Comparison of the Clinico-Demographic and Molecular Profile of SARS-CoV-2 Omicron Variants BA.1 and BA.2 from North-East India

Purpose: The present study investigated the clinical and demographic characteristics of SARS-CoV-2 infected patients in North-East India during the SARS-CoV-2 Omicron wave from December 2021 to January 2022. Methods: An in-house real-time RT-PCR assay was used to screen the Omicron sub-variants BA.1 and BA.2. The Omicron positive samples underwent whole genome sequencing to confirm the presence of sub-variants BA.1 and BA.2. Further, a retrospective study based on questionnaire survey was conducted to compare the clinico-demographic characteristics of patients infected with SARS-CoV-2 Omicron variants BA.1 and BA.2. Results: Out of a total of 349 participants, 26 were positive for sub-lineage BA.1, while 323 were positive for sub-lineage BA.2. Overall, 77.90% of cases (272/349) exhibited symptoms, with fever being the most common. Patients infected with BA.2 sub-lineage experienced higher symptoms compared to BA.1 sub-lineage (79.87%, p=0.002). Among SARS-CoV-2 vaccinated individuals, 92.83% were infected with the Omicron variant and of those, 79.32% experienced symptoms (p=0.025). Of the individuals with a prior COVID-19 history, 37 out of 349 were re-infected with the Omicron variant, with only one case requiring hospitalization and none needing ICU care. Furthermore, all 37 SARS-CoV-2 re-infection cases reported in this study were positive for the BA.2 variant suggesting that BA.2 can evade and circumvent the herd immunity established through prior infections. Conclusion: The predominant SARS-CoV-2 Omicron variant observed in the region during the period was BA.2. The lower number of hospitalizations including the need for ICU indicated a milder severity of the Omicron variant, potentially attributed to the protective immunity developed during pre-Omicron waves. Notably, re-infection cases demonstrated less severe infections indicating the active role of hybrid immunity derived from a combination of immunity from past infections and vaccination.