Vaccination coverage and breakthrough infections of COVID-19 during the second wave among staff of selected medical institutions in India.

India experienced the second wave of SARS-CoV-2 infection from April 3 to June 10, 2021. During the second wave, Delta variant B.1617.2 emerged as the predominant strain, spiking cases from 12.5 million to 29.3 million (cumulative) by the end of the surge in India. Vaccines against COVID-19 are a potent tool to control and end the pandemic in addition to other control measures. India rolled out its vaccination programme on January 16, 2021, initially with two vaccines that were given emergency authorization-Covaxin (BBV152) and Covishield (ChAdOx1 nCoV- 19). Vaccination was initially started for the elderly (60+) and front-line workers and then gradually opened to different age groups. The second wave hit when vaccination was picking up pace in India. There were instances of vaccinated people (fully and partially) getting infected, and reinfections were also reported. We undertook a survey of staff (front line health care workers and supporting) of 15 medical colleges and research institutes across India to assess the vaccination coverage, incidence of breakthrough infections, and reinfections among them from June 2 to July 10, 2021. A total of 1876 staff participated, and 1484 forms were selected for analysis after removing duplicates and erroneous entries (n = 392). We found that among the respondents at the time of response, 17.6% were unvaccinated, 19.8% were partially vaccinated (received the first dose), and 62.5% were fully vaccinated (received both doses). Incidence of breakthrough infections was 8.7% among the 801 individuals (70/801) tested at least 14 days after the 2nd dose of vaccine. Eight participants reported reinfection in the overall infected group and reinfection incidence rate was 5.1%. Out of (N = 349) infected individuals 243 (69.6%) were unvaccinated and 106 (30.3%) were vaccinated. Our findings reveal the protective effect of vaccination and its role as an essential tool in the struggle against this pandemic.

Seroprevalence of anti SARS-CoV-2 IgG antibodies among adults in Jammu district, India: A community-based study.

Background & objectives: Serology testing is essential for immunological surveillance in the population. This serosurvey was conducted to ascertain the cumulative population immunity against SARS-CoV-2 among adults in Jammu district and to understand the association of seropositivity with sociodemographic and clinical correlates. Methods: On September 30 and October 1, 2020, a household survey was done in 20 villages/wards chosen from 10 health blocks in district Jammu, India. Demographic, clinical and exposure information was collected from 2000 adults. Serum samples were screened for IgG antibodies using COVID Kavach MERILISA kit. Tests of association were used to identify risk factors associated with IgG positivity. Crude odds ratio with 95 per cent confidence intervals (CIs) was calculated during univariate analysis followed by logistic regression. Results: Overall adjusted seroprevalence for SARS-CoV-2 was 8.8 per cent (95% CI: 8.78-8.82); it varied from 4.1 per cent in Chauki choura to 16.7 per cent Pallanwalla across 10 blocks in the district. Seropositivity was observed to be comparatively higher in 41-50 and 61-70 yr age groups, among males and in rural areas. Fever, sore throat, cough, dyspnoea, myalgias, anosmia, ageusia, fatigue, seizures, history of exposure, medical consultation, hospitalization and missing work showed significant association with seropositivity on univariate analysis. On logistic regression, only sore throat, myalgia and missing work showed significant adjusted odds of IgG positivity. Extrapolation to adult population suggested that exposure to SARS-CoV-2 was 14.4 times higher than reported cases, translating into Infection fatality rate of 0.08 per cent. Interpretation & conclusions: Since a major part of population was immunologically naive, all efforts to contain COVID-19 need to be vigorously followed while these baseline results provide an important yardstick to monitor the trends of COVID-19 and guide locally appropriate control strategies in the region.

Optimization and validation of RT-LAMP assay for diagnosis of SARS-CoV2 including the globally dominant Delta variant.

