibodies signifies a past infection, even in asymptomatic subjects. Antibodies against SARS-CoV-2 provide a potential therapeutic option via transfer from antibody rich plasma of a recovered subject to an infected individual. Nucleic acid identification may not absolutely confirm the infection because of frequent SARS-CoV-2 genome mutations and possible technical errors, while specific antibody detection also needs at least (8-14) days for detectable screening of B-cell generated antibodies. Nucleic acid and antibody tests are complementary to each other as an early stage diagnostic assay for SARS-CoV-2 infection and possible therapy (antibodies). Sufferers with a high clinical suspicion but negative RT-PCR screening could be examined via combined imaging and repeated swab test.

Laboratory-Based Resources for COVID-19 Diagnostics: Traditional Tools and Novel Technologies. A Perspective of Personalized Medicine

The coronavirus infection 2019 (COVID-19) pandemic, caused by the highly contagious SARS-CoV-2 virus, has provoked a global healthcare and economic crisis. The control over the spread of the disease requires an efficient and scalable laboratory-based strategy for testing the population based on multiple platforms to provide rapid and accurate diagnosis. With the onset of the pandemic, the reverse transcription polymerase chain reaction (RT-PCR) method has become a standard diagnostic tool, which has received wide clinical use. In large-scale and repeated examinations, these tests can identify infected patients with COVID-19, with their accuracy, however, dependent on many factors, while the entire process takes up to 6–8 h. Here we also describe a number of serological systems for detecting antibodies against SARS-CoV-2. These are used to assess the level of population immunity in various categories of people, as well as for retrospective diagnosis of asymptomatic and mild COVID-19 in patients. However, the widespread use of traditional diagnostic tools in the context of the rapid spread of COVID-19 is hampered by a number of limitations. Therefore, the sharp increase in the number of patients with COVID-19 necessitates creation of new rapid, inexpensive, sensitive, and specific tests. In this regard, we focus on new laboratory technologies such as loop mediated isothermal amplification (LAMP) and lateral flow immunoassay (LFIA), which have proven to work well in the COVID-19 diagnostics and can become a worthy alternative to traditional laboratory-based diagnostics resources. To cope with the COVID-19 pandemic, the healthcare system requires a combination of various types of laboratory diagnostic testing techniques, whodse sensitivity and specificity increases with the progress in the SARS-CoV-2 research. The testing strategy should be designed in such a way to provide, depending on the timing of examination and the severity of the infection in patients, large-scale and repeated examinations based on the principle: screening–monitoring–control. The search and development of new methods for rapid diagnostics of COVID-19 in laboratory, based on new analytical platforms, is still a highly important and urgent healthcare issue. In the final part of the review, special emphasis is made on the relevance of the concept of personalized medicine to combat the COVID-19 pandemic in the light of the recent studies carried out to identify the causes of variation in individual susceptibility to SARS-CoV-2 and increase the efficiency and cost-effectiveness of treatment.

Current advances in the detection of COVID-19 and evaluation of the humoral response

The new outbreak caused by coronavirus SARS-CoV-2 started at the end of 2019 and was declared a pandemic in March 2020. Since then, several diagnostic approaches have been re-adapted, and also improved from the previous detections of SARS and MERS coronavirus. The best strategy to handle this situation seems to rely on a triad of detection methods: (i) highly sensitive and specific techniques as the gold standard method, (ii) easier and faster point of care tests accessible for large population screening, and (iii) serology assays to complement the direct detection and to use for surveillance. In this study, we assessed the techniques and tests described in the literature, their advantages and disadvantages, and the interpretation of the results. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) is undoubtedly the gold standard technique utilized not only for diagnostics, but also as a standard for comparison and validation of newer approaches. Other nucleic acid amplification methods have been shown to be adequate as point of care (POC) diagnostic tests with similar performance as RT-qPCR. The analysis of seroconversion with immunotests shows the complexity of the immune response to COVID-19. The detection of anti-SARS-CoV-2 antibodies can also help to detect previously infected asymptomatic individuals with negative RT-qPCR tests. Nevertheless, more controlled serology cohort studies should be performed as soon as possible to understand the immune response to SARS-CoV-2.

