Background India has experienced the second largest outbreak of COVID-19 globally, yet there is a paucity of studies analysing contact tracing data in the region which can optimise public health interventions (PHI’s). Methods We analysed contact tracing data from Karnataka, India between 9 March and 21 July 2020. We estimated metrics of transmission including the reproduction number (R), overdispersion (k), secondary attack rate (SAR), and serial interval. R and k were jointly estimated using a Bayesian Markov Chain Monte Carlo approach. We studied determinants of risk of further transmission and risk of being symptomatic using Poisson regression models. Findings Up to 21 July 2020, we found 111 index cases that crossed the super-spreading threshold of ≥8 secondary cases. Among 956 confirmed traced cases, 8.7% of index cases had 14.4% of contacts but caused 80% of all secondary cases. Among 16715 contacts, overall SAR was 3.6% [95% CI, 3.4–3.9] and symptomatic cases were more infectious than asymptomatic cases (SAR 7.7% vs 2.0%; aRR 3.63 [3.04–4.34]). As compared to infectors aged 19–44 years, children were less infectious (aRR 0.21 [0.07–0.66] for 0–5 years and 0.47 [0.32–0.68] for 6–18 years). Infectors who were confirmed ≥4 days after symptom onset were associated with higher infectiousness (aRR 3.01 [2.11–4.31]). As compared to asymptomatic cases, symptomatic cases were 8.16 [3.29–20.24] times more likely to cause symptomatic infection in their secondary cases. Serial interval had a mean of 5.4 [4.4–6.4] days, and case fatality rate was 2.5% [2.4–2.7] which increased with age. Conclusion We found significant heterogeneity in the individual-level transmissibility of SARS-CoV-2 which could not be explained by the degree of heterogeneity in the underlying number of contacts. To strengthen contact tracing in over-dispersed outbreaks, testing and tracing delays should be minimised and retrospective contact tracing should be implemented. Targeted measures to reduce potential superspreading events should be implemented. Interventions aimed at children might have a relatively small impact on reducing transmission owing to their low symptomaticity and infectivity. We propose that symptomatic cases could cause a snowballing effect on clinical severity and infectiousness across transmission generations; further studies are needed to confirm this finding.

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India is among the top three countries in the world both in COVID-19 case and death counts. With the pandemic far from over, timely, transparent, and accessible reporting of COVID-19 data continues to be critical for India’s pandemic efforts. We systematically analyze the quality of reporting of COVID-19 data in over one hundred government platforms (web and mobile) from India. Our analyses reveal a lack of granular data in the reporting of COVID-19 surveillance, vaccination, and vacant bed availability. As of 5 June 2021, age and gender distribution are available for less than 22% of cases and deaths, and comorbidity distribution is available for less than 30% of deaths. Amid rising concerns of undercounting cases and deaths in India, our results highlight a patchy reporting of granular data even among the reported cases and deaths. Furthermore, total vaccination stratified by healthcare workers, frontline workers, and age brackets is reported by only 14 out of India’s 36 subnationals (states and union territories). There is no reporting of adverse events following immunization by vaccine and event type. By showing what, where, and how much data is missing, we highlight the need for a more responsible and transparent reporting of granular COVID-19 data in India.

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— A comprehensive analysis of more than 100 digital platforms (web and mobile) from India shows a lack of granular data in the reporting of COVID-19 surveillance, vaccination monitoring, and bed availability.— As of 5 June 2021, age and gender distribution is available for less than 22% of cases and deaths; and comorbidity distribution is available for less than 30% of deaths.— Total vaccination stratified by healthcare workers, frontline workers, and age brackets is reported by only 14 out of the 36 subnationals (states and union territories) in India. — There is no reporting of adverse events following immunization by vaccine and event type. — By showing what, where, and how much data is missing, we join the Indian scientific community in pushing for a more responsible and transparent reporting of granular data.

Daily positivity rates (DPR) are a popular metric to judge the prevalence of an infection in the population and the testing response to it as a single number. It has been widely implicated in predicting future course of the SARS CoV-2 pandemic in India. With increasing use of multiple testing protocols with varying sensitivity and specificity in various proportions, the naive calculation loses meaning particularly during comparison between states/countries with large daily variations in contribution of different testing protocols to the testing response. We propose an adjustment to the naive DPR based on the testing parameters and the relative proportional use of each such protocol. Such a correction has become essential for comparing testing response of Indian states from Jun 2020 to Aug 2020 because of steep variations in testing protocol in certain states.

