•A novel ORF1a-based RT-PCR assay (Viroselect) for detection of severe acute respiratory syndrome coronavirus-2.•Viroselect displayed high concordance with manual and automated real-time RT-PCR ...detection assays.•Viroselect demonstrated utility in resolving inconclusive samples.
India bears the second largest burden of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. A multitude of reverse transcription polymerase chain reaction (RT-PCR) detection assays with disparate gene targets, including automated high-throughput platforms, are available. Varying concordance and interpretation of diagnostic results in this setting can result in significant reporting delays, leading to suboptimal disease management. This article reports the development of a novel ORF1a-based SARS-CoV-2 RT-PCR assay – Viroselect – that shows high concordance with conventional assays and the ability to resolve inconclusive results generated during the peak of the epidemic in Mumbai, India.
A unique target region within SARS-CoV-2 ORF1a – the non-structural protein 3 (nsp3) region – was used to design and develop the assay. This hypervariable region (1923–3956) between SARS-CoV-2, SARS-CoV-1 and Middle East respiratory syndrome coronavirus was utilized to design the primers and probes for the RT-PCR assay. The concordance of this assay with commonly used emergency use authorization (US Food and Drug Administration) manual kits and an automated high-throughput testing platform was evaluated. Further, a retrospective analysis was carried out using Viroselect on samples reported as ‘inconclusive’ between April and October 2020.
In total, 701 samples were tested. Concordance analysis of 477 samples demonstrated high overall agreement of Viroselect with both manual (87.6%) and automated (84.7%) assays. Also, in the retrospective analysis of 224 additional samples reported as ‘inconclusive’, Viroselect was able to resolve 100% (19/19) and 93.7% (192/205) of samples which had inconclusive results on manual and automated high-throughput platforms, respectively.
Viroselect had high concordance with conventional assays, both manual and automated, and has potential to resolve inconclusive samples.
Dirofilariasis is a worldwide zoonotic filariasis. Human dirofilariasis is a zoonotic infection most commonly caused by
. Dirofilariasis, caused by
, has been reported to occur widely throughout ...Asia, Europe, and Africa. It has not been widely recognized in India; however, several cases have been reported in the last few years. Ease and frequency of international travel has probably contributed to the increase in the number of cases. There is probably a focus of human infection with
in Kerala, India. We report a case of ocular dirofilariasis, from the Western part of India. Among the Indian case reports of human dirofilariasis caused by
, majority had ocular infections and few had subcutaneous involvement of the face.
The role of sMAdCAM, an important gut immune migratory marker, remains unexplored in COVID-19 pathogenesis considering recent studies positing the gut as a sanctuary site for SARS-CoV-2 persistence. ...Thus, assimilating profiles of systemic inflammatory mediators with sMAdCAM levels may provide insights into the progression of COVID-19 disease. Also, the role of these markers in governing virus specific immunity following infection remains largely unexplored. A cohort (n = 84) of SARS-C0V-2 infected individuals included a group of in-patients (n = 60) at various stages of disease progression together with convalescent individuals (n = 24) recruited between April and June 2020 from Mumbai, India. Follow-up of 35 in-patients at day 7 post diagnosis was carried out. Th1/Th2/Th17 cytokines along with soluble MAdCAM (sMAdCAM) levels in plasma were measured. Also, anti-viral humoral response as measured by rapid antibody test (IgG, IgM), Chemiluminescent Immunoassay (IgG), and antibodies binding to SARS-CoV-2 proteins were measured by Surface Plasmon Resonance (SPR) from plasma. IL-6 and sMAdCAM levels among in-patients inversely correlated with one another. When expressed as a novel integrated marker—sMIL index (sMAdCAM/IL-6 ratio)—these levels were incrementally and significantly higher in various disease states with convalescents exhibiting the highest values. Importantly, sMAdCAM levels as well as sMIL index (fold change) correlated with peak association response units of receptor binding domain and fold change in binding to spike respectively as measured by SPR. Our results highlight key systemic and gut homing parameters that need to be monitored and investigated further to optimally guide therapeutic and prophylactic interventions for COVID-19.
COVID-19 severity is disproportionately high in the elderly and people with comorbidities. However, other factors that predispose individuals to increased chances of infection are unclear.
Data from ...18,600 people screened for COVID-19 in Mumbai during the outbreak's initial phase, March 7 to June 30, 2020, were used to assess risk factors associated with COVID-19 using the odds ratio analysis.