Genetic analysis of the 2019 coronavirus pandemic with from real-time reverse transcriptase polymerase chain reaction

Corona viruses (CoV) are known to cause extreme pandemics in the globe. The year 2020 will be a pandemic with the spread of the novel coronavirus (SARS-CoV-2) across the globe. Coronavirus 2019 (COVID-19) has been a part of our scary life for more than a quarter of a year in 2020. The Wuhan market and China have been the most commonly used terms in the world for at least a quarter of 2020. A zoonotic coronavirus has entered organisms to affect organisms for the third season in several centuries. CoV is a global pandemic prompted a drastic and rapid reconfiguration of society. CoV have extraordinary broad genomes of about 30 kilobases of RNA. There is no genetic relationship between the SARS-CoV, MERS and SARS-CoV-2. For health care strategies and for anticipating and preventing potential outbreaks, adequate description of the international spread of COVID-19 virus is imperative. The WHO has declared COVID-19 as endemic to pandemic in the first trimester of 2020. The biggest issues for diagnosis COVID-19 is not established apart from Real-time reverse transcriptase polymerase chain reaction (RT-PCR). In order to monitor the COVID-19 pandemic, testing of active SARS-CoV-2 infections is a fundamental public health method. The vast use of SARS-CoV-2 RT-PCR tests around the world has led to increased availability of test kits, which is also a major bottleneck. The technique RT-PCR was generally agreed in the present scenario to detect SARS-CoV-2 in the human body. This review discusses about the importance of molecular technique for diagnosing the pandemic disease of 2019. In conclusion, RT-PCR was found to be an apt technique for identification of SARS-CoV-2.

Sensitivity-Enhancing Strategies in Optical Biosensing

High-sensitivity detection of minute quantities or concentration variations of analytes of clinical importance is critical for biosensing to ensure accurate disease diagnostics and reliable health monitoring. A variety of sensitivity-improving concepts have been proposed from chemical, physical, and biological perspectives. In this review, elements that are responsible for sensitivity enhancement are classified and discussed in accordance with their operating steps in a typical biosensing workflow that runs through sampling, analyte recognition, and signal transduction. With a focus on optical biosensing, exemplary sensitivity-improving strategies are introduced, which can be developed into "plug-and-play" modules for many current and future sensors, and discuss their mechanisms to enhance biosensing performance. Three major strategies are covered: i) amplification of signal transduction by polymerization and nanocatalysts, ii) diffusion-limit-breaking systems for enhancing sensor-analyte contact and subsequent analyte recognition by fluid-mixing and analyte-concentrating, and iii) combined approaches that utilize renal concentration at the sampling and recognition steps and chemical signal amplification at the signal transduction step.

Colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a visual diagnostic platform for the detection of the emerging coronavirus SARS-CoV-2

RT-LAMP to detect SARS-CoV-2: in a positive sample, RT-LAMP leads to a color change from pink to yellow.

State-of-the-art equipment for rapid and accurate diagnosis of COVID-19

The World Health Organization (WHO) declared COVID-19 as a pandemic worldwide. Containment of this pandemic requires the diagnosis of the disease at an early stage. Extensive accessibility to accurate and rapid testing procedures is the need of the hour to control SARS-CoV-2 virus infection and to check the amount of immunity in the community. As such, scientists, doctors, and individual laboratories and companies around the world have been working tirelessly to develop the critically needed test kits in huge numbers. The ready to use test kits are based on different principles including detection of viral proteins in samples obtained from feces, sputum, nasopharyngeal or oropharyngeal samples, etc., or in blood or serum, by detection of antibodies produced in the human body to fight the infection. The first kind involves molecular assays like polymerase chain reaction-based techniques for the detection of severe acute respiratory syndrome coronavirus viral RNA. The second one involves serological and immunological assays which mostly rely upon antibody detection in an individual produced as a result of exposure to the virus. While the nucleic acid-based viral RNA can detect current infection in a sample, the serological tests can give an estimate of the already infected population. Medical imaging, specially chest computed tomography (CT), is another kind of technique that is becoming a supplement to the reverse transcriptase-polymerase chain reaction, especially when the results by the former technique are not certain or take time to arrive. Apart from being a diagnostic tool, the CT scan can also help in prediction, assessing the disease progression and checking whether the patient is responsive to administered therapy. This chapter will provide a comprehensive overview of the various rapid and accurate diagnosis methods for SARS COVID-19 suggested by WHO for current infection, for example, detection of viral proteins, medical imaging, and previous infection, and detection of antibodies generated during COVID-19 infections and others that are currently being researched.

