Associations between genetic mutations in different SARS-CoV-2 strains and negative conversion time of viral RNA among imported cases in Hangzhou: A cross-sectional study

Abstract

Purpose: Previous studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have focused on factors that influence the achievement of negative conversion of viral RNA. This study aimed to investigate the effects of the genetic mutations in different SARS-CoV-2 strains on the negative conversion time (NCT) among imported cases in Hangzhou, Zhejiang Province, China, in order to provide valuable insights for developing targeted epidemic prevention guidelines.

Methods: This retrospective study involved 146 imported SARS-CoV-2 cases in Hangzhou from 8 April 2021 to 11 June 2022. We compared the SARS-CoV-2-specific indicators, clinical indexes, and NCT among the wild-type (WT), Delta, and Omicron groups. Spearman correlation analysis was used to identify the correlations of NCT with mutation types/frequencies.

Results: The mean age of the imported cases was 35.3 (SD: 12.3) years, with 71.92 % males and 28.08 % females. The mean cycle threshold (Ct) values of open reading frame 1ab (ORF1ab) and nucleocapsid (N) RNA were 25.17 (SD: 6.44) and 23.4 (SD: 6.76), respectively. The mutations of SARS-CoV-2 strains were mainly located in N, membrane (M), spike (S), ORF1a, ORF1b, ORF3a, ORF6, and ORF9b genes among the WT, Delta, and Omicron groups. NCT was significantly prolonged in the WT and Delta groups compared to the Omicron group. T lymphocyte, white blood cell, eosinophil, and basophil counts were dramatically higher in the WT group than the Delta group. White blood cell, red blood cell, and basophil counts were significantly lower in the Delta group than the Omicron group. Spearman correlation analysis revealed a significant correlation between the NCT of viral RNA and mutation types of viral genes of WT and Omicron strains. Additionally, NCT was markedly negatively correlated with the frequencies of five mutations in Omicron strains (ORF1b:P1223L, ORF1b:R1315C, ORF1b:T2163I, ORF3a:T223I, and ORF6:D61L).

Conclusions: This study indicates that five mutations in Omicron strains (ORF1b:P1223L/R1315C/T2163I, ORF3a:T223I and ORF6:D61L) shortened NCT in imported SARS-CoV-2 cases.

Keywords: Genetic mutation; Imported cases; Negative conversion; SARS-CoV-2 strain.

Fig. 1

Study flow diagram. In total, 146 imported cases were included in the mutation analysis and 108 imported cases were included in the clinical comparisons and correlation analyses. Abbreviations: WT: wild-type; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2.

Fig. 2

Numbers and frequencies of mutations in all the significant genomic regions of SARS-CoV-2 WT strain (A), Delta variant (B) and Omicron variant (C) among our population. Abbreviations: WT: wild-type; N: nucleocapsid; M: membrane; S: spike; ORF: open reading frame.

Fig. 3

Comparisons of SARS-CoV-2-specific indicators among WT, Delta, and Omicron groups. Differences in cycle threshold values for N (A) or ORF1ab (B) on admission, (C) NCT of viral RNA, and serum IgG (D), IgM (E), and NAb (F) levels among WT, Delta, and Omicron groups. Abbreviations: N: nucleocapsid; WT: wild-type; IgG: immunoglobulin G; IgM: immunoglobulin M; Ab: antibody; NAb: neutralizing antibody; NCT: negative conversion time.

Fig. 4

Comparisons of clinical indexes among WT, Delta, and Omicron groups. Differences in T lymphocyte (A), white blood cell (B), red blood cell (C), neutrophil (D), eosinophil (E), and basophil (F) counts, and serum CRP (G), SAA (H) and IL-6 (I) levels, among WT, Delta, and Omicron groups. Abbreviations: CRP: C-reactive protein; SAA: serum amyloid A; IL-6: interleukin 6; WT: wild-type.

Fig. 5

Correlations of NCT with mutation frequencies in imported cases involving SARS-CoV-2 (A) WT or Delta strain (B) or Omicron strain (C). Abbreviations: NCT: negative conversion time; WT: wild-type.