Showing papers by "Lalit Dar published in 2020"

First isolation of SARS-CoV-2 from clinical samples in India

Abstract: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has, as on March 31, 2020, spread to over 207 countries around the world1,2, with a total of 896,475 confirmed cases and 45,525 deaths2. The number of reported SARS-CoV-2 cases in India is also on an increase with 1,636 cases and 38 deaths2. In the current pandemic situation, the isolation of SARS-CoV-2 is important for developing and evaluating diagnostic reagents, for antiviral studies and for screening of vaccine candidates. Earlier studies showed that SARS-CoV-2 could not replicate in several cell lines, which are routinely used for isolation of respiratory viruses3. Human and animal cell lines that were found to support SARS-CoV-1 replication during the first outbreak of SARS in China, 20024, are currently being studied. The virus was first isolated in the human airway epithelial cells from clinical specimens as part of early attempts to identify the aetiologic agent of infection5. We describe here the successful isolation and characterization of SARS-CoV-2 from clinical samples in India using Vero CCL-81 cells by observing cytopathic effects (CPEs) and cycle threshold (Ct) values in real-time reverse transcription-polymerase chain reaction (RT-PCR), electron microscopy and next-generation sequencing (NGS).

Clinico-demographic profile & hospital outcomes of COVID-19 patients admitted at a tertiary care centre in north India.

Abstract: Background & objectives: In December 2019, a novel coronavirus (SARS-CoV-2) emerged in China and rapidly spread globally including India. The characteristic clinical observations and outcomes of this disease (COVID-19) have been reported from different countries. The present study was aimed to describe the clinico-demographic characteristics and in-hospital outcomes of a group of COVID-19 patients in north India. Methods: This was a prospective, single-centre collection of data regarding epidemiological, demographic, clinical and laboratory parameters, management and outcome of COVID-19 patients admitted in a tertiary care facility in north India. Patient outcomes were recorded as death, discharge and still admitted. Results: Data of 144 patients with COVID-19 were recorded and analyzed. The mean age of the patients was 40.1±13.1 yr, with 93.1 per cent males, and included 10 (6.9%) foreign nationals. Domestic travel to or from affected States (77.1%) and close contact with COVID-19 patients in congregations (82.6%) constituted the most commonly documented exposure. Nine (6.3%) patients were smokers, with a median smoking index of 200. Comorbidities were present in 23 (15.9%) patients, of which diabetes mellitus (n=16; 11.1%) was the most common. A significant proportion of patients had no symptoms (n=64; 44.4%); among the symptomatic, cough (34.7%) was the most common symptom followed by fever (17.4%) and nasal symptoms (2.15%). Majority of the patients were managed with supportive treatment with hydroxychloroquine and azithromycin given on a case-to-case basis. Only five (3.5%) patients required oxygen supplementation, four (2.8%) patients had severe disease requiring intensive care, one required mechanical ventilation and mortality occurred in two (1.4%) patients. The time to reverse transcription-polymerase chain reaction (RT-PCR) negativity was 16-18 days. Interpretation & conclusions: In this single-centre study of 144 hospitalized patients with confirmed COVID-19 in north India, the characteristic findings included younger age, high proportion of asymptomatic patients, long time to PCR negativity and low need for intensive care unit care.

Poor outcomes in patients with cirrhosis and Corona Virus Disease-19.