Clinical correlation of severe acute respiratory syndrome-coronavirus-2 cases in selected districts of Uttar Pradesh: A cross-sectional hospital-based study

BACKGROUND

The novel coronavirus (CoV) has resulted in a global pandemic despite drastic measures to avoid contagious spread. On April 3, 2020, there were around 1 million reported cases and 51,515 deaths due to CoV disease 2019. The disease presents with flu-like symptoms such as fever, dry cough, and fatigue. India being a resource-limited country, it is very important to differentiate the suspected cases clinically.

AIM

The aim was to know the correlation of various clinical features of severe acute respiratory syndrome CoV 2 (SARS-CoV-2)-infected cases in selected districts of UP.

SETTING AND DESIGN

This was a retrospective cross-sectional hospital-based study.

MATERIALS AND METHODS

This was a retrospective cross-sectional study performed on 1243 suspected cases of SARS-CoV-2 infection from March 25, 2020 to April 17, 2020 in the department of microbiology of our institute to know the incidence of SARS-CoV-2 infection in selected districts of Uttar Pradesh. These cases were analyzed to see the association of various clinical symptoms with SARS-CoV-2 infection. For statistical analysis, Pearson's Chi-square test was performed using SPSS version 23.

RESULTS

Out of total suspected cases, 4.5% were positive. Travel history was present in 80.4% of positive cases. About 83.9% had fever, 28.6% had shortness of breath, 35.7% had dry cough, 17.9% had either Type I or II diabetes mellitus, 12.5% had chronic kidney disease, and 7.1% had obstructive pulmonary diseases.

CONCLUSION

Negative clinical history is very important in ruling out the suspected cases who came out to be free from the infection.

COVID-19 diagnostic laboratory strategies: modern technologies and development trends (review of literature)

The COVID-19 pandemic, associated with the new coronavirus SARS-CoV-2, has caused a surge in incidence worldwide, as well as a severe crisis in global health and economy. Therefore, fast and accurate diagnosis of infection is key to timely treatment and elimination of the spread of the virus. Currently, the standard method for detecting coronavirus is reverse transcription polymerase chain reaction (RT-PCR). However, this method requires expensive equipment and trained personnel, which limits the conduct of mass testing and lengthens the time to obtain a research result. Serological tests for antibodies against SARS-CoV-2 and the determination of protective immunity in various populations are used to retrospectively identify patients with asymptomatic and mild forms of infection, monitor the course of infection in hospitalized patients, and also track contacts and epidemiological surveillance. The use of standard methods for diagnosing COVID-19 in conditions of mass morbidity, especially in conditions of insufficient resources and lack of appropriate infrastructure, is associated with a number of limitations. Therefore, the search and development of new, fast, inexpensive, simple, device-free and no less sensitive and specific tests is an urgent task. Therefore, the search and development of new, fast, inexpensive, simple, device-free and no less sensitive and specific tests is an urgent task. The review examines new laboratory technologies for diagnosing a new infection - loop isothermal amplification (LAMP) and immunochromatographic analysis (ICA), which can become a real alternative to the used molecular and enzyme immunoassay methods. The dynamic development of these methods in recent years expands the prospects for their use both for diagnosing COVID-19 and monitoring a pandemic.

A Study on Understanding Potential Gold and Silver Nanoparticle : An Overview

This paper highlights on the coronavirus outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At the time of writing this paper, there has been over 6 million confirmed cases worldwide. It is a person–person transmittable infection but there have been cases of asymptomatic carriers. Hence, development of an effective biosensing diagnostic tool can curb its rapid transmission rate. The first part of the paper highlights on the SARS-CoV-2 structure and its resemblance to SARS-CoV. The second part of the paper analyzes on the potential application of gold and silver nanoparticles to generate a red shift that had enhanced the calorimetric property of the MERS-CoV analysis due to transition in its optical property. Other electrochemical techniques that utilized the application of gold nanoparticles are also reviewed. Gold and silver nanoparticles (AuNP and Ag NP) can accelerate the sensitivity upon electrodeposition on the diagnostic tool.

