Abstract:
Background: The SARS-CoV-2 Delta variant (B.1.617.2) was first detected in India in late 2020 and soon became the
predominant lineage owing to its high transmissibility. Over time, the virus has acquired mutations and has evolved into
many new sub-lineages. AY.4 is one such sub-lineage that grew in frequency globally. Therefore, we aimed to compare the
severity of infection due to Delta sub-lineages to Delta infections in Pune, Maharashtra, India.
Material and Methods: Whole-genome sequencing and analysis of 255 SARS-CoV-2 positive samples, collected between
1
st August to 1st September 2021, by BJ Government Medical College, Pune, was carried out at the Indian Institute of
Science Education and Research (IISER), Pune and the Council of Scientific and Industrial Research–Institute of Genomics
and Integrative Biology (CSIR-IGIB), New Delhi. Individual-level data on these patients were collected from ICMR
COVID-19 Data Portal. Additional information regarding the presence of any symptoms, comorbidities, hospitalization,
international travel history within 14 days and vaccination status was collected by telephonic interview with each patient by
the BJGMC Sequencing Team.
Results: Of the 255 samples sequenced, 161 (63.13%) had VOC B.1.617.2, 90 (35.29%) had AY.*. The AY.4 (51.1%) was
the predominant Delta sub-lineage, followed by AY.12 (22.2%) and AY.16 (15.6%). A total of 201 patients were contacted
telephonically, of which 30 (14.93%) cases were asymptomatic, and 171 (85.07%) cases were symptomatic. Of the
symptomatic cases, 58.21% had Delta, 11.94% had AY.4 and 14.93% were infected with other Delta sub-lineages. Oxygen
therapy by mask/nasal prongs was required in 13.18% of Delta cases, and one (0.78%) case required mechanical ventilation.
In contrast, only 3.03% and 5.13% cases of AY.4 and other Delta sub-lineages, respectively, needed oxygen therapy. Of 49
individuals vaccinated with two vaccine doses, 71.43% were infected with Delta, 20.41% with other Delta-sub-lineages and
8.16% with AY.4. There was no evidence of a significant difference in hospital attendance, disease severity, oxygen therapy
requirement, hospitalization days, vaccination status, and disease outcome among patients infected with Delta and AY.*
Delta sub-lineages.
Conclusion: The preliminary results suggest that the disease severity in patients with Delta sub-lineages is not markedly
different from those infected with Delta variant. Therefore, currently, it shares the same public health concern as those of
Delta.