Abstract: There is a paucity of data on the clinical presentations and outcomes of Corona Virus Disease-19 (COVID-19) in patients with underlying liver disease. We aimed to summarize the presentations and outcomes of COVID-19-positive patients and compare with historical controls. Patients with known chronic liver disease who presented with superimposed COVID-19 (n = 28) between 22 April 2020 and 22 June 2020 were studied. Seventy-eight cirrhotic patients without COVID-19 were included as historical controls for comparison. A total of 28 COVID-19 patients (two without cirrhosis, one with compensated cirrhosis, sixteen with acute decompensation [AD], and nine with acute-on-chronic liver failure [ACLF]) were included. The etiology of cirrhosis was alcohol (n = 9), non-alcoholic fatty liver disease (n = 2), viral (n = 5), autoimmune hepatitis (n = 4), and cryptogenic cirrhosis (n = 6). The clinical presentations included complications of cirrhosis in 12 (46.2%), respiratory symptoms in 3 (11.5%), and combined complications of cirrhosis and respiratory symptoms in 11 (42.3%) patients. The median hospital stay was 8 (7–12) days. The mortality rate in COVID-19 patients was 42.3% (11/26), as compared with 23.1% (18/78) in the historical controls (p = 0.077). All COVID-19 patients with ACLF (9/9) died compared with 53.3% (16/30) in ACLF of historical controls (p = 0.015). Mortality rate was higher in COVID-19 patients with compensated cirrhosis and AD as compared with historical controls 2/17 (11.8%) vs. 2/48 (4.2%), though not statistically significant (p = 0.278). Requirement of mechanical ventilation independently predicted mortality (hazard ratio 13.68). Both non-cirrhotic patients presented with respiratory symptoms and recovered uneventfully. COVID-19 is associated with poor outcomes in patients with cirrhosis, with worst survival rates in ACLF. Mechanical ventilation is associated with a poor outcome.

Rapid chromatographic immunoassay-based evaluation of COVID-19: A cross-sectional, diagnostic test accuracy study & its implications for COVID-19 management in India.

Abstract: Background & objectives: Coronavirus disease 2019 (COVID-19) has so far affected over 41 million people globally. The limited supply of real-time reverse transcription-polymerase chain reaction (rRT-PCR) kits and reagents has made meeting the rising demand for increased testing incompetent, worldwide. A highly sensitive and specific antigen-based rapid diagnostic test (RDT) is the need of the hour. The objective of this study was to evaluate the performance of a rapid chromatographic immunoassay-based test (index test) compared with a clinical reference standard (rRT-PCR). Methods: A cross-sectional, single-blinded study was conducted at a tertiary care teaching hospital in north India. Paired samples were taken for RDT and rRT-PCR (reference standard) from consecutive participants screened for COVID-19 to calculate the sensitivity and specificity of the RDT. Further subgroup analysis was done based on the duration of illness and cycle threshold values. Cohen's kappa coefficient was used to measure the level of agreement between the two tests. Results: Of the 330 participants, 77 were rRT-PCR positive for SARS-CoV-2. Sixty four of these patients also tested positive for SARS-CoV-2 by RDT. The overall sensitivity and specificity were 81.8 and 99.6 per cent, respectively. The sensitivity of RDT was higher (85.9%) in participants with a duration of illness ≤5 days. Interpretation & conclusions: With an excellent specificity and moderate sensitivity, this RDT may be used to rule in COVID-19 in patients with a duration of illness ≤5 days. Large-scale testing based on this RDT across the country would result in quick detection, isolation and treatment of COVID-19 patients.

Laboratory preparedness for SARS-CoV-2 testing in India: Harnessing a network of Virus Research & Diagnostic Laboratories.

Abstract: Background & objectives: An outbreak of respiratory illness of unknown aetiology was reported from Hubei province of Wuhan, People's Republic of China, in December 2019. The outbreak was attributed to a novel coronavirus (CoV), named as severe acute respiratory syndrome (SARS)-CoV-2 and the disease as COVID-19. Within one month, cases were reported from 25 countries. In view of the novel viral strain with reported high morbidity, establishing early countrywide diagnosis to detect imported cases became critical. Here we describe the role of a countrywide network of VRDLs in early diagnosis of COVID-19. Methods: The Indian Council of Medical Research (ICMR)-National Institute of Virology (NIV), Pune, established screening as well as confirmatory assays for SARS-CoV-2. A total of 13 VRDLs were provided with the E gene screening real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay. VRDLs were selected on the basis of their presence near an international airport/seaport and their past performance. The case definition for testing included all individuals with travel history to Wuhan and symptomatic individuals with travel history to other parts of China. This was later expanded to include symptomatic individuals returning from Singapore, Japan, Hong Kong, Thailand and South Korea. Results: Within a week of standardization of the test at NIV, all VRDLs could initiate testing for SARS-CoV-2. Till February 29, 2020, a total of 2,913 samples were tested. This included both 654 individuals quarantined in the two camps and others fitting within the case definition. The quarantined individuals were tested twice - at days 0 and 14. All tested negative on both occasions. Only three individuals belonging to different districts in Kerala were found to be positive. Interpretation & conclusions: Sudden emergence of SARS-CoV-2 and its potential to cause a pandemic posed an unsurmountable challenge to the public health system of India. However, concerted efforts of various arms of the Government of India resulted in a well-coordinated action at each level. India has successfully demonstrated its ability to establish quick diagnosis of SARS-CoV-2 at NIV, Pune, and the testing VRDLs.