Point-of-Care Biosensor-Based Diagnosis of COVID-19 Holds Promise to Combat Current and Future Pandemics

Efficient and rapid detection of viruses plays an extremely important role in disease prevention, diagnosis, and environmental monitoring. Early screening of viral infection among the population has the potential to combat the spread of infection. However, the traditional methods of virus detection being used currently, such as plate culturing and quantitative RT-PCR, give promising results, but they are time-consuming and require expert analysis and costly equipment and reagents; therefore, they are not affordable by people in low socio-economic groups in developing countries. Further, mass or bulk testing chosen by many governments to tackle the pandemic situation has led to severe shortages of testing kits and reagents and hence are affecting the demand and supply chain drastically. We tried to include all the reported current scenario-based biosensors such as electrochemical, optical, and microfluidics, which have the potential to replace mainstream diagnostic methods and therefore could pave the way to combat COVID-19. Apart from this, we have also provided information on commercially available biosensors for detection of SARS-CoV-2 along with the challenges in development of better diagnostic approaches. It is therefore expected that the content of this review will help researchers to design and develop more sensitive advanced commercial biosensor devices for early diagnosis of viral infection, which can open up avenues for better and more specific therapeutic outcomes.

Rapid Differential Diagnosis of Seven Human Respiratory Coronaviruses Based on Centrifugal Microfluidic Nucleic Acid Assay

With the global outbreak of the coronavirus disease 2019 (COVID-19), the highly infective, highly pathogenic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has attracted great attention. Currently, a method to simultaneously diagnose the seven known types human coronaviruses remains lacking and is urgently needed. In this work, we successfully developed a portable microfluidic system for the rapid, accurate, and simultaneous detection of SARS-CoV, middle east respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2, and four other human coronaviruses (HCoVs) including HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1. The disk-like microfluidic platform integrated with loop-mediated isothermal amplification provides highly accurate, sensitive, and specific results with a wide linear range within 40 min. The diagnostic tool achieved 100% consistency with the "gold standard" polymerase chain reaction in detecting 54 real clinical samples. The integrated system, with its simplicity, is urgently needed for the diagnosis of SARS-CoV-2 during the COVID-19 pandemic.

Quasi-species nature and differential gene expression of severe acute respiratory syndrome coronavirus 2 and phylogenetic analysis of a novel Iranian strain

A novel coronavirus related to severe acute respiratory syndrome virus, (SARS-CoV-2) is the causal agent of the COVID-19 pandemic. Despite the genetic mutations across the SARS-CoV-2 genome being recently investigated, its transcriptomic genetic polymorphisms at inter-host level and the viral gene expression level based on each Open Reading Frame (ORF) remains unclear. Using available High Throughput Sequencing (HTS) data and based on SARS-CoV-2 infected human transcriptomic data, this study presents a high-resolution map of SARS-CoV-2 single nucleotide polymorphism (SNP) hotspots in a viral population at inter-host level. Four throat swab samples from COVID-19 infected patients were pooled, with RNA-Seq read retrieved from SRA NCBI to detect 21 SNPs and a replacement across the SARS-CoV-2 genomic population. Twenty-two RNA modification sites on viral transcripts were identified that may cause inter-host genetic diversity of this virus. In addition, the canonical genomic RNAs of N ORF showed higher expression in transcriptomic data and reverse transcriptase quantitative PCR compared to other SARS-CoV-2 ORFs, indicating the importance of this ORF in virus replication or other major functions in virus cycle. Phylogenetic and ancestral sequence analyses based on the entire genome revealed that SARS-CoV-2 is possibly derived from a recombination event between SARS-CoV and Bat SARS-like CoV. Ancestor analysis of the isolates from different locations including Iran suggest shared Chinese ancestry. These results propose the importance of potential inter-host level genetic variations to the evolution of SARS-COV-2, and the formation of viral quasi-species. The RNA modifications discovered in this study may cause amino acid sequence changes in polyprotein, spike protein, product of ORF8 and nucleocapsid (N) protein, suggesting further insights to understanding the functional impacts of mutations in the life cycle and pathogenicity of SARS-CoV-2.

