Extensive genetic diversity of severe fever with thrombocytopenia syndrome virus circulating in Hubei Province, China, 2018-2022

Abstract

Severe fever with thrombocytopenia syndrome virus (SFTSV), an etiological agent causing febrile human disease was identified as an emerging tick-borne bunyavirus. The clinical disease characteristics and case fatality rates of SFTSV may vary across distinct regions and among different variant genotypes. From 2018 to 2022, we surveyed and recruited 202 severe fever with thrombocytopenia syndrome (SFTS) patients in Hubei Province, a high-incidence area of the epidemic, and conducted timely and systematic research on the disease characteristics, SFTSV diversity, and the correlation between virus genome variation and clinical diseases. Our study identified at least 6 genotypes of SFTSV prevalent in Hubei Province based on the analysis of the S, M, and L genome sequences of 88 virus strains. Strikingly, the dominant genotype of SFTSV was found to change during the years, indicating a dynamic shift in viral genetic diversity in the region. Phylogenetic analysis revealed the genetic exchange of Hubei SFTSV strains was relatively frequent, including 3 reassortment strains and 8 recombination strains. Despite the limited sample size, SFTSV C1 genotype may be associated with higher mortality compared to the other four genotypes, and the serum amyloid A (SAA) level, an inflammatory biomarker, was significantly elevated in these patients. Overall, our data summarize the disease characteristics of SFTSV in Hubei Province, highlight the profound changes in viral genetic diversity, and indicate the need for in-depth monitoring and exploration of the relationship between viral mutations and disease severity.

Fig 1. Epidemiological data of SFTS cases in Hubei Province from 2018 to 2022.

(A) Confirmed cases of SFTS in Hubei Province from 2018 to 2022. (B) Month distribution of confirmed SFTS cases. (C) Ratio of nonfatal to fatal cases by age group with the case fatality rate (CFR) showed with the datapoints. Blue represented non-fatal cases and red represented fatal cases. (D) Spatial arrangement of confirmed SFTS patients (n = 202) residing in Hubei Province. The map was created in ArcGIS 10.2 software (ESRI Inc., Redlands, CA, USA) and modified using Adobe illustrator, Version CC2018 (Adobe, San Jose, CA, USA). The source of the base layer shapefile was from the open access platform: National Platform for Common Geospatial Information Services (www.tianditu.gov.cn). The black dots indicate the residential regions of confirmed SFTS patients in this study.

Fig 2. Phylogenetic relationships of the partial sequence of L, M and S segments of SFTSV strains.

The ML trees were constructed based on the partial sequence alignment of L (700bp, A), M (500bp, B), and S (770bp, C) segments. The SFTSV strains detected in this study are indicated by bold black spots. The ML trees were constructed and tested by bootstrap analysis with 1000 iterations and only bootstrap values above 70% are shown. Ten genotypes, colored in pink, purple, red, yellow, green, cyan, blue, fuchsia, gray and brown evolutionary branches were designated as genotype J1, J2, J3, J4, C1, C2, C3, C4, C5 and C6, respectively. (D) The number and proportion of different genotypes obtained from patients with SFTS in each studied year.

Fig 3. Phylogenetic analysis based on the complete ORF sequences of L, M and S gene segments of Hubei SFTSVs.

(A) Segment shift events were specially marked including S1 (HBHG2020-02), S2 (HBHG2020-08), S3 (HBHG2021-02), S4 (HBHG2022-12), S5 (HBSZ2022-11), S6 (HBHG2022-36), S7 (HBSZ2022-54) and S8 (HBHG2021-4). The bars indicate pure groups of genotypes colored with green (C1), cyan (C2), blue (C3), fuchsia (C4), gray (C5), brown (C6), pink (J1), purple (J2), red (J3), yellow (J4). The ML trees were constructed and tested by bootstrap analysis with 1000 replications, and these phylogenic trees were mid-point rooted. The scale bars (0.005) indicate the number of nucleotide substitutions per site. “*” representing that the phylogenetic branches were supported with greater than 70% bootstrap values. (B) Genotypes of Hubei SFTSVs detected in human sera and the graphic representation of reassortment events in SFTSV genome sequences obtained from patients. The SFTSVs were assigned to different genotypes based on the genetic origin of each segment as determined by phylogenic analysis. Gene segments from top to bottom are L, M, and S.

Fig 4. Fatality rates, viral loads and laboratory index of patients infected with five viral genotypes.

(A) Red columns represent dead patients and blue column represent survival patient. Datapoints show CFRs; error bars show 95% CIs; (B) Horizontal and dotted lines indicate the mean value and IQR. The statistical significance (p<0.05) of the comparison of viral load among these five genotypes used the ANOVA test. (C) Intermediate lines show mean value; error bars show standard deviation (SD). The star indicates the statistical significance (p<0.05) of the comparison of laboratory variables between the patients infected with genotype C1 and other four genotypes determined by the ANOVA test. “*” indicate 0.01<p<0.05, “**” indicate 0.001<p<0.01, “***” indicate p<0.001 (detailed in S8 and S9 Tables).