In-vitro and in silico activity of Cyamopsis tetragonoloba (Gaur) L. supercritical extract against the dengue-2 virus.

Abstract: Our health and wealth are highly influenced by a number of viruses. Dengue is one of them having a global influence in absence of vaccines and antiviral. WHO suggested that the morbidity of dengue is increasing more than 6 times from 0.5 million in 2010 to over 3.34 million in 2016, following a sharp increase in 2019. The aim of the present study is to check the in vitro and in silico anti-dengue activity of Cyamopsis tetragonoloba supercritical extract in cell lines. The optimum yield of supercritical extract was obtained 0.13 g/10 g (1.3% w/w) at 40 °C temp and 15 MPa pressure and further characterized by GC–MS. The antiviral assay was performed on C6/36 cell lines with 100 copies of dengue-2 virus and maximum non-toxic dose (31.25 µg/ml) of supercritical extract and their effect was detected by real-time RT-PCR. This study revealed that C. tetragonoloba supercritical extract inhibited the dengue-2 virus (99.9%). GC–MS analysis of C. tetragonoloba supercritical extract showed the presence of 10 compounds. The major compounds identified were Hexadecanoic acid, 15-methyl–methyl ester (24.498%); 9,12-octadecadienoyl chloride, (z,z)- (23.718%); methyl dodecanoic acid (13.228%); methyl-stearate (8.696%); Tridecanoic acid, 12-methyl-, methyl-ester (8.426%), dodecanoic acid (6.102%). The study reveals that C. tetragonoloba can be exploited to develop an effective, inexpensive, and specific anti-dengue. The molecular docking study demonstrated the binding energy of 1,2-benzenedicarboxylic acid, bis(2-methylpropyl) ester (− 4.1 kcal/mol), 9,12-octadecadienoyl chloride (z,z) (− 4.0 kcal/mol) ligands were higher than others. It is concluded that C. tetragonoloba can play a major role to inhibit dengue-2 virus.

COVID-19: Possible Cause of Induction of Relapse of Plasmodium vivax Infection.

Abstract: To the Editor: In ongoing pandemic of novel corona virus disease (COVID-19), clinicians are observing atypical manifestations of the disease. We hereby report a case of COVID19 co-infection with vivax malaria in a 10-y-old boy, who previously had received incomplete radical cure with primaquine for vivax infection, suggesting a possible role of COVID-19 in inducing current malarial relapse. A 10-y-old boy, resident of Delhi, presented to the pediatric emergency department of a tertiary care hospital with history of high grade fever with chills and rigors, headache, cold, cough and pain abdomen. Past history revealed admission with a similar episode of febrile illness six months back. Medical records from previous admission revealed that he was diagnosed with P. vivax infection and had not completed primaquine therapy as per history. At presentation, child was febrile with fever of 104 F, maintained saturation of 97–98% on room air. Rest of systemic examination was normal. Investigations revealed Hb of 11.7/dl, total leucocyte count (TLC) of 4500/mm with 15% neutrophils, 53% lymphocytes and 28% eosinophils (absolute eosinophil count of 1260/mm), and platelet count of 52,000/mm. Rapid diagnostic test for malaria was faintly positive for pan antigen and smear examination showed all stages of Plasmodium vivax (P. vivax), confirming it to be malaria. Nasal and pharyngeal swabs RT-PCR for corona virus 2 (SARS-CoV-2) were positive. Other investigations were normal. The child was admitted and treated for malaria and supportive care for COVID-19 infection [1]. Primaquine eradication therapy was given for 14 d after ruling out G6PD deficiency. He was discharged after complete recovery. This boy had been diagnosed with P. vivax infection six months back and had now reactivation of malaria. Relapse rates after P. vivax infection vary geographically from 8 to 80%, with considerable proportion of population harboring dormant but activatable hypnozoites in endemic areas [2]. Exact mechanism causing this activation is though unclear, associated cytokine response with systemic illness has been postulated in P vivax relapse [3]. COVID-19 leads to a cytokine storm, which is responsible for the more severe manifestations of the disease [4, 5]. Hence, we postulate that the COVID-19 infection, with its cytokine response was responsible for induction of P. vivax relapse in our patient. Our hypothesis is based on circumstantial evidence in form of documented malaria in past, a possibility of re-activation in natural course or re-infection cannot be ruled out.