South Indian medicinal plants can combat deadly viruses along with COVID-19? - A review

SARS-CoV-2 is a causative agent of Coronavirus disease-19 (COVID-19), which is considered as a fatal disease for public health apprehension worldwide. This pathogenic virus can present everywhere. As it is a virus it can extend easily and cause severe illness to humans. Hence, an efficient international attentiveness of plan is necessary to cure and prevent. In this review, epidemic outbreak, clinical findings, prevention recommendations of COVID-19 and suggestive medicinal value of south Indian plant sources have been discussed. Though the varieties of improved approaches have been taken in scientific and medicinal concern, we have to pay attention to the medicinal value of the plant-based sources to prevent these types of pandemic diseases. This is one of the suggestive and effective ways to control the spreading of viruses. In the future, it is required to provide medicinal plant-based clinical products (Masks, sanitizers, soap, etc.,) with better techniques by clinicians to contend the scarcity and expose towards the nature-based medicine rather than chemical drugs. This may be a benchmark for the economical clinical trials of specific plant material to treat the viral diseases in the future.

Trends in MERS-CoV, SARS-CoV, and SARS-CoV-2 (COVID-19) Diagnosis Strategies: A Patent Review

The emergence of a new coronavirus (SARS-CoV-2) outbreak represents a challenge for the diagnostic laboratories responsible for developing test kits to identify those infected with SARS-CoV-2. Methods with rapid and accurate detection are essential to control the sources of infection, to prevent the spread of the disease and to assist decision-making by public health managers. Currently, there is a wide variety of tests available with different detection methodologies, levels of specificity and sensitivity, detection time, and with an extensive range of prices. This review therefore aimed to conduct a patent search in relation to tests for the detection of SARS-CoV, MERS-CoV, and SARS-CoV-2. The greatest number of patents identified in the search were registered between 2003 and 2011, being mainly deposited by China, the Republic of Korea, and the United States. Most of the patents used the existing RT-PCR, ELISA, and isothermal amplification methods to develop simple, sensitive, precise, easy to use, low-cost tests that reduced false-negative or false-positive results. The findings of this patent search show that an increasing number of materials and diagnostic tests for the coronavirus are being produced to identify infected individuals and combat the growth of the current pandemic; however, there is still a question in relation to the reliability of the results of these tests.

CRISPR-based assays for rapid detection of SARS-CoV-2

COVID-19 pandemic posed an unprecedented threat to global public health and economies. There is no effective treatment of the disease, hence, scaling up testing for rapid diagnosis of SARS-CoV-2 infected patients and quarantine them from healthy individuals is one the best strategies to curb the pandemic. Establishing globally accepted easy-to-access diagnostic tests is extremely important to understanding the epidemiology of the present pandemic. While nucleic acid based tests are considered to be more sensitive with respect to serological tests but present gold standard qRT-PCR-based assays possess limitations such as low sample throughput, requirement for sophisticated reagents and instrumentation. To overcome these shortcomings, recent efforts of incorporating LAMP-based isothermal detection, and minimizing the number of reagents required are on rise. CRISPR based novel techniques, when merge with isothermal and allied technologies, promises to provide sensitive and rapid detection of SARS-CoV-2 nucleic acids. Here, we discuss and present compilation of state-of-the-art detection techniques for COVID-19 using CRISPR technology which has tremendous potential to transform diagnostics and epidemiology.

Recent advances in the nucleic acid-based diagnostic tool for coronavirus

Abstract

Recently in China, a novel coronavirus outbreak took place which caused pneumonia-like symptoms. This coronavirus belongs to the family of SARS and MERS and causes respiratory system disease known as COVID-19. At present we use polymerase chain reaction (PCR) based molecular biology methods for the detection of coronavirus. Other than these PCR based methods, some improved methods also exist such as microarray-based techniques, Real time-quantitative PCR, CRISPR-Cas13 based tools but almost all of the available methods have advantages and disadvantages. There are many limitations associated with this method and hence there is a need for a fast, more sensitive, and specific diagnostic tool which can detect a greater number of samples in less time. Here we have summarised currently available nucleic acid-based diagnostic methods for the detection of coronavirus and the need for developing a better technique for a fast and sensitive detection of coronavirus infections.

Graphic abstract

Nucleic acid based detection tool for SARS-CoV-2.

A Characteristic Chest Radiographic Pattern in the Setting of the COVID-19 Pandemic

PURPOSE

To determine the utility of chest radiography in aiding clinical diagnosis of coronavirus disease 2019 (COVID-19) utilizing reverse-transcription polymerase chain reaction (RT-PCR) as the standard of comparison.