Background and Aims Glomerular diseases pose a substantial burden on the healthcare system. While the medical and economic burden of glomerular diseases is well established, the data on the health-related quality of life impact is scant. Method We used the PROMIS 29 v2.1 (Patient-Reported Outcomes Measurement Information System) tool to assess HRQOL impact of primary glomerular diseases in adult Indian patients [1], under the domains: physical function, anxiety, fatigue, depression, sleep disturbance, ability to participate in social roles and activities and pain interference in daily activities. The questionnaire was administered in English and Hindi. Patient responses were then used to calculate T-scores with a mean of 50 and an SD of 10 with the score having positive correlation with the quantum of the outcome measured. Results 141 adult patients were recruited (39 minimal change disease/ focal segmental glomerulosclerosis, 36 membranous nephropathy, 56 IgA nephropathy, 9 membrano-proliferative glomerulonephritis). Mean T-scores across domains were as follows: physical function- 48.2 (46.8-49.6), fatigue- 49.2 (47.5-51), anxiety- 52.3 (50.6-53.9), sleep impairment- 43.5 (41.9-45.1), depression- 50.7 (49-52.4), ability to participate in social roles and activities- 55 (53.3-56.7), hindrance in daily activities due to pain 51.2 (49.7-52.8). Better physical function was associated with higher eGFR (T-score of 44 at eGFR<45 ml/min/1.73m2 and 49.8 at eGFR>45 ml/min/1.73m2, p<0.001), lower BMI (42.4 in obese vs 48.6 in non-obese, p = 0.02), and male sex (50.2 vs 44.5 in females, p<0.001). Fatigue was associated with eGFR<45 ml/min/1.73m2 (52.2 vs 48.1 at eGFR>45 ml/min/1.73m2, p = 0.04), and female sex (53.2 vs 47.1 in males, p<0.001). Worse anxiety was seen in females (55.8 vs 50.4 in males, p = 0.002) and patients with eGFR<45 ml/min/1.73m2 (55.4 vs 51.1 at eGFR>45 ml/min/1.73m2, p = 0.02). Sleep impairment was seen in patients having a history of steroid usage in the last 2 months (45.8 vs 42.1, p = 0.02), females (45.8 vs 42.3, p = 0.04), and patients with eGFR<45 ml/min/1.73m2 (46.2 vs 42.5 at eGFR>45 ml/min/1.73m2, p = 0.04). Pain interference was higher in females (55.9 vs 48.8 in males, p<0.001) and patients with eGFR<45 ml/min/1.73m2 (54 vs 50.2 at eGFR>45 ml/min/1.73m2, p = 0.03). eGFR>45 ml/min/1.73m2 (56.4 vs 51.4 at eGFR<45 ml/min/1.73m2, p = 0.008) was associated with better involvement in social roles. Depression was associated with female sex (54.2 vs 48.9 in males, p = 0.003). Degree of proteinuria, serum albumin, duration of disease, immunosuppressive drug use, age, patient-reported edema, and socio-economic status were not associated with a significant decrease in HRQOL. Multivariable linear regression models were evaluated for all domains. Physical function was negatively associated with eGFR<45ml/min/1.73m2 (β = -5.46), female sex (β = -5.16), and obesity (β = -6.36). Fatigue was associated with eGFR<45ml/min/1.73m2 (β = 3.89), female sex (β = 5.76), and obesity (β = 9.62). Worse anxiety was associated with eGFR<45ml/min/1.73m2 (β = 3.82) and female sex (β = 4.97). Sleep impairment was associated with eGFR<45ml/min/1.73m2 (β = 3.46) and female sex (β = 3.24). Pain interference was associated with eGFR<45ml/min/1.73m2 (β = 3.39) and female sex (β = 7.19) Ability to participate in social roles and activities was negatively associated with eGFR<45ml/min/1.73m2 (β = -4.86) and female sex (β = −3). Depression was associated with obesity (β = 6.16) and female sex (β = 5.22). Conclusion Glomerular diseases adversely impact the quality of life. Female sex, lower renal function (eGFR), higher BMI and history of recent steroid use correlated with higher morbidity.