BACKGROUND: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19 pandemic, has infected more than 179 million people worldwide. Testing of infected individuals is crucial for identification and isolation, thereby preventing further spread of the disease. Presently, Taqman™ Reverse Transcription Real Time PCR is considered gold standard, and is the most common technique used for molecular testing of COVID-19, though it requires sophisticated equipments, expertise and is also relatively expensive. OBJECTIVE: Development and optimization of an alternate molecular testing method for the diagnosis of COVID-19, through a two step Reverse Transcription Loop-mediated isothermal AMPlification (RT-LAMP). RESULTS: Primers for LAMP were carefully designed for discrimination from other closely related human pathogenic coronaviruses. Care was also taken that primer binding sites are present in conserved regions of SARS-CoV2. Our analysis shows that the primer binding sites are well conserved in all the variants of concern (VOC) and variants of interest (VOI), notified by World Health Organization (WHO). These lineages include B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427/B.1.429, P.2, B.1.525, P.3, B.1.526 and B.1.617.1. Various DNA polymerases with strand displacement activity were evaluated and conditions were optimized for LAMP amplification and visualization. Different LAMP primer sets were also evaluated using synthetic templates as well as patient samples. CONCLUSION: In a double blind study, the RT-LAMP assay was validated on more than 150 patient samples at two different sites. The RT-LAMP assay appeared to be 89.2% accurate when compared to the Taqman™ rt-RT-PCR assay.

Estimation of Baseline Widal Antibody Titers among Apparently Healthy Urban Population of District Jammu.

INTRODUCTION: Definitive diagnosis of Enteric fever is by blood culture for Salmonella enterica serotype Typhi, Paratyphi A, and Paratyphi B which takes long turnaround time and is costly, whereas Widal test is simple, rapid, and cost-effective test whose interpretation depends on the baseline Widal titers among healthy individuals in a defined population. OBJECTIVES: To determine the baseline Widal titers among apparently healthy urban population of district Jammu (J&K). MATERIALS AND METHODS: 302 individuals in the age group of 18-50 years were recruited. A pretested questionnaire was used to collect demographic and clinical details. The Widal testing was done using commercial Salmonella antigen kit. RESULTS: A total of 302 samples were screened by Widal test. 138 samples (45.69%) were reactive for TO antigen and 64 (21.19%) tested reactive for TH antigen, 3 (0.01%) samples showed agglutination for AH antigen and 3 (0.01%) were positive for BH antigen. Majority of seropositive samples were in dilutions of 1:40 for both TO and TH antigens. CONCLUSIONS: Hence, next higher dilutions showing positivity for both TO and TH antigens, i.e., ≥1:80 may be considered diagnostic for enteric fever in the urban population of Jammu district.

Educational interventions to improve knowledge and skills of interns towards prevention and control of hospital-associated infections.

CONTEXT: We believe that there is significant educational deficit amongst interns regarding up-to-date formal knowledge and skills on healthcare-associated infections (HAIs) which might compromise patient safety. This urgently requires curriculum innovations to ensure their formal training on HAIs prevention and control. AIM: Education of interns to improve their knowledge and skills toward HAIs prevention and control. SUBJECTS AND METHODS: This pilot study was conducted in interns using a multimodal approach consisting of a combination of videos, PowerPoint presentation, and hands-on demonstration to provide applied and practical teaching on prevention and control of HAIs. Pre- and post-test assessment of knowledge, attitude, and skills was carried out by multiple choice questions, 5-point Likert scale, and Objective Structured Practical Examination respectively. STATISTICAL ANALYSIS USED: Paired t-test. RESULTS: A statistically significant improvement in the overall score rates between pre- and post-test of intern's was seen, suggesting that educational programs have a positive effect. Intern's felt benefitted from interventions focused on HAIs prevention and control and hoped that such sessions are integrated in the regular undergraduate curriculum. A majority of the students felt that their learning style assessment matched well with their own perception of learning preference. CONCLUSIONS: Assessment drives learning; hence strengthening the contribution of health-care workers to HAIs prevention programs should include measures that enhance knowledge, improve skills and develop appropriate attitudes, resulting in safety and quality of patient care.

Inbreeding as a cause for deafness: Dadhkai study.

BACKGROUND: We report on the higher prevalence of deaf-mutes from a village in Jammu and Kashmir State of India. MATERIALS AND METHODS: A cross-sectional study among 79 deaf mutes using pedigree analysis, audiometry, imaging and molecular analysis. RESULTS: A high rate of hereditary deafness with 79 individuals diagnosed to be suffering from non-syndrome deafness in a total population of 2452 individuals residing in the village. INTERPRETATION: Flourishing of intermarriages led to a population with high prevalence of deafness.

