Genetic analysis of the 2019 coronavirus pandemic with from Real-time reverse transcriptase polymerase chain reaction
ABSTRACT: 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.
Project description:Highlights • The urgent need for rapid and sensitive SARS-CoV-2 detection is highlighted.• Working principle of LAMP assay for nucleic acid detection is introduced.• RT-LAMP enabled isothermal amplification methods for COVID-19 diagnosis are summarized.• Future trends for COVID-19 detection was presented and discussed. The coronavirus disease 2019 (COVID-19) pandemic has infected millions of people around the globe. The outbreak caused by the novel coronavirus (SARS-CoV-2) poses a great health risk to the public. Therefore, rapid and accurate diagnosis of the virus plays a crucial role in treatment of the disease and saving lives. The current standard method for coronavirus detection is the reverse transcription polymerase chain reaction (RT-PCR) method. However, laboratory-based RT-PCR test for SARS-COV-2 requires complex facilities and elaborate training of operators, thus suffering from limit testing capacity and delayed results. Consequently, isothermal PCR such as loop-mediated isothermal amplification (LAMP) has been emerging as a great alternative to the RT-PCR method. LAMP possesses some fundamental advantages such as amplification at a constant temperature, exclusion of a thermal cycler, a faster test result, and potentially a larger diagnostic capacity, while maintaining similar sensitivity and specificity, thus making it more suitable than the RT-PCR for monitoring a pandemic. Starting with a brief introduction of the working principle of LAMP method, this review summarizes recent progress in LAMP-enabled SARS-CoV-2 viral RNA detection. Lastly, future research directions are discussed. This critical review will motivate biosensor community in furthering the present research, which may pave the road for rapid and large-scale screening of SARS-CoV-2.
Project description:OBJECTIVE:This study aimed to investigate the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients presenting with only sudden sensorineural hearing loss (SSHNL) during the COVID-19 pandemic. METHODS:The study included five male patients who presented with the sole complaint of unilateral SSNHL to the otolaryngology outpatient clinic between 03-12 April 2020. The patients were referred to the infectious diseases clinic to be evaluated for SARS-CoV-2 by real time polymerase chain reaction (RT-PCR) testing. RESULTS:RT-PCR testing for SARS-CoV-2 was positive in one of the patients and negative in the other four patients. A positive response to COVID-19-specific treatment in the SARS-CoV-2 positive SSNHL patient was noted. CONCLUSION:It should be remembered that non-specific symptoms such as SSNHL could be the only sign with which to recognize a COVID-19 case. Awareness of such a non-specific presentation of COVID-19 patients is crucial during this pandemic period for preventing infectious spread through isolation and early initiation of COVID-19 targeted treatment.
Project description:BACKGROUND:The Coronavirus disease 2019 (COVID-19) pandemic continues to spread across the world. Hence, there is an urgent need for rapid, simple, and accurate tests to diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Performance characteristics of the rapid SARS-CoV-2 antigen detection test should be evaluated and compared with the gold standard real-time reverse transcription-polymerase chain reaction (RT-PCR) test for diagnosis of COVID-19 cases. METHODS:The rapid SARS-CoV-2 antigen detection test, Standard™ Q COVID-19 Ag kit (SD Biosensor®, Republic of Korea), was compared with the real-time RT-PCR test, Allplex™ 2019-nCoV Assay (Seegene®, Korea) for detection of SARS-CoV-2 in respiratory specimens. Four hundred fifty-four respiratory samples (mainly nasopharyngeal and throat swabs) were obtained from COVID-19 suspected cases and contact individuals, including pre-operative patients at Siriraj Hospital, Bangkok, Thailand during March-May 2020. RESULTS:Of 454 respiratory samples, 60 (13.2%) were positive, and 394 (86.8%) were negative for SARS-CoV-2 RNA by real-time RT-PCR assay. The duration from onset to laboratory test in COVID-19 suspected cases and contact individuals ranged from 0 to 14 days with a median of 3 days. The rapid SARS-CoV-2 antigen detection test's sensitivity and specificity were 98.33% (95% CI, 91.06-99.96%) and 98.73% (95% CI, 97.06-99.59%), respectively. One false negative test result was from a sample with a high real-time RT-PCR cycle threshold (Ct), while five false positive test results were from specimens of pre-operative patients. CONCLUSIONS:The rapid assay for SARS-CoV-2 antigen detection showed comparable sensitivity and specificity with the real-time RT-PCR assay. Thus, there is a potential use of this rapid and simple SARS-CoV-2 antigen detection test as a screening assay.
Project description:Containment strategies and clinical management of coronavirus disease (COVID-19) patients during the current pandemic depend on reliable diagnostic PCR assays for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we compare 11 different RT-PCR test systems used in seven diagnostic laboratories in Germany in March 2020. While most assays performed well, we identified detection problems in a commonly used assay that may have resulted in false-negative test results during the first weeks of the pandemic.