MATERIALS AND METHODS

A retrospective study was performed of persons under investigation for COVID-19 presenting to this institution during the exponential growth phase of the COVID-19 outbreak in New Orleans (March 13-25, 2020). Three hundred seventy-six in-hospital chest radiographic examinations for 366 individual patients were reviewed along with concurrent RT-PCR tests. Two experienced radiologists categorized each chest radiograph as characteristic, nonspecific, or negative in appearance for COVID-19, utilizing well-documented COVID-19 imaging patterns. Chest radiograph categorization was compared against RT-PCR results to determine the utility of chest radiography in diagnosing COVID-19.

RESULTS

Of the 366 patients, the study consisted of 178 male (49%) and 188 female (51%) patients with a mean age of 52.7 years (range, 17 to 98 years). Of the 376 chest radiographic examinations, 37 (10%) exhibited the characteristic COVID-19 appearance; 215 (57%) exhibited the nonspecific appearance; and 124 (33%) were considered negative for a pulmonary abnormality. Of the 376 RT-PCR tests evaluated, 200 (53%) were positive and 176 (47%) were negative. RT-PCR tests took an average of 2.5 days ± 0.7 to provide results. Sensitivity and specificity for correctly identifying COVID-19 with a characteristic chest radiographic pattern was 15.5% (31/200) and 96.6% (170/176), with a positive predictive value and negative predictive value of 83.8% (31/37) and 50.1% (170/339), respectively.

CONCLUSION

The presence of patchy and/or confluent, bandlike ground-glass opacity or consolidation in a peripheral and mid to lower lung zone distribution on a chest radiograph obtained in the setting of pandemic COVID-19 was highly suggestive of severe acute respiratory syndrome coronavirus 2 infection and should be used in conjunction with clinical judgment to make a diagnosis.© RSNA, 2020.

SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies

In December 2019, an outbreak of atypical pneumonia (Coronavirus disease 2019 -COVID-19) associated with a novel coronavirus (SARS-CoV-2) was reported in Wuhan city, Hubei province, China. The outbreak was traced to a seafood wholesale market and human to human transmission was confirmed. The rapid spread and the death toll of the new epidemic warrants immediate intervention. The intra-host genomic variability of SARS-CoV-2 plays a pivotal role in the development of effective antiviral agents and vaccines, as well as in the design of accurate diagnostics. We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify small- and large-scale intra-host variations in the viral genome. We identified tens of low- or higher- frequency single nucleotide variations (SNVs) with variable density across the viral genome, affecting 7 out of 10 protein-coding viral genes. The majority of these SNVs (72/104) corresponded to missense changes. The annotation of the identified SNVs but also of all currently circulating strain variations revealed colocalization of intra-host as well as strain specific SNVs with primers and probes currently used in molecular diagnostics assays. Moreover, we de-novo assembled the viral genome, in order to isolate and validate intra-host structural variations and recombination breakpoints. The bioinformatics analysis disclosed genomic rearrangements over poly-A / poly-U regions located in ORF1ab and spike (S) gene, including a potential recombination hot-spot within S gene. Our results highlight the intra-host genomic diversity and plasticity of SARS-CoV-2, pointing out genomic regions that are prone to alterations. The isolated SNVs and genomic rearrangements reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays.

Fighting COVID-19: Integrated Micro- and Nanosystems for Viral Infection Diagnostics

The pandemic of coronavirus disease 2019 (COVID-19) highlights the importance of rapid and sensitive diagnostics of viral infection that enables the efficient tracing of cases and the implementation of public health measures for disease containment. The immediate actions from both academia and industry have led to the development of many COVID-19 diagnostic systems that have secured fast-track regulatory approvals and have been serving our healthcare frontlines since the early stage of the pandemic. On diagnostic technologies, many of these clinically validated systems have significantly benefited from the recent advances in micro- and nanotechnologies in terms of platform design, analytical method, and system integration and miniaturization. The continued development of new diagnostic platforms integrating micro- and nanocomponents will address some of the shortcomings we have witnessed in the existing COVID-19 diagnostic systems. This Perspective reviews the previous and ongoing research efforts on developing integrated micro- and nanosystems for nucleic acid-based virus detection, and highlights promising technologies that could provide better solutions for the diagnosis of COVID-19 and other viral infectious diseases. With the summary and outlook of this rapidly evolving research field, we hope to inspire more research and development activities to better prepare our society for future public health crises.

Re-positive coronavirus disease 2019 PCR test: could it be a reinfection?