Brief AbstractWe analysed SARS-CoV-2 surveillance and contact tracing data from Karnataka, India up to 21 July 2020. We estimated metrics of infectiousness and the tendency for superspreading (overdispersion), and evaluated potential determinants of infectiousness and symptomaticity in COVID-19 cases. Among 956 cases confirmed to be forward-traced, 8.7% of index cases had 14.4% of contacts but caused 80% of all secondary cases, suggesting significant heterogeneity in individual-level transmissibility of SARS-CoV-2 which could not be explained by the degree of heterogeneity in underlying number of contacts. Secondary attack rate was 3.6% among 16715 close contacts. Transmission was higher when index case was aged >18 years, or was symptomatic (adjusted risk ratio, aRR 3.63), or was lab-confirmed ≥4 days after symptom onset (aRR 3.01). Probability of symptomatic infection increased with age, and symptomatic infectors were 8.16 times more likely to generate symptomatic secondaries. This could potentially cause a snowballing effect on infectiousness and clinical severity across transmission generations; further studies are suggested to confirm this. Mean serial interval was 5.4 days. Adding backward contact tracing and targeting control measures to curb super-spreading may be prudent. Due to low symptomaticity and infectivity, interventions aimed at children might have a relatively small impact on reducing transmission.Structured AbstractBackgroundIndia has experienced the second largest outbreak of COVID-19 globally, yet there is a paucity of studies analysing contact tracing data in the region. Such studies can elucidate essential transmission metrics which can help optimize disease control policies.MethodsWe analysed contact tracing data collected under the Integrated Disease Surveillance Programme from Karnataka, India between 9 March and 21 July 2020. We estimated metrics of disease transmission including the reproduction number (R), overdispersion (k), secondary attack rate (SAR), and serial interval. R and k were jointly estimated using a Bayesian Markov Chain Monte Carlo approach. We evaluated the effect of age and other factors on the risk of transmitting the infection, probability of asymptomatic infection, and mortality due to COVID-19.FindingsUp to 21 July, we found 111 index cases that crossed the super-spreading threshold of ≥8 secondary cases. R and k were most reliably estimated at R 0.75 (95% CI, 0.62-0.91) and k 0.12 (0.11-0.15) for confirmed traced cases (n=956); and R 0.91 (0.72-1.15) and k 0.22 (0.17-0.27) from the three largest clusters (n=394). Among 956 confirmed traced cases, 8.7% of index cases had 14.4% of contacts but caused 80% of all secondary cases. Among 16715 contacts, overall SAR was 3.6% (3.4-3.9) and symptomatic cases were more infectious than asymptomatic cases (SAR 7.7% vs 2.0%; aRR 3.63 [3.04-4.34]). As compared to infectors aged 19-44 years, children were less infectious (aRR 0.21 [0.07-0.66] for 0-5 years and 0.47 [0.32-0.68] for 6-18 years). Infectors who were confirmed ≥4 days after symptom onset were associated with higher infectiousness (aRR 3.01 [2.11-4.31]). Probability of symptomatic infection increased with age, and symptomatic infectors were 8.16 (3.29-20.24) times more likely to generate symptomatic secondaries. Serial interval had a mean of 5.4 (4.4-6.4) days with a Weibull distribution. Overall case fatality rate was 2.5% (2.4-2.7) which increased with age.ConclusionWe found significant heterogeneity in the individual-level transmissibility of SARS-CoV-2 which could not be explained by the degree of heterogeneity in the underlying number of contacts. To strengthen contact tracing in over-dispersed outbreaks, testing and tracing delays should be minimised, retrospective contact tracing should be considered, and contact tracing performance metrics should be utilised. Targeted measures to reduce potential superspreading events should be implemented. Interventions aimed at children might have a relatively small impact on reducing SARS-CoV-2 transmission owing to their low symptomaticity and infectivity. There is some evidence that symptomatic cases produce secondary cases that are more likely to be symptomatic themselves which may potentially cause a snowballing effect on infectiousness and clinical severity across transmission generations; further studies are needed to confirm this finding.FundingGiridhara R Babu is funded by an Intermediate Fellowship by the Wellcome Trust DBT India Alliance (Clinical and Public Health Research Fellowship); grant number: IA/CPHI/14/1/501499.