Molecular Evolution and Spatial Transmission of Severe Fever with Thrombocytopenia Syndrome Virus Based on Complete Genome Sequences

Ecological Changes Exacerbating the Spread of Invasive Ticks has Driven the Dispersal of Severe Fever with Thrombocytopenia Syndrome Virus Throughout Southeast Asia

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne virus recognized by the World Health Organization as an emerging infectious disease of growing concern. Utilizing phylodynamic and phylogeographic methods, we have reconstructed the origin and transmission patterns of SFTSV lineages and the roles demographic, ecological, and climatic factors have played in shaping its emergence and spread throughout Asia. Environmental changes and fluctuations in tick populations, exacerbated by the widespread use of pesticides, have contributed significantly to its geographic expansion. The increased adaptability of Lineage L2 strains to the Haemaphysalis longicornis vector has facilitated the dispersal of SFTSV through Southeast Asia. Increased surveillance and proactive measures are needed to prevent further spread to Australia, Indonesia, and North America.

Molecular surveillance of zoonotic pathogens from wild rodents in the Republic of Korea

BACKGROUND

Rodents are recognized as major reservoirs of numerous zoonotic pathogens and are involved in the transmission and maintenance of infectious diseases. Furthermore, despite their importance, diseases transmitted by rodents have been neglected. To date, there have been limited epidemiological studies on rodents, and information regarding their involvement in infectious diseases in the Republic of Korea (ROK) is still scarce.

METHODOLOGY/PRINCIPAL FINDINGS

We investigated rodent-borne pathogens using nested PCR/RT-PCR from 156 rodents including 151 Apodemus agrarius and 5 Rattus norvegicus from 27 regions in eight provinces across the ROK between March 2019 and November 2020. Spleen, kidney, and blood samples were used to detect Anaplasma phagocytophilum, Bartonella spp., Borrelia burgdorferi sensu lato group, Coxiella burnetii, Leptospira interrogans, and severe fever with thrombocytopenia syndrome virus (SFTSV). Of the 156 rodents, 73 (46.8%) were infected with Bartonella spp., 25 (16.0%) with C. burnetii, 24 (15.4%) with L. interrogans, 21 (13.5%) with A. phagocytophilum, 9 (5.8%) with SFTSV, and 5 (3.2%) with Borrelia afzelii. Co-infections with two and three pathogens were detected in 33 (21.1%) and 11 rodents (7.1%), respectively. A. phagocytophilum was detected in all regions, showing a widespread occurrence in the ROK. The infection rates of Bartonella spp. were 83.3% for B. grahamii and 16.7% for B. taylorii.

CONCLUSIONS/SIGNIFICANCE

To the best of our knowledge, this is the first report of C. burnetii and SFTSV infections in rodents in the ROK. This study also provides the first description of various rodent-borne pathogens through an extensive epidemiological survey in the ROK. These results suggest that rodents harbor various pathogens that pose a potential threat to public health in the ROK. Our findings provide useful information on the occurrence and distribution of zoonotic pathogens disseminated among rodents and emphasize the urgent need for rapid diagnosis, prevention, and control strategies for these zoonotic diseases.

Current Progress of Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) Vaccine Development

SFTSV is an emerging tick-borne virus causing hemorrhagic fever with a case fatality rate (CFR) that can reach up to 27%. With endemic infection in East Asia and the recent spread of the vector tick to more than 20 states in the United States, the SFTSV outbreak is a globally growing public health concern. However, there is currently no targeted antiviral therapy or licensed vaccine against SFTSV. Considering the age-dependent SFTS pathogenesis and disease outcome, a sophisticated vaccine development approach is required to safeguard the elderly population from lethal SFTSV infection. Given the recent emergence of SFTSV, the establishment of animal models to study immunogenicity and protection from SFTS symptoms has only occurred recently. The latest research efforts have applied diverse vaccine development approaches-including live-attenuated vaccine, DNA vaccine, whole inactivated virus vaccine, viral vector vaccine, protein subunit vaccine, and mRNA vaccine-in the quest to develop a safe and effective vaccine against SFTSV. This review aims to outline the current progress in SFTSV vaccine development and suggest future directions to enhance the safety and efficacy of these vaccines, ensuring their suitability for clinical application.