A cluster of SARS-CoV-2 infection among Italian tourists visiting India, March 2020.

Abstract: Background & objectives: A cluster of SARS-CoV-2 infection occurred among Italian tourists visiting India. We report here the epidemiological, clinical, radiological and laboratory findings of the first cluster of SARS-CoV-2 infection among the tourists. Methods: Information was collected on demographic details, travel and exposure history, comorbidities, timelines of events, date of symptom onset and duration of hospitalization from the 16 Italian tourists and an Indian with laboratory-confirmed SARS-CoV-2 infection. The clinical, laboratory, radiologic and treatment data was abstracted from their medical records and all tourists were followed up till their recovery or discharge or death. Throat and deep nasal swab specimens were collected on days 3, 8, 15, 18, 23 and 25 to evaluate viral clearance. Results: A group of 23 Italian tourists reached New Delhi, India, on February 21, 2020 and along with three Indians visited several tourist places in Rajasthan. By March 3, 2020, 17 of the 26 (attack rate: 65.4%) had become positive for SARS-CoV-2 infection. Of these 17 patients, nine were symptomatic, while eight did not show any symptoms. Of the nine who developed symptoms, six were mild, one was severe and two were critically ill. The median duration between the day of confirmation for COVID-19 and RT-PCR negativity was 18 days (range: 12-23 days). Two patients died with a case fatality of 11.8 per cent. Interpretation & conclusions: This study reconfirms higher rates of transmission among close contacts and therefore, public health measures such as physical distancing, personal hygiene and infection control measures are necessary to prevent transmission.

Diagnosing Herpetic Genital Ulcers in a Resource-Limited Setting- What Works?

Abstract: Aims: Globally, viral agents, especially herpes simplex virus (HSV), have overtaken the bacterial causes of genital ulcers. Very few laboratories in India, perform culture techniques and polymerase chain reaction (PCR) for diagnosis of genital ulcers. This study aimed to establish the utility of existing tests, which are cheaper and need less technical expertise, when compared to newer tests such as PCR. Study Design: This cross sectional study was carried out to determine the aetiology of genital ulcers, with emphasis on diagnosis of herpetic ulcers, using newer and more accurate methods of Original Research Article Singh et al.; ISRR, 9(1): 58-67, 2020; Article no.ISRR.56585 59 diagnosis and evaluating their performance by comparing against viral culture as gold standard test. Place and Duration of the Study: The study was carried out over a period of one year in the Apex Regional Sexually Transmitted Diseases (STD) Centre at Safdarjung Hospital, New Delhi and the Department of Microbiology, AIIMS, New Delhi. Methodology: Fifty three patients with genital ulcers were included in the study. Specimens from ulcers were taken for various tests, including Giemsa stain, ELISA for HSV-1 & 2, PCR and Viral culture for HSV. Results: HSV was identified in 31 of 53 cases (58.5%), including 03 cases of HSV-1, and 28 cases of HSV-2. Sensitivity and specificity of PCR was 90.0% and 84.85%, respectively. Viral culture positivity was 37.7%. Conclusion: Genital herpes is associated with an increased risk of Human Immunodeficiency Virus (HIV) acquisition, and clinical manifestations are diverse; hence a presumptive diagnosis should be confirmed by reliable laboratory tests. Nucleic acid amplification tests (NAAT) are the most sensitive methods for direct detection of HSV. The extensive validation of these tests allows for their application in routine laboratory settings with consistency and greater diagnostic accuracy. When standardised and used, PCR is a highly reproducible, rapid and labour efficient method for HSV detection.