Epidemiological and molecular characteristics of SARS-CoV-2 Delta variant-caused pneumonia in Henan Province in 2021

ABSTRACT

Objective To analyze and summarize the epidemiological and molecular characteristics of SARS-CoV-2 Delta variant, a variant of concern (VOC), in Henan Province in 2021 in order to provide a basis for epidemic prevention and control. Methods According to the feedback of sequencing results from Chinese Center for Disease Control and Prevention, 111 patients infected with SARS-CoV-2 Delta VOC were selected from the Henan imported and local cases in 2021. Basic patient information was obtained from the pandemic website. The differences in age, gender, vaccination history, the number of vaccine doses and different clinical types were analyzed. Moreover, the differences in RT-qPCR results of ORF1ab gene and N gene Ct values between cases of different genders and symptoms were analyzed statistically. Sequencing results of the nucleotide and S protein mutation sites were analyzed. Results There was no significant difference in the gender distribution of 111 cases between different age groups (χ2 = 2. 217, P = 0. 529). There was also no significant difference in clinical types between patients with different vaccination history (χ2 = 12. 074, P = 0. 209). The Ct values of most SARS-CoV-2 nucleic acid-positive specimens were distributed in the lower range and the viral loads were higher. The difference in the Ct value of ORF1ab gene between different gender groups was not statistically significant (χ2 = 1. 646, P = 0. 439), but were significantly different among asymptomatic, mild, normal, and severe cases (χ2 = 13. 257, P = 0. 039). There was no significant difference in N gene Ct value among cases of different genders or different symptoms (all P>0. 05). The 111 patients in this study were mainly found through close-contact screening and full-staff nucleic acid screening and accounted for 62. 2% (69 cases) of the total. The sequencing length coverage was basically greater than 99% (accounting for 90. 1%, 100 / 111);the total number of nucleotide mutation sites was mostly in the range of 46-50 (86. 4%, 89 / 103);the total number of S protein mutation sites was mostly 12 (82. 5%, 85 / 103). The 103 Delta mutants all contained nine mutation sites, which were T19R, R158G, L452R, T478K, D614G, P681R, D950N, E156del and F157del, with a mutation rate of 100%. Conclusions People were highly susceptible to the SARS-CoV-2 Delta in Henan Province in 2021. High viral load and increase in the ORF1ab gene load would aggravate the clinical symptoms.