Emerging tickborne viruses vectored by Amblyomma americanum (Ixodida: Ixodidae): Heartland and Bourbon viruses

Heartland (HRTV) and Bourbon (BRBV) viruses are newly identified tick-borne viruses, isolated from serious clinical cases in 2009 and 2014, respectively. Both viruses originated in the lower Midwest United States near the border of Missouri and Kansas, cause similar disease manifestations, and are presumably vectored by the same tick species, Amblyomma americanum Linnaeus (Ixodida: Ixodidae). In this article, we provide a current review of HRTV and BRBV, including the virology, epidemiology, and ecology of the viruses with an emphasis on the tick vector. We touch on current challenges of vector control and surveillance, and we discuss future directions in the study of these emergent pathogens.

Emerging Tick-Borne Dabie bandavirus: Virology, Epidemiology, and Prevention

Severe Fever with Thrombocytopenia Syndrome (SFTS), caused by Dabie bandavirus (SFTSV), is an emerging infectious disease first identified in China. Since its discovery, infections have spread throughout East Asian countries primarily through tick bites but also via transmission between animals and humans. The expanding range of ticks, the primary vectors for SFTSV, combined with migration patterns of tick-carrying birds, sets the stage for the global spread of this virus. SFTSV rapidly evolves due to continuous mutation and reassortment; currently, no approved vaccines or antiviral drugs are available. Thus, the threat this virus poses to global health is unmistakable. This review consolidates the most recent research on SFTSV, including its molecular characteristics, transmission pathways through ticks and other animals, as well as the progress in antiviral drug and vaccine development, encompassing animal models and clinical trials.

Genome-informed investigation of the molecular evolution and genetic reassortment of severe fever with thrombocytopenia syndrome virus

BACKGROUND

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a viral pathogen causing significant clinical signs from mild fever with thrombocytopenia to severe hemorrhages. World Health Organization has paid special attention to the dramatic increase in human SFTS cases in China, Japan, and South Korea since the 2010s. The present study investigated the molecular evolution and genetic reassortment of SFTSVs using complete genomic sequences.

METHODS/PRINCIPAL FINDING

We collected the complete genome sequences of SFTSVs globally isolated until 2019 (L segment, n = 307; M segment, n = 326; and S segment, n = 564) and evaluated the evolutionary profiles of SFTSVs based on phylogenetic and molecular selection pressure analyses. By employing a time-scaled Bayesian inference method, we found the geographical heterogeneity of dominant SFTSV genotypes in China, Japan, and South Korea around several centuries before and locally spread by tick-born spillover with infrequent long-distance transmission. Purifying selection predominated the molecular evolution of SFTSVs with limited gene reassortment and fixed substitution, but almost all three gene segments appeared to harbor at least one amino acid residue under positive selection. Specifically, the nonstructural protein and glycoprotein (Gn/Gc) genes were preferential selective targets, and the Gn region retained the highest number of positively selected residues.

CONCLUSION/SIGNIFICANCE

Here, the large-scale genomic analyses of SFTSVs improved prior knowledge of how this virus emerged and evolved in China, Japan, and South Korea. Our results highlight the importance of SFTSV surveillance in both human and non-human reservoirs at the molecular level to fight against fatal human infection with the virus.

Genomic diversity and evolution analysis of severe fever with thrombocytopenia syndrome in East Asia from 2010 to 2022

Background

Conducting an up-to-date analysis on the genomic diversity and evolution patterns of severe fever with thrombocytopenia syndrome virus (SFTSV) is crucial for elucidating the underlying mechanisms of its emergency and pathogenicity, as well as assessing the extent of its threat to public health.

Methods

Complete genome sequences of SFTSV were obtained from GenBank until December 19, 2022. A thorough phylogenetic analysis was conducted using comprehensive bioinformatics methods to estimate the genomic diversity and evolution.