T-cell assays for tuberculosis infection: deriving cut-offs for conversions using reproducibility data.

BACKGROUND: Although interferon-gamma release assays (IGRA) are promising alternatives to the tuberculin skin test, interpretation of repeated testing results is hampered by lack of evidence on optimal cut-offs for conversions and reversions. A logical start is to determine the within-person variability of T-cell responses during serial testing. METHODOLOGY/PRINCIPAL FINDINGS: We performed a pilot study in India, to evaluate the short-term reproducibility of QuantiFERON-TB Gold In Tube assay (QFT) among 14 healthcare workers (HCWs) who underwent 4 serial QFT tests on day 0, 3, 9 and 12. QFT ELISA was repeated twice on the same sets of specimens. We assessed two types of reproducibility: 1) test-retest reproducibility (between-test variability), and 2) within-person reproducibility over time. Test-retest reproducibility: with dichotomous test results, extremely high concordance was noticed between two tests performed on the same sets of specimens: of the 56 samples, the test and re-test results agreed for all but 2 individuals (kappa = 0.94). Discordance was noted in subjects who had IFN-gamma values around the cut-off point, with both increases and decreases noted. With continuous IFN-gamma results, re-test results tended to produce higher estimates of IFN-gamma than the original test. Within-person reproducibility: when continuous IFN-gamma data were analyzed, the within-person reproducibility was moderate to high. While persons with negative QFT results generally stayed negative, positive results tended to vary over time. Our data showed that increases of more than 16% in the IFN-gamma levels are statistically improbable in the short-term. CONCLUSIONS: Conservatively assuming that long-term variability might be at least twice higher than short-term, we hypothesize that a QFT conversion requires two conditions to be met: 1) change from negative to positive result, and 2) at least 30% increase in the baseline IFN-gamma response. Larger studies are needed to confirm our preliminary findings, and determine the conversion thresholds for IGRAs.

Evaluation of diagnostic accuracy, feasibility and client preference for rapid oral fluid-based diagnosis of HIV infection in rural India.

BACKGROUND: Oral fluid-based rapid tests are promising for improving HIV diagnosis and screening. However, recent reports from the United States of false-positive results with the oral OraQuick ADVANCE HIV1/2 test have raised concerns about their performance in routine practice. We report a field evaluation of the diagnostic accuracy, client preference, and feasibility for the oral fluid-based OraQuick Rapid HIV1/2 test in a rural hospital in India. METHODOLOGY/PRINCIPAL FINDINGS: A cross-sectional, hospital-based study was conducted in 450 consenting participants with suspected HIV infection in rural India. The objectives were to evaluate performance, client preference and feasibility of the OraQuick Rapid HIV-1/2 tests. Two Oraquick Rapid HIV1/2 tests (oral fluid and finger stick) were administered in parallel with confirmatory ELISA/Western Blot (reference standard). Pre- and post-test counseling and face to face interviews were conducted to determine client preference. Of the 450 participants, 146 were deemed to be HIV sero-positive using the reference standard (seropositivity rate of 32% (95% confidence interval [CI] 28%, 37%)). The OraQuick test on oral fluid specimens had better performance with a sensitivity of 100% (95% CI 98, 100) and a specificity of 100% (95% CI 99, 100), as compared to the OraQuick test on finger stick specimens with a sensitivity of 100% (95% CI 98, 100), and a specificity of 99.7% (95% CI 98.4, 99.9). The OraQuick oral fluid-based test was preferred by 87% of the participants for first time testing and 60% of the participants for repeat testing. CONCLUSION/SIGNIFICANCE: In a rural Indian hospital setting, the OraQuick Rapid- HIV1/2 test was found to be highly accurate. The oral fluid-based test performed marginally better than the finger stick test. The oral OraQuick test was highly preferred by participants. In the context of global efforts to scale-up HIV testing, our data suggest that oral fluid-based rapid HIV testing may work well in rural, resource-limited settings.

Comparison of a whole blood interferon-gamma assay with tuberculin skin testing for the detection of tuberculosis infection in hospitalized children in rural India.