The coronavirus disease 2019 (COVID-19) outbreak started in December 2019 and rapidly spread around the globe as a major health threat. Several reports on re-positive cases subsequent to discharge from hospitals caught our attention. We aimed to highlight RT-qPCR positivity re-detection after discharge from isolation, with special consideration of the possible reasons behind it. We found that re-positive RT-qPCR assays for severe acute respiratory syndrome coronavirus 2 after previous negative results might be attributed to false-negative laboratory results and prolonged viral shedding, rather than to re-infection. These findings are encouraging and should be validated in a larger cohort.

Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection

The new coronavirus SARS-CoV-2, the cause of COVID-19, has become a public health emergency of global concern. Like the SARS and influenza pandemics, there have been a large number of cases coinfected with other viruses, fungi, and bacteria, some of which originate from the oral cavity. Capnocytophaga, Veillonella, and other oral opportunistic pathogens were found in the BALF of the COVID-19 patients by mNGS. Risk factors such as poor oral hygiene, cough, increased inhalation under normal or abnormal conditions, and mechanical ventilation provide a pathway for oral microorganisms to enter the lower respiratory tract and thus cause respiratory disease. Lung hypoxia, typical symptoms of COVID-19, would favor the growth of anaerobes and facultative anaerobes originating from the oral microbiota. SARS-CoV-2 may aggravate lung disease by interacting with the lung or oral microbiota via mechanisms involving changes in cytokines, T cell responses, and the effects of host conditions such as aging and the oral microbiome changes due to systemic diseases. Because the oral microbiome is closely associated with SARS-CoV-2 co-infections in the lungs, effective oral health care measures are necessary to reduce these infections, especially in severe COVID-19 patients. We hope this review will draw attention from both the scientific and clinical communities on the role of the oral microbiome in the current global pandemic.

A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2

Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically analyse the data. Our assay could detect to a limit of 15 copies of SARS-CoV-2 transcripts-based on experiments performed by spiking total human RNA with in vitro synthesized viral transcripts. The assay was evaluated by performing 184 validations for the SARS-CoV-2 Nucleocapsid gene and human RNase P as an internal control reference gene with dilutions ranging from 1-100 ng for human RNA on a cohort of 26 clinical samples. 5 of 26 patients were confirmed to be infected with SARS-CoV-2, while 21 tested negative, consistent with the standards. The accuracy of the assay was found to be 100% sensitive and 100% specific based on the 26 clinical samples that need to be further verified using a large number of clinical samples. In summary, we present a rapid, easy to implement real-time PCR based assay with automated analysis using a novel COVID qPCR Analyzer tool with graphical user interface (GUI) to analyze the raw qRT-PCR data in an unbiased manner at a cost of under $3 per reaction and turnaround time of less than 2h, to enable in-house SARS-CoV-2 testing across laboratories.

Clinical-Forensic Autopsy Findings to Defeat COVID-19 Disease: A Literature Review

The severe acute respiratory syndrome (SARS)-CoV-2 was identified for the first time in China, in December 2019. Confirmed cases of COVID-19 have been reported around the world; indeed, this infection has been declared a pandemic. Consequently, the scientific community is working hard to gain useful information about the history of this virus, its transmission, diagnosis, clinical features, radiological findings, research and development of candidate therapeutics as well as vaccines. This review aims to analyze the diagnostic techniques used to ascertain the COVID-19 infection, critically reviewing positive points and criticism for forensic implications, obviously including autopsy. Finally, this review proposes a practical workflow to be applied in the management of corpses during this outbreak of the COVID-19 infection, which could be useful in cases of future infectious disease emergencies. Analyzing the diagnostic methods, to date, virus nucleic acid RT-PCR represents the standard method used to ascertain the COVID-19 infection in living subjects and corpses, even if this technique has several criticisms: mainly, the staff should be highly specialized, working in high-throughput settings, able to handle high workloads and aware of health risks and the importance of the results. Thus, IgG/IgM serological tests have been developed, overcoming RT-qPCR duration, costs, and management, not requiring highly trained personnel. Nevertheless, serological tests present problems; the WHO recommends the use of these new point-of-care immunodiagnostic tests only in research settings. Furthermore, nothing has yet been published regarding the possibility of applying these methods during post-mortem investigations. In light of this scenario, in this review, we suggest a flow chart for the pathologist called on to ascertain the cause of death of a subject with historical and clinical findings of COVID-19 status or without any anamnestic, diagnostic, or exposure information. Indeed, the literature data confirmed the analytical vulnerabilities of the kits used for laboratory diagnosis of COVID-19, particularly during postmortem examinations. For these reasons, autopsy remains the gold standard method to ascertain the exact cause of death (from or with COVID-19 infection, or other causes), to consequently provide real data for statistical evaluations and to take necessary measures to contain the risks of the infection. Moreover, performing autopsies could provide information on the pathogenesis of the COVID-19 infection with obvious therapeutic implications.

