An Early and Preliminary Assessment of the Clinical Severity of the Emerging SARS-CoV-2 Omicron Variants in Maharashtra, India

Abstract

Background: The SARS-CoV-2 Omicron variants BA.2.74, BA.2.75 and BA.2.76 have appeared recently in India and have already spread to over 40 countries. They have acquired additional mutations in their spike protein compared to BA.2, branching away on the SARS-CoV-2 phylogenetic tree. These added mutations, over and above those of the parental BA.2 variant, have raised concerns about the impact on viral pathogenicity, transmissibility, and immune evasion properties of the new variants. Material and Methods: A total of 990 RT-PCR positive SARS-CoV-2 samples, with a cycle threshold value (Ct) less than 25, were processed for SARS-CoV-2 whole genome sequencing between 3rd June 2022 to 7th August 2022. All corresponding demographic and clinical data were recorded and analyzed using Microsoft Excel. Results: Out of 990 samples sequenced, BA.2.75 (23.03%) was the predominant Omicron sublineage, followed by BA.2.38 (21.01%), BA.5 (9.70%), BA.2 (9.09%), BA.2.74 (8.89%) and BA.2.76 (5.56%). A total of 228 cases of BA.2.74, BA.2.75 and BA.2.76 were contacted by telephone, of which 215 (94.30%) were symptomatic with mild symptoms, and 13 (5.70%) had no symptoms. Fever (82.02%) was the most common symptom, followed by cough (49.12%), cold (35.97%), fatigue (27.19%), headache (21.05%) and myalgia (20.61%). Of the 228 cases, 195 (85.53%) cases recovered at home, and 33 (14.47%) required institutional quarantine. Recovery with conservative treatment was observed in 92.98% of cases, while 4.83% required additional oxygen therapy. Only 03 (1.32%) cases had poor outcomes resulting in death, and the remaining 225 (98.68%) had a good outcome. Among the 228 cases, 219 (96.05%) cases were vaccinated with COVID-19 vaccine; of these 72.60% had received both doses, 26.03% had also received the precautionary booster dose, while 1.37% were incompletely vaccinated with a single dose of vaccine. Conclusion: The current study indicates that the three BA.2 sublineages are causing mild disease in India. However, BA.2.75 has key mutations that are notable for accelerated growth and transmission and require close and effective monitoring. Keywords: Omicron, BA.2.74, BA.2.75, BA.2.76, SARS-CoV-2 whole-genome sequencing

Cross‐reactivity of SARS‐CoV‐2 with other pathogens, especially dengue virus: A historical perspective

“…Conversely, whether DENV Abs will still have cross‐protective effects on the newer SARS‐CoV‐2 variants is also a pertinent question. Again, the present day epidemiological observations suggest that the spread, severity, and mortality due to Omicron variants are much reduced in the Indian subcontinent and Southeast Asia compared to dengue non‐endemic countries 63–65 . It is a well‐established fact that DENV Abs last over years while SARS‐CoV‐2 Abs are much short‐lived and gradually wanes out in a year or so, in general 66–68 .…”

Vaccine- and BTI-elicited pre-Omicron immunity more effectively neutralizes Omicron sublineages BA.1, BA.2, BA.4 and BA.5 than pre-Omicron infection alone

“…While Omicron strains are less pathogenic and associated with lower fatality rates than Delta, the later strains BA.2.75 and BA.5 seem to gain pathogenicity compared to the early BA.1 and BA.2 (6,(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18). The Omicron lineage typically features strongly enhanced transmissibility compared to Delta and pre-Omicron variants (3-6, 19, 20).…”