OBJECTIVE: In vitro interferon-gamma (IFN-gamma) assays have emerged as novel alternatives to the tuberculin skin test (TST) for the diagnosis of latent tuberculosis (TB) infection. These assays have been evaluated in low incidence countries, mainly in adults, and have been shown to be more specific than TST. Because few studies have been done in high incidence countries, and because paediatric data are limited, we compared a whole-blood IFN-gamma assay with TST among hospitalized Indian children. METHODS: Between July 2004 and June 2005, a total of 105 consecutively admitted children (median age 6 years; 82% had BCG scars) in whom TB was suspected or had history of contact with an index case were recruited at a rural hospital in India. All children underwent TST, and the QuantiFERON-TB-Gold In Tube (QFT) assay. RESULTS: The overall prevalence of TB infection was similar with both tests. With a TST cut-off point of > or =10mm, 10 of 105 (9.5%; 95% CI 3.8, 15.2) children were TST positive. With a cut-off point of IFN-gamma> or =0.35IU/ml, 11 of 105 (10.5%; 95% CI 4.5, 16.4) were QFT positive. The concordance between TST and QFT was substantial (agreement 95.2%; kappa [kappa] 0.73; 95% CI for kappa 0.53, 0.92). Agreement between TST and QFT results was 100% (kappa 1.0) in BCG scar-negative children as compared to 94% (kappa 0.63) in scar-positive children. BCG was not associated with the results of either TST or QFT (P>0.05 for both tests). The number of children with bacteriologically confirmed active TB was too small to permit the estimation of sensitivity of the tests. CONCLUSIONS: In a rural, predominantly BCG-vaccinated paediatric population in India, the TST and QFT assay produced comparable results. BCG vaccination did not significantly affect either TST or QFT results. Larger studies are needed to compare the sensitivity of the IFN-gamma assay with that of the TST in children with bacteriologically and/or clinically confirmed TB.

Serial testing of health care workers for tuberculosis using interferon-gamma assay.

RATIONALE: Although interferon-gamma (IFN-gamma) assays are promising alternatives to the tuberculin skin test (TST), their serial testing performance is unknown. OBJECTIVE: To compare TST and IFN-gamma conversions and reversions in healthcare workers. METHODS: We prospectively followed-up 216 medical and nursing students in India who underwent baseline and repeat testing (after 18 mo) with TST and QuantiFERON-TB Gold In-Tube (QFT). TST conversions were defined as reactions greater than or equal to 10 mm, with increments of 6 or 10 mm over baseline. QFT conversions were defined as baseline IFN-gamma less than 0.35 and follow-up IFN-gamma greater than or equal to 0.35 or 0.70 IU/ml. QFT reversions were defined as baseline IFN-gamma greater than or equal to 0.35 and follow-up IFN-gamma less than 0.35 IU/ml. RESULTS: Of the 216 participants, 48 (22%) were TST-positive, and 38 (18%) were QFT-positive at baseline. Among 147 participants with concordant baseline negative results, TST conversions occurred in 14 (9.5%; 95% confidence interval [CI] = 5.3-15.5) using the 6 mm increment definition, and 6 (4.1%; 95% CI = 1.5-8.7) using the 10 mm increment definition. QFT conversions occurred in 17/147 participants (11.6%; 95% CI = 6.9-17.9) using the definition of IFN-gamma greater than or equal to 0.35 IU/ml, and 11/147 participants (7.5%; 95% CI = 3.8-13.0) using IFN-gamma greater than or equal to 0.70 IU/ml. Agreement between TST (10 mm increment) and QFT conversions (>or= 0.70 IU/ml) was 96% (kappa = 0.70). QFT reversions occurred in 2/28 participants (7%) with baseline concordant positive results, as compared with 7/10 participants (70%) with baseline discordant results (p < 0.001). CONCLUSIONS: IFN-gamma assay shows promise for serial testing, but repeat results need to be interpreted carefully. To meaningfully interpret serial results, the optimal thresholds to distinguish new infections from nonspecific variations must be determined.

Persistently elevated T cell interferon-gamma responses after treatment for latent tuberculosis infection among health care workers in India: a preliminary report.

