To meet the unprecedented requirement of diagnostic testing for SARS-CoV-2, a large number of diagnostic kits were authorized by concerned authorities for diagnostic use within a short period of time during the initial phases of the ongoing pandemic. We undertook this study to evaluate the inter-test agreement and other key operational features of 5 such commercial kits that have been extensively used in India for routine diagnostic testing for COVID-19. The five commercial kits were evaluated, using a panel of positive and negative respiratory samples, considering the kit provided by National Institute of Virology, Indian Council of Medical Research (2019-nCoV Kit) as the reference. The positive panel comprised of individuals who fulfilled the 3 criteria of being clinically symptomatic, having history of contact with diagnosed cases and testing positive in the reference kit. The negative panel included both healthy and disease controls, the latter being drawn from individuals diagnosed with other respiratory viral infections. The same protocol of sample collection, same RNA extraction kit and same RT-PCR instrument were used for all the kits. Clinical samples were collected from a panel of 92 cases and 60 control patients, who fulfilled our inclusion criteria. The control group included equal number of healthy individuals and patients infected with other respiratory viruses (n = 30, in each group). We observed varying sensitivity and specificity among the evaluated kits, with LabGun COVID-19 RT-PCR kit showing the highest sensitivity and specificity (94% and 100% respectively), followed by TaqPath COVID-19 Combo and Allplex 2019-nCoV assays. The extent of inter-test agreement was not associated with viral loads of the samples. Poor correlation was observed between Ct values of the same genes amplified using different kits. Our findings reveal the presence of wide heterogeneity and sub-optimal inter-test agreement in the diagnostic performance of the evaluated kits and hint at the need of adopting stringent standards for fulfilling the quality assurance requirements of the COVID-19 diagnostic process.
Objective:We are presently going through a historic and unprecedented crisis for humanity with SARS-CoV-2 causing immense damage to life and world economics. It has been 3 months, since we had the first cluster in China and we felt the need to look into certain regional patterns of transmission of the virus with respect to some distinctive living conditions, incidence of malaria, the genomics of different strains, and its impact on severity.Material and Methods: Data for 107 countries was compiled and correlation analysis was done between incidence of malaria and number of SARS-CoV-2 cases. Possibility of genetic similarity between SARS-CoV-2 and reported zoonotic RNA viruses found associated previously with some Plasmodium species was explored by utilizing NCBI database. Results:We found a significant inverse correlation between SARS-CoV-2 disease burden and incidence of Malaria. Our analysis also showed that a 12 base pair region encoding a part of surface glycoprotein of SARS-CoV-2 aligned with the Plasmodium associated zoonotic viral genome. Conclusion:Our analysis suggests a significantly lower SARS-CoV-2 disease burden in Malaria endemic regions and an inverse correlation with incidence of Malaria. The possibility of a pre-existing immunological memory for SARS-CoV-2 in Indians is possible and needs to be explored further
Lung cancer, one of the most frequently diagnosed cancers worldwide has long relied on testing for the molecular biomarkers EGFR/ALK. However, achieving superior clinical outcomes for patients with lung cancer requires developing comprehensive techniques beyond contemporary EGFR/ALK testing. Current technologies are on par with molecular testing for EGFR/ALK in terms of efficacy, most of them failing to offer improvements perhaps primarily due to skepticism among clinicians, despite being recommended in the NCCN guidelines. The present study endeavored to minimize chemotherapy-dependence in EGFR/ALK-negative patient cohorts, and use evidence-based methods to identify ways to improve clinical outcomes. In total, 137 lung cancer cases obtained from 'PositiveSelect NGS data', comprising 91 males and 46 females, were investigated. EGFR-and ALK-positivity was used for data dichotomization to understand the therapeutic utility of rare gene alterations beyond just EGFR/ALK. Statistics obtained from PositiveSelect were collated with data from international studies to construct a meta-analysis intended to achieve better clinical outcomes. Upon dichotomization, 23% of cases harbored EGFR variants indicating that treating with EGFR TKIs would be beneficial; the remaining 77% exhibited no EGFR variants that would indicate favorable results using specific currently available chemotherapy practices. Similarly, 28% of cases had EGFR+ALK variants favoring EGFR/ALK-based targeted therapeutics; the remaining 72% harbored no EGFR/ALK variants with known beneficial chemotherapy routes. The present study aimed to overcome current inadequacies of targeted therapies in patients with a conventional EGFR/ALK-positive diagnosis and those in EGFR+ALK-negative cohorts. Upon analysis of the negative cohorts, significant and clinically relevant single nucleotide variants were identified in KRAS, ERBB2, MET and RET, with frequencies of 7, 1, 2 and 3% in patients who were EGFR-negative and 6, 1, 1, and 3% in patients who were EGFR and ALK-negative, respectively, enabling the use of targeted therapeutics aside from EGFR/ALK TKIs. From the results of the current study only 35% of the two negative arms (EGFR negative and EGFR+ALK negative) would be recommended NCCN or off-label chemotherapy; prior to the current study, the entire cohorts would have been recommended this treatment. The present study emphasizes the potential of comprehensive genomics in identifying hallmarks of lung cancer beyond EGFR/ALK, using broad-spectrum genetic testing and data-sharing among medical professionals to circumvent ineffective chemotherapy.
Introduction: We present data from a systematic survey on conflict of interest (COI) disclosure and its interpretation by the doctors participating in continuing medical education (CME). Methods: A brief 12 question online Google survey with multiple choice options (read, select, and click) was done among Indian practicing doctors using links shared through WhatsApp through the internet over a 72 h period. Results: Of the 386 replies, 373 unique replies were eligible for evaluation. The majority found CME activities beneficial. About 73% of participants would watch out for bias, even if the speaker shows COI disclosure slide. The use of brand/trade names was considered as a flag for bias by the majority. About 99% wanted the speaker to show a final take home message slide. Cross verification of the data presented by comparing to published data was done in more than 75% of instances by only 25% of the participating doctors. A significantly higher number of doctors found bias when CME activities were being organized by the health-care industry as compared to programs of medical bodies/societies/organizations. Discussion: COI considerations are given due to the importance of medical professionals. However, doctors are smart enough to understand the limitations of such disclosures and remain alert to ensure they are not influenced by any bias. Take home message slide gives the presenters opportunity to share their insights and allows the audience to make their own judgment on the impartiality of the data presented. The doctors are aware that bias could be more when CME activities are organized by healthcare industry and take appropriate precautions. Conclusion: COI is is given due importance by the medical professionals. COI disclosures are often incomplete. Doctors remain alert to ensure they are not influenced by biased presentations. Concluding take home message slide is unanimously recommended. Presentation bias is more when healthcare industry is directly organizing educational and promotional activities.
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