Prognostic factors for the outcomes of COVID-19 patients infected with SARS-CoV-2 Omicron and Delta variants

Abstract

Background: The SARS-CoV-2 Omicron variant has replaced the previously dominant Delta variant because of high transmissibility. However, studies on the impact of the Omicron variant on the severity of COVID-19 are still limited in developing countries. Our study aimed to determine the prognostic factors for the outcomes of patients infected with SARS-CoV-2 Omicron and Delta variants, including age, sex, comorbidities, and smoking.

Methods: In this retrospective cross-sectional study, we involved 352 patients with COVID-19 from Yogyakarta and Central Java provinces, Indonesia, from May 2021 to February 2022, consisting of 164 males and 188 females. We included all patients with the PCR's Ct value of less than 30 for further whole-genome sequencing.

Results: Ct value and mean age of COVID-19 patients were not significantly different between both groups (p = 0.146 and 0.273, respectively). Patients infected with Omicron (n = 139) and Delta (n = 213) variants showed similar hospitalization (p = 0.396) and mortality rates (p = 0.565). Multivariate analysis of both groups showed that older age (≥ 65 years) had a higher risk for hospitalization (OR = 3.86 [95% CI = 1.29-11.5]; p = 0.015) and fatalities (OR = 3.91 [95% CI = 1.35-11.42]; p = 0.012). In both groups, patients with cardiovascular disease had a higher risk for hospitalization (OR = 5.36 [95% CI = 1.08-26.52]; p = 0.039), whereas patients with diabetes revealed a higher risk for fatalities (OR = 9.47 [95% CI = 3.23-27.01]; p = < 0.001).

Conclusions: Our study shows that patients infected with Omicron and Delta variants reveal similar clinical outcomes, including hospitalization and mortality. Our findings further confirm that older age, cardiovascular disease, and diabetes are substantial prognostic factors for the outcomes of COVID-19 patients. Our findings imply that COVID-19 patients with older age, cardiovascular disease, or diabetes should be treated comprehensively and cautiously to prevent further morbidity and mortality. Furthermore, incomplete data on vaccination status hampered us from analyzing further its impact on hospitalization and mortality in our patients.

Keywords: COVID-19 outcomes; Delta variant; Hospitalization; Mortality; Omicron variant; SARS-CoV-2; Whole-genome sequencing.

Fig. 1

Phylogenetic analysis of Omicron and Delta variants of SARS-CoV-2 virus collected from Central Java and Yogyakarta regions from 2021–2022. Phylogenetic trees are displayed in rectangular (a) and polar (b) layouts. The evolutionary history was inferred using the Neighbor-Joining method [19, 20] and computed using the Kimura 2-parameter [21] method with 1000 bootstrap replication in MEGA X [23]. The number of base substitutions per site (0.0001) is shown on the left of the rectangular tree, where the rate variation among sites was modeled with a gamma distribution. This analysis involved 392 nucleotide sequences, a total of 29.409 positions in the final dataset. Moreover, all ambiguous positions were removed for each sequence pair (pairwise deletion option). Samples from our study were color-coded as follows: the Delta variant taxa are indicated in red, followed by Omicron-BA.1-like in blue, Omicron-BA.2-like in green, Omicron-BA.3-like in purple, and other variants previously circulating in Indonesia that are involved in this analysis are indicated in black

Fig. 2

Vaccination coverage in Indonesia during Delta and Omicron surges