BACKGROUND: T cell-based interferon-gamma (IFN-gamma) release assays (IGRAs) are novel tests for latent tuberculosis infection (LTBI). It has been suggested that T cell responses may be correlated with bacterial burden and, therefore, IGRAs may have a role in monitoring treatment response. We investigated IFN-gamma responses to specific TB antigens among Indian health care workers (HCWs) before, and after LTBI preventive therapy. METHODS: In 2004, we established a cohort of HCWs who underwent tuberculin skin testing (TST) and a whole-blood IGRA (QuantiFERON-TB-Gold In-Tube [QFT-G], Cellestis Ltd, Victoria, Australia) at a rural hospital in India. HCWs positive by either test were offered 6 months of isoniazid (INH) preventive therapy. Among the HCWs who underwent therapy, we prospectively followed-up 10 nursing students who were positive by both tests at baseline. The QFT-G assay was repeated 4 and 10 months after INH treatment completion (i.e. approximately 12 months and 18 months after the initial testing). IFN-gamma responses to ESAT-6, CFP-10 and TB7.7 peptides were measured using ELISA, and IFN-gamma >/=0.35 IU/mL was used to define a positive QFT-G test result. RESULTS: All participants (N = 10) reported direct contact with smear-positive TB patients at baseline, during and after LTBI treatment. All participants except one started treatment with high baseline IFN-gamma responses (median 10.0 IU/mL). The second QFT-G was positive in 9 of 10 participants, but IFN-gamma responses had declined (median 5.0 IU/mL); however, this difference was not significant (P = 0.10). The third QFT-G assay continued to be positive in 9 of 10 participants, with persistently elevated IFN-gamma responses (median 7.9 IU/mL; P = 0.32 for difference against baseline average). CONCLUSION: In an environment with ongoing, intensive nosocomial exposure, HCWs had strong IFN-gamma responses at baseline, and continued to have persistently elevated responses, despite LTBI treatment. It is plausible that persistence of infection and/or re-infection might account for this phenomenon. Our preliminary findings need confirmation in larger studies in high transmission settings. Specifically, research is needed to study T cell kinetics during LTBI treatment, and determine the effect of recurrent exposures on host cellular immune responses.

Mycobacterium tuberculosis infection in health care workers in rural India: comparison of a whole-blood interferon gamma assay with tuberculin skin testing.

CONTEXT: Mycobacterium tuberculosis infection in health care workers has not been adequately studied in developing countries using newer diagnostic tests. OBJECTIVES: To estimate latent tuberculosis infection prevalence in health care workers using the tuberculin skin test (TST) and a whole-blood interferon gamma (IFN-gamma) assay; to determine agreement between the tests; and to compare their correlation with risk factors. DESIGN, SETTING, AND PARTICIPANTS: A cross-sectional comparison study of 726 health care workers aged 18 to 61 years (median age, 22 years) with no history of active tuberculosis conducted from January to May 2004, at a rural medical school in India. A total of 493 (68%) of the health care workers had direct contact with patients with tuberculosis and 514 (71%) had BCG vaccine scars. INTERVENTIONS: Tuberculin skin testing was performed using 1-TU dose of purified protein derivative RT23, and the IFN-gamma assay was performed by measuring IFN-gamma response to early secreted antigenic target 6, culture filtrate protein 10, and a portion of tuberculosis antigen TB7.7. MAIN OUTCOME MEASURES: Agreement between TST and the IFN-gamma assay, and comparison of the tests with respect to their association with risk factors. RESULTS: A large proportion of the health care workers were latently infected; 360 (50%) were positive by either TST or IFN-gamma assay, and 226 (31%) were positive by both tests. The prevalence estimates of TST and IFN-gamma assay positivity were comparable (41%; 95% confidence interval [CI], 38%-45% and 40%; 95% CI, 37%-43%, respectively). Agreement between the tests was high (81.4%; kappa = 0.61; 95% CI, 0.56-0.67). Increasing age and years in the health profession were significant risk factors for both IFN-gamma assay and TST positivity. BCG vaccination had little impact on TST and IFN-gamma assay results. CONCLUSIONS: Our study showed high latent tuberculosis infection prevalence in Indian health care workers, high agreement between TST and IFN-gamma assay, and similar association between positive test results and risk factors. Although TST and IFN-gamma assay appear comparable in this population, they have different performance and operational characteristics; therefore, the decision to select one test over the other will depend on the population, purpose of testing, and resource availability.