Males aged ≥60 years having both diabetes and hypertension were at the highest risk of COVID-19 infection (M vs. F OR=2.5, 95% CI=1.34–4.67, p = 0.0049). People having both diabetes and hypertension in ≥20 years (OR=4.11, 95% CI=3.26–5.20, p <0.0001), diabetes and hypertension independently in 20–39 (OR=4.13, 95% CI=2.22–7.70, p <0.0001, OR=4.32, 95% CI=2.10–8.88, p = 0.0001) and ≥60 years (OR=2.69, 95% CI=1.87–3.87, p <0.0001, OR=2.03, 95% CI=1.46–2.82, p <0.0001), chronic renal disease in 20–39 years (OR=5.38, 95% CI=1.91–15.09, p = 0.0007) age groups had significantly higher risk of COVID-19 infection than those without comorbidity. Quarantined people had significantly lower positive odds (OR=0.59, 95% CI=0.53–0.66, p <0.001) than non-quarantined people.
Our research indicates that the risk of getting COVID-19 disease is not equal. When considering sex, age, and comorbidity together, we found that males aged ≥60 years and having both diabetes and hypertension had a significantly high risk of COVID-19 infection. Therefore, remedial measures such as vaccination programs should be prioritized for at-risk individuals.
SERB, India: SB/S1/COVID-2/2020 and Seed grant RD/0520-IRCCHC0–006 from IRCC, IIT Bombay.
Abstract
INTRODUCTION:
Dengue virus (DENV) causes a wide range of diseases in humans, from acute febrile illness Dengue fever (DF) to life-threatening Dengue hemorrhagic fever (DHF) or Dengue shock ...syndrome (DSS). Factors believed to be responsible for spread of Dengue virus infection include explosive population growth, unplanned urban overpopulation with inadequate public health systems, poor standing water and vector control, climate changes and increased international recreational, business, military travel to endemic areas. All of these factors must be addressed to control the spread of Dengue and other mosquito-borne infections. The detection of Dengue virus RNA by reverse transcriptase PCR (RT-PCR) in human serum or plasma samples is highly indicative of acute Dengue fever. Moreover, the method is able to identify the Dengue virus serotype by demonstrating defined sequence homologies in the viral genomic RNA.
METHODS AND RESULTS:
During the nine year period of this study analysis, 6767 strongly suspected cases were tested by RT-PCR. 1685 (24.9%) were Dengue PCR positive and confirmed as Dengue cases. Observations on the seasonality were based on the nine year's data as the intensity of sampling was at its maximum during monsoon season. Dengue typing was done on 100 positive samples after storage of Dengue RNA at – 80°C. Dengue serotypes were detected in 69 samples of which Dengue 2 was most predominant. 576 samples were processed for NS1 antigen and PCR simultaneously. 19/576 were positive (3.3 %) for NS1 as well as by PCR. 23/576 samples were negative for NS1 antigen, but were positive by RT-PCR. The remaining 534 samples which were negative for NS1 antigen were also negative by Dengue RT-PCR.
CONCLUSION:
In this study we sought to standardize rapid, sensitive, and specific fluorogenic probe-based RT-PCR assay to screen and serotype a representative range of Dengue viruses that are found in and around Mumbai. Qualitative Dengue virus TaqMan assays could have tremendous utility for the epidemiological investigation of Dengue illness and especially for the study of the viremic response with candidate live-attenuated dengue virus vaccines.
ABSTRACT
Background:
Chikungunya fever (CHIK) is an arboviral disease. Dengue fever (DENG) and CHIK are indistinguishable clinically and need to be differentiated by laboratory investigations.
...Purpose:
This study aimed at estimating the seroprevalence of CHIK mono-infection and CHIK and DENG dual infection in suspected patients. We also analyzed the age, sex distribution, joint involvement, and relation of joint movement restriction with visual analog scale (VAS).
Materials and Methods:
Two hundred patients clinically suspected with DENG and CHIK were enrolled from a Tertiary Care Hospital in Mumbai from April 2012 to October 2013. The detailed history and examination findings were recorded. Serum samples were subjected to DENG and CHIK immunoglobulin G (IgM) enzyme-linked immunosorbent assay (ELISA).
Results:
The seroprevalence of CHIK was 12.5%. Mono-infection of CHIK was 3%, and CHIK and DENG dual infection was 9.5%. Most affected age group in CHIK cases was 46–60 years wherein female preponderance was seen. All 6 patients with CHIK mono-infection had fever and joint involvement; knee and elbow were the most commonly affected joints. All CHIK patients had VAS score of 6–10 with restricted joint movement. Of the patients with dual infection, the majorities were from 31 to 45 years with male preponderance; all had fever and joint pain mainly affecting knee and elbow. Of patients who had VAS score 6–10 in patients with dual infection, only 5.26% had restricted joint movement.
