Is the infection of the SARS-CoV-2 Delta variant associated with the outcomes of COVID-19 patients?

BackgroundSARS-CoV-2 Delta variant (B.1.617.2) has been responsible for the current increase in COVID-19 infectivity rate worldwide. We compared the impact of the Delta variant and non-Delta variant on the COVID-19 outcomes in patients from Yogyakarta and Central Java provinces, Indonesia. MethodsWe ascertained 161 patients, 69 with the Delta variant and 92 with the non-Delta variant. The Illumina MiSeq next-generation sequencer was used to perform the whole genome sequences of SARS-CoV-2. ResultsThe mean age of patients with Delta and the non-Delta variant was 27.3 {+/-} 20.0 and 43.0 {+/-} 20.9 (p=3x10-6). The patients with Delta variant consisted of 23 males and 46 females, while the patients with the non-Delta variant involved 56 males and 36 females (p=0.001). The Ct value of the Delta variant (18.4 {+/-} 2.9) was significantly lower than the non-Delta variant (19.5 {+/-} 3.8) (p=0.043). There was no significant difference in the hospitalization and mortality of patients with Delta and non-Delta variants (p=0.80 and 0.29, respectively). None of the prognostic factors was associated with the hospitalization, except diabetes with an OR of 3.6 (95% CI=1.02-12.5; p=0.036). Moreover, the patients with the following factors have been associated with higher mortality rate than patients without the factors: age [≥]65 years, obesity, diabetes, hypertension, and cardiovascular disease with the OR of 11 (95% CI=3.4-36; p=8x10-5), 27 (95% CI=6.1-118; p=1x10-5), 15.6 (95% CI=5.3-46; p=6x10-7), 12 (95% CI=4-35.3; p=1.2x10-5), and 6.8 (95% CI=2.1-22.1; p=0.003), respectively. Multivariate analysis showed that age [≥]65 years, obesity, diabetes, and hypertension were the strong prognostic factors for the mortality of COVID-19 patients with the OR of 3.6 (95% CI=0.58-21.9; p=0.028), 16.6 (95% CI=2.5-107.1; p=0.003), 5.5 (95% CI=1.3-23.7; p=0.021), and 5.8 (95% CI=1.02-32.8; p=0.047), respectively. ConclusionsWe show that the patients infected by the SARS-CoV-2 Delta variant have a lower Ct value than the patients infected by the non-Delta variant, implying that the Delta variant has a higher viral load, which might cause a more transmissible virus among humans. However, the Delta variant does not affect the COVID-19 outcomes in our patients. Our study also confirms the older age and comorbidity increase the mortality rate of COVID-19 patients.

The emergence of COVID-19 in Indonesia: analysis of predictors of infection and mortality using independent and clustered data approaches

BackgroundAnalyses of correlates of SARS-CoV-2 infection or mortality have usually assessed individual predictors. This study aimed to determine if patterns of combined predictors may better identify risk of infection and mortality MethodsFor the period of March 2nd to 10th 2020, the first 9 days of the COVID-19 pandemic in Indonesia, we selected all 18 confirmed cases, of which 6 died, and all 60 suspected cases, of which 1 died; and 28 putatively negative patients with pneumonia and no travel history. We recorded data for travel, contact history, symptoms, haematology, comorbidities, and chest x-ray. Hierarchical cluster analyses (HCA) and principal component analyses (PCA) identified cluster and covariance patterns for symptoms or haematology which were analysed with other predictors of infection or mortality using logistic regression. ResultsFor univariate analyses, no significant association with infection was seen for fever, cough, dyspnoea, headache, runny nose, sore throat, gastrointestinal complaints (GIC), or haematology. A PCA symptom component for fever, cough, and GIC tended to increase risk of infection (OR 3.41; 95% CI 1.06-14; p=0.06), and a haematology component with elevated monocytes decreased risk (OR 0.26; 0.07-0.79; 0.027). Multivariate analysis revealed that an HCA cluster of 3-5 symptoms, typically fever, cough, headache, runny nose, sore throat but little dyspnoea and no GIC tended to reduce risk (aOR 0.048; <0.001-0.52; 0.056). In univariate analyses for death, an HCA cluster of cough, fever and dyspnoea had increased risk (OR 5.75; 1.06 - 31.3, 0.043), but no other individual predictor, cluster or component was associated. Other significant predictors of infection were age [≥] 45, international travel, contact with COVID-19 patient, and pneumonia. Diabetes and history of contact were associated with higher mortality. ConclusionsCluster groups and co-variance patterns may be stronger correlates of SARS-CoV-2 infection than individual predictors. Comorbidities may warrant careful attention as would COVID-19 exposure levels.