Is the Infection of the SARS-CoV-2 Delta Variant Associated With the Outcomes of COVID-19 Patients?

Abstract

Background: Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) has been responsible for the current increase in Coronavirus disease 2019 (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.Methods: In this cross-sectional study, we 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.Results: The mean age of patients with the Delta variant and the non-Delta variant was 27.3 ± 20.0 and 43.0 ± 20.9 (p = 3 × 10−6). 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 that of 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 were 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 the patients without the factors: age ≥65 years, obesity, diabetes, hypertension, and cardiovascular disease with the OR of 11 (95% CI = 3.4–36; p = 8 × 10−5), 27 (95% CI = 6.1–118; p = 1 × 10−5), 15.6 (95% CI = 5.3–46; p = 6 × 10−7), 12 (95% CI = 4–35.3; p = 1.2 × 10−5), 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.Conclusions: We 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 that older age and comorbidity increase the mortality rate of patients with COVID-19.

Comparative analysis of the outcomes of COVID-19 between patients infected with SARS-CoV-2 Omicron and Delta variants: a retrospective cohort study

“…Previous studies showed that older age and comorbidities are significant prognostic factors for hospitalization and mortality [13-15,33,34]. Our study further provides evidence that older age, diabetes, and cardiovascular diseases as strong prognostic factors for the outcomes of COVID-19 patients.…”

“…We conducted whole-genome sequencing (WGS) of SARS-CoV-2 for all samples with PCR's Ct value of less than 30. As described in our previous studies [13,14,18,119], singlestranded cDNA was synthesized from total RNA extracted from the samples of COVID-19 patients by SuperScript™ III First-Strand Synthesis System (Thermo Fisher Scientific, MA, United States). Subsequently, the second strand was synthesized by COVID-19 ARTIC v3 primer pool design by SARS-CoV-2 ARTIC Network using Phusion™ High-Fidelity DNA Polymerase (Thermo Fisher Scientific, MA, United States).…”

“…We associated the outcomes of COVID-19 patients with the following prognostic variables: sex; age; comorbidities, including obesity, diabetes, hypertension, cardiovascular disease, and chronic kidney disease; and smoking. According to the previous reports, those prognostic factors were selected [13][14][15][16][17].…”

“…Several factors have been associated with the clinical severity of infection, including vaccination status and the previous SARS-CoV-2 infection. In addition, we and others have shown that several prognostic factors have been associated with the outcomes of COVID-19 [13][14][15][16][17]. Therefore, to further comprehend the impact of the Omicron wave in developing countries, we performed a comparative analysis of the outcomes of COVID-19 patients infected with Delta and Omicron variants and associated them with several prognostic factors, including age, sex, comorbidities, and smoking.…”

Tracking the molecular evolution and transmission patterns of SARS-CoV-2 lineage B.1.466.2 in Indonesia based on genomic surveillance data

“…Under this system, a multitude of SARS-CoV-2 lineages and sub-lineages are identified and named accurately, including four variants of concern (VOCs: B.1.1.7, B.1.351, P.1 and B.1.617.2 corresponding to Alpha, Beta, Gamma and Delta labelled by WHO) and several variants of interest (VOIs) [12]. Since 2020, several teams and institutions (e. g., the Yogyakarta-Central Java COVID-19 Study Group and the West Java Health Laboratory) have conducted whole-genome sequencing (WGS) of SARS-CoV-2 strains circulating in various parts of Indonesia, and have shared genetic data and related metadata via the Global Initiative on Sharing Avian Influenza Data (GISAID) platform [13][14][15][16][17]. These efforts make it possible to gain insights into Indonesia's COVID-19 epidemic from a micro perspective.…”