Conclusion:
IgM ELISA for Chikungunya infection should be included in the routine laboratory tests for acute febrile illness.
Access to reproductive health services in Human Immunodeficiency Virus (HIV) programs can greatly enhance program's potential to limit the spread of disease, reduce unintended pregnancies and ...safeguard the health of infected people.
To assess (i) knowledge, attitude, and use regarding contraceptives; safe sex and dual protection; (ii) fertility desires and unintended pregnancies post HIV and (iii) symptoms of reproductive tract infection/sexually transmitted infection (RTI/STI) among women infected with HIV.
A cross-sectional study among 300 currently married HIV-positive women who had not undergone permanent sterilization with no immediate desire for pregnancy. Study site was Integrated Counseling and Testing Centers (ICTC) in tertiary hospitals of Mumbai and women were interviewed using a semistructured questionnaire.
In spite of good awareness about modern methods, 42.7 felt that contraceptives other than condoms were harmful to use due to their HIV status. Knowledge on dual protection was limited to condom (75%). Condom use increased from 5.7% pre-HIV to 71.7% post-HIV, with 89.6% reporting regular use. Future fertility desire was expressed by 8.7% women. Induced abortions post-HIV was reported by16.6% women, as pregnancies were unintended. About 69% wished to use dual contraceptive methods for effective protection if it was not harmful to be used by people living with HIV (PLHIV).
Data reveals a need to promote modern contraceptive methods along with regular condom use to prevent unintended pregnancies and improve health-seeking behavior for contraception. Health system models that converge or link HIV services with other reproductive health services need to be tested to provide comprehensive reproductive healthcare to infected women in India.
The coronavirus disease 2019 (COVID-19) pandemic continues to ravage the world, with many hospitals overwhelmed by the large number of patients presenting during major outbreaks. A rapid triage for ...COVID-19 patient requiring hospitalization and intensive care is urgently needed. Age and comorbidities have been associated with a higher risk of severe COVID-19 but are not sufficient to triage patients. Here, we investigated the potential of attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy as a rapid blood test for classification of COVID-19 disease severity using a cohort of 160 COVID-19 patients. A simple plasma processing and ATR-FTIR data acquisition procedure was established using 75% ethanol for viral inactivation. Next, partial least-squares-discriminant analysis (PLS-DA) models were developed and tested using data from 130 and 30 patients, respectively. Addition of the ATR-FTIR spectra to the clinical parameters (age, sex, diabetes mellitus, and hypertension) increased the area under the ROC curve (C-statistics) for both the training and test data sets, from 69.3% (95% CI 59.8–78.9%) to 85.7% (78.6–92.8%) and 77.8% (61.3–94.4%) to 85.1% (71.3–98.8%), respectively. The independent test set achieved 69.2% specificity (42.4–87.3%) and 94.1% sensitivity (73.0–99.0%). Diabetes mellitus was the strongest predictor in the model, followed by FTIR regions 1020–1090 and 1588–1592 cm–1. In summary, this study demonstrates the potential of ATR-FTIR spectroscopy as a rapid, low-cost COVID-19 severity triage tool to facilitate COVID-19 patient management during an outbreak.
Severe coronavirus disease 2019 (COVID-19) infection may lead to lung injury, multi-organ failure, and eventually death. Cytokine storm due to excess cytokine production has been associated with ...fatality in severe infections. However, the specific molecular signatures associated with the elevated immune response are yet to be elucidated. We performed a mass-spectrometry-based proteomic and metabolomic analysis of COVID-19 plasma samples collected at two time points. Using Orbitrap Fusion LC–MS/MS-based label-free proteomic analysis, we identified around 10 significant proteins, 32 significant peptides, and 5 metabolites that were dysregulated at the severe time points. Few of these proteins identified by quantitative proteomics were validated using the multiple reaction monitoring (MRM) assay. Integrated pathway analysis using distinct proteomic and metabolomic signatures revealed alterations in complement and coagulation cascade, platelet aggregation, myeloid leukocyte activation pathway, and arginine metabolism. Further, we highlight the role of leukocyte activation and arginine metabolism in COVID-19 pathogenesis and targeting these pathways for COVID-19 therapeutics.
PDF