Loop mediated isothermal amplification (LAMP) assays as a rapid diagnostic for COVID-19

Recently, a novel coronavirus (SARS-CoV-2; coronavirus disease 2019, COVID-19) has emerged, rapidly spreading and severely straining the capacity of the global health community. Many nations are employing combinations of containment and mitigation strategies, where early diagnosis of COVID-19 is vital in controlling illness progression and limiting viral spread within the population. Thus, rapid and accurate methods of early detection are vital to contain COVID-19 and prevent further spread and predicted subsequent infectious waves of viral recurrence in future. Immediately after its initial characterization, Chinese and American Centers for Disease Control and Prevention (CDCs) rapidly employed molecular assays for detection of COVID-19, mostly employing real-time polymerase chain reaction (RT-PCR) methods. However, such methods require specific expensive items of equipment and highly trained analysts, requiring upwards of 4–8 h to process. These requirements coupled with associated financial pressures may prevent effective deployment of such diagnostic tests. Loop mediated isothermal amplification (LAMP) is method of nucleic acid amplification which exhibits increased sensitivity and specificity are significantly rapid, and do not require expensive reagents or instruments, which aids in cost reduction for coronavirus detection. Studies have shown the successful application of LAMP assays in various forms to detect coronavirus RNA in patient samples, demonstrating that 1–10 copies of viral RNA template per reaction are sufficient for successful detection, ~100-fold more sensitive than conventional RT-PCR methods. Importantly, studies have also now demonstrated the effectiveness of LAMP methodology in the detection of SARS-CoV-2 RNA at significantly low levels, particularly following numerous improvements to LAMP assay protocols. We hypothesise that recent advancements in enhanced LAMP protocols assay perhaps represent the best chance for a rapid and robust assay for field diagnosis of COVID-19, without the requirement of specialized equipment and highly trained professionals to interpret results. Herein, we present our arguments with a view to disseminate such findings, to assist the combat of this virus that is proving so devastating. We hope that this strategy could be applied rapidly, and confirmed for viability with clinical samples, before being rolled out for mass-diagnostic testing in these current times.

Measures for diagnosing and treating infections by a novel coronavirus responsible for a pneumonia outbreak originating in Wuhan, China

On 10 January 2020, a new coronavirus causing a pneumonia outbreak in Wuhan City in central China was denoted as 2019-nCoV by the World Health Organization (WHO). As of 24 January 2020, there were 887 confirmed cases of 2019-nCoV infection, including 26 deaths, reported in China and other countries. Therefore, combating this new virus and stopping the epidemic is a matter of urgency. Here, we focus on advances in research and development of fast diagnosis methods, as well as potential prophylactics and therapeutics to prevent or treat 2019-nCoV infection.

Recent advances and perspectives of nucleic acid detection for coronavirus

The recent pneumonia outbreak caused by a novel coronavirus (SARS-CoV-2) is posing a great threat to global public health. Therefore, rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people’s lives and preventing epidemics. It is important to establish a quick standard diagnostic test for the detection of the infectious disease (COVID-19) to prevent subsequent secondary spread. Polymerase chain reaction (PCR) is regarded as a gold standard test for the molecular diagnosis of viral and bacterial infections with high sensitivity and specificity. Isothermal nucleic acid amplification is considered to be a highly promising candidate method due to its fundamental advantage in quick procedure time at constant temperature without thermocycler operation. A variety of improved or new approaches also have been developed. This review summarizes the currently available detection methods for coronavirus nucleic acid. It is anticipated that this will assist researchers and clinicians in developing better techniques for timely and effective detection of coronavirus infection.

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This review summarizes the currently available detection methods for coronavirus nucleic acid.

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It will assist researchers in developing better techniques for timely and effective detection of coronavirus infection.

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It will help the establishment of SARS-CoV-2 RNA detection method which is useful for the early diagnosis of COVID-19.