A comparison of SARS-CoV-2 rapid antigen testing with realtime RT-PCR among symptomatic and asymptomatic individuals.

BACKGROUND: Identification of SARS-CoV-2 positive patients with rapid and cost-effective test methods is the key for isolating infected individuals, interrupting the transmission chain, and thus, containment of the CoVID-19 disease. In this regard, Rapid Antigen Test (RAT) plays an important role at point of care testing but the low sensitivity attributing towards escape of positive cases is reported as a major disadvantage of RAT which led us to evaluate a RAT kit among symptomatic and asymptomatic individuals suspected of CoVID-19. METHODS: We analyzed 329 parallel nasopharyngeal swabs for RAT (Zydus Cadila, India) at the point of collection in a hospital-based facility and RealTime RT-PCR in the laboratory. The performance parameters were analyzed by evaluating the specificity, sensitivity, Negative Predictive Value (NPV), Positive Predictive Value (PPV), and Kappa coefficient. RESULTS: The sensitivity and specificity were found to be 75.17% and 98.89% respectively. Positive Predictive value was 98.25% and the negative predictive value was 82.79%. The accuracy between the two techniques was found to be 88.14% with a kappa coefficient of 0.756 (SE: 0.036 and CI at 95%: 0.686 to 0.826) with a good strength of agreement (0.61-0.80) between the two testing techniques. Among the false-negative cases, 22 (59.5%) were asymptomatic having the Cycle Threshold (Ct) range 27 to 32.9 including 12 cases with a history of close contact with the known positive cases (i.e. household contact). The remaining 15 cases (40.5%) were symptomatic having low to moderate Ct values. CONCLUSION: It is observed from the results that the false negative result for symptomatic individuals is a matter of concern as it was noted in 4 cases of our study subjects who required hospitalisation later. Also the positives among asymptomatic contacts are important from epidemiological point of view for isolation and curtailing the infection from spreading in a community. These results support the fact that RAT showing sensitivity below 80% can be used for mass screening purposes with provision for additional testing in case of false negative with symptomatic individuals. Also false-negative results should be interpreted cautiously considering the epidemiological link as well as the clinical condition of the patients.

Yielding quality viral RNA by using two different chemistries: a comparative performance study.

Purity and integrity are two important criteria for any RNA extraction process to qualify the RNA for meaningful gene expression analysis. This study compares four commercially available RNA extraction kits using silica membrane and magnetic bead separation methods. The performance was evaluated in terms of both quantity (total RNA amount in µg/µl) and purity (260/280 ratio). The concentration and purity of each kit was significantly different from those of the others (p < 0.001). Although quantity obtained from Mag MAX is comparatively lower than QIAGEN, the quality is comparable as evident from real-time PCR performance. This study suggests that there are practical differences between these RNA extraction kits that should be taken into account while isolating RNA required for gene expression analysis.

Prevalence and trend of emerging and re-emerging arboviral infections in the state of Odisha.

Newly emerging or re-emerging infections are posing continuous threat to both public health system and clinical care globally. The emergence of infections especially caused by arboviruses can be linked to several mechanisms which include geographical expansion linked to human development and transportation, global warming, enhanced transmission in peridomestic area and close proximity of human habitations to domestic as well as wild animals. The co-circulation of Dengue, Chikungunya and Zika is a matter of public health priority due to the fact that they are transmitted by the same vector as well as increase in the number of reported cases of severe dengue, post-chikungunya chronic joint disease and microcephaly related to Zika virus disease. The study was designed to estimate the prevalence of these arboviral infections in Odisha. About 5198 cases presenting with common clinical symptoms of fever, arthralgia, headache, myalgia and malaise were screened during 2016-2019. A total of 42.2% patients tested positive for dengue NS1 antigen (n = 4154), 30.2% for dengue IgM (n = 2161) and 14.3% for chikungunya IgM (n = 1816). A total of 1684 samples were subjected to Zika RT-PCR and none was tested positive. Peak in the numbers of dengue/ chikungunya cases was evident in the post-monsoon months of July - October. Circulation of all four serotypes of dengue i.e. DEN 1, 2, 3, and 4 was noticed in the state. Molecular investigation of suspected Chik cases in early phases showed circulation of Eastern Central Southern African genotype (E1:226A). There is dearth of knowledge about disease severity during arbovirus co-infections and importance of adequate management of patients at an early stage residing in risk areas. It is the first study in Odisha to study the pattern and status of these three arboviral diseases Dengue, Chikungunya and Zika. The outcome of this study will help in focusing and improvement of existing surveillance systems and vector control tools, as well as on the development of suitable antiviral agents and formulating candidate vaccine.

An outbreak of hepatitis E virus infection caused by genotype 1 in an urban setting in eastern India: a probe into risk factors for transmission.

The study was undertaken to find out the cause and etiology of an outbreak presumed to be due to water contamination that caused high morbidity in the western part of the state of Odisha during May, 2014. In this investigation 56 blood samples were collected and tested for HEV IgM through ELISA. Blood sample of 22 patients collected within 1 weeks post onset of symptoms and were subjected to RT-PCR and sequencing followed by phylogenetic analysis. Water samples were also analyzed for viral and bacterial contamination. A total of 290 individuals were examined for suspected jaundice. Out of 56 blood samples in 41 (73.2%) IgM for HEV was found. 12 samples out of 22 early phase samples were positive for RT-PCR and through phylogenetic analysis all were found to be of Genotype 1 and subtype A. This large outbreak was confirmed due to Hepatitis E virus and transmission was fast due to contamination of drinking water sources and lack of hygienic practices. The outcome of this investigation has created alertness among state health and municipal authorities to be prepared for the similar kind of situation for other part of the state.