Project description:The emergence of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for causing coronavirus disease 2019 (COVID-19), marked the third time in the twenty-first century when a new, highly pathogenic human coronavirus outbreak has led to an epidemic. The COVID-19 epidemic has emerged in late December 2019 in Wuhan city of China and spread rapidly to other parts of the world. This quick spread of SARS-CoV-2 infection to many states across the globe affecting many people has led WHO to declare it a pandemic on March 12, 2020. As of July 4, 2020, more than 523,011 people lost their lives worldwide because of this deadly SARS-CoV-2. The current situation becomes more frightening as no FDA-approved drugs or vaccines are available to treat or prevent SARS-CoV-2 infection. The current therapeutic options for COVID-19 are limited only to supportive measures and non-specific interventions. So, the need of the hour is to search for SARS-CoV-2-specific antiviral treatments and to develop vaccines for SARS-CoV-2. Also, it is equally important to maintain our immunity, and natural products and Ayurvedic medicines are indispensable in this regard. In this review, we discuss recent updates regarding various therapeutic approaches to combat COVID-19 pandemic and enlist the major pipeline drugs and traditional medicines that are under trial for COVID-19. Also, possible mechanisms involved in viral pathogenesis are discussed, which further allow us to understand various drug targets and helps in discovering novel therapeutic approaches for COVID-19. Altogether, the information provided in this review will work as an intellectual groundwork and provides an insight into the ongoing development of various therapeutic agents.
Project description:The novel Coronavirus disease of 2019 (nCOV-19) is a viral outbreak noted first in Wuhan, China. This disease is caused by Severe Acute Respiratory Syndrome (SARS) Coronavirus (CoV)-2. In the past, other members of the coronavirus family, such as SARS and Middle East Respiratory Syndrome (MERS), have made an impact in China and the Arabian peninsula respectively. Both SARS and COVID-19 share similar symptoms such as fever, cough, and difficulty in breathing that can become fatal in later stages. However, SARS and MERS infections were epidemic diseases constrained to limited regions. By March 2020 the SARS-CoV-2 had spread across the globe and on March 11th, 2020 the World Health Organization (WHO) declared COVID-19 as pandemic disease. In severe SARS-CoV-2 infection, many patients succumbed to pneumonia. Higher rates of deaths were seen in older patients who had co-morbidities such as diabetes mellitus, hypertension, cardiovascular disease (CVD), and dementia. In this review paper, we discuss the effect of SARS-CoV-2 on CNS diseases, such as Alzheimer's-like dementia, and diabetes mellitus. We also focus on the virus genome, pathophysiology, theranostics, and autophagy mechanisms. We will assess the multiorgan failure reported in advanced stages of SARS-CoV-2 infection. Our paper will provide mechanistic clues and therapeutic targets for physicians and investigators to combat COVID-19.
Project description:Coronavirus disease 2019 (COVID-19) is an infection caused by the novel coronavirus severe acute respiratory coronavirus 2 (SARS-CoV-2). The infection manifests as a mild flu to severe acute respiratory infection. The World Health Organization (WHO) declared COVID-19 as a global pandemic on March 11, 2020. The disease spreads by droplet infection from person to person. Early diagnosis is the key for prompt management of cases and control of the spread of the virus. Currently, the laboratory diagnosis of SARS-CoV-2 is based on nucleic acid amplification tests (NAAT) like real-time reverse transcriptase (RT-PCR). Various genes like E, N, S, ORF and RdRp are targeted as a part of screening and confirmation of cases. Furthermore, nucleic acid sequencing may be done for the identification of mutation in the genome of SARS-CoV-2. The development of serological assays and point of care molecular test will further intensify the diagnostic modalities of SARS-CoV-2.
Project description:The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The objective of this study was to determine the clinical course and risk factors for patients showing recurrent SARS-CoV-2 RNA positivity. A total of 1087 COVID-19 patients confirmed by RT-PCR from February 24, 2020 to March 31, 2020 were retrospectively enrolled. Advanced age was significantly associated with mortality. In addition, 81 (7.6%) of the discharged patients tested positive for SARS-CoV-2 RNA during the isolation period. For patients with recurrent RT-PCR positivity, the median duration from illness onset to recurrence was 50 days. Multivariate regression analysis identified elevated serum IL-6, increased lymphocyte counts and CT imaging features of lung consolidation during hospitalization as the independent risk factors of recurrence. We hypothesized that the balance between immune response and virus toxicity may be the underlying mechanism of this phenomenon. For patients with a high risk of recurrence, a prolonged observation and additional preventative measures should be implemented for at least 50 days after illness onset to prevent future outbreaks.
Project description:Background. International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods. We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results. In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (?Ct) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions. Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings.
Project description:To understand how COVID-19 alters the platelet transcriptome. Overall design: A cohort of eight hospitalized COVID-19 patients (n=8) were recruited from NYU Langone Health between May 11-21, 2020. SARS-CoV-2 infection was confirmed by RT-PCR, in accordance with current standards. All COVID-19 patients and , age-, and sex-matched control donors were recruited under study protocols approved by the NYU Langone Health Institutional Review Board. Each study participant or their Legal Authorized Representative gave written informed consent for study enrollment in accordance with the Declaration of Helsinki. For COVID-19 patients, enrollment criteria included age greater than 18, hospital admission, positive SARS-CoV-2 testing, and informed consent. COVID-19 patients were monitored until discharge or death.