Results

The phylogenetic classification of SFTSV strains yielded seven lineages (A-G) for each genome segment. SFTSV displayed notable variations in evolutionary patterns among different regions and segments, without a linear accumulation of nucleotide substitutions within segments and regions. The comprehensive analysis revealed 54 recombination events and 17 reassortment strains, including the first discovery of recombination events involving sea-crossing and species-crossing. Selection analysis identified three positive sites (2, 671, 1353) in RNA-dependent RNA polymerase, three positive sites (22, 298, 404) in glycoprotein, and two positive sites (9, 289) in nonstructural protein. No positive selection sites were found in nucleoprotein.

Conclusion

Our study unveiled the existence of multiple evolutionary forces influencing SFTSV, contributing to its increasing genetic diversity, which had the potential to modify its antigenicity and pathogenicity. Furthermore, our study highlights the importance of tracking the spread of SFTSV across regions and species.

Advancements in the Worldwide Detection of Severe Fever with Thrombocytopenia Syndrome Virus Infection from 2009 to 2023

Severe fever with thrombocytopenia syndrome (SFTS) is a growing concern as an emerging tick-borne infectious disease originating from the SFTS virus (SFTSV), a recent addition to the Phlebovirus genus under the family of bunyaviruses. SFTS is typically identified by symptoms such as fever, thrombocytopenia, leukopenia, and gastrointestinal problems, accompanied by a potentially high case fatality rate. Thus, early and accurate diagnosis is essential for effective treatment and disease management. This review delves into the existing methodologies for SFTS detection, including pathogenic, molecular, and immunological technologies.

Genetic variants of Dabie bandavirus: classification and biological/clinical implications

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by Dabie bandavirus (DBV), a novel Bandavirus in the family Phenuiviridae. The first case of SFTS was reported in China, followed by cases in Japan, South Korea, Taiwan and Vietnam. With clinical manifestations including fever, leukopenia, thrombocytopenia, and gastrointestinal symptoms, SFTS has a fatality rate of approximately 10%. In recent years, an increasing number of viral strains have been isolated and sequenced, and several research groups have attempted to classify the different genotypes of DBV. Additionally, accumulating evidence indicates certain correlations between the genetic makeup and biological/clinical manifestations of the virus. Here, we attempted to evaluate the genetic classification of different groups, align the genotypic nomenclature in different studies, summarize the distribution of different genotypes, and review the biological and clinical implications of DBV genetic variations.

In silico study on miRNA regulation and NSs protein interactome characterization of the SFTS virus

Severe fever with thrombocytopenia syndrome causing virus i.e. SFTS virus has increased in the last few years. The underlying cause and mechanism of disease progression and development of symptoms is not well known. Many viruses including Hepatitis B, Hepatitis C, HIV-1, Herpes virus, Dengue virus and many others have been seen to regulate their functions at the miRNA level. This study aimed to find out those cellular miRNAs, which can be mimicked or antagonized by the viral genome and analyze the effect of these miRNAs on various gene functions. Investigations in this study suggest a correlation between miRNA regulation with the disease symptoms and progression. By exhaustive literature survey we have tried to identify the interacting partners of the Non Structural S (NSs) protein and characterized the protein-protein interactions. The binding interface that can serve as target for therapeutic studies involving the interfacial residues was analyzed. This study would serve as an avenue to design therapeutics making use of not only protein-protein interactions but also miRNA based regulation as well.

[The molecular evolution of Dabie bandavirus (Phenuiviridae: Bandavirus: Dabie bandavirus), the agent of severe fever with thrombocytopenia syndrome]

Since the Dabie bandavirus (DBV; former SFTS virus, SFTSV) was identified, the epidemics of severe fever with thrombocytopenic syndrome (SFTS) caused by this virus have occurred in several countries in East Asia. The rapid increase in incidence indicates that this infectious agent has a pandemic potential and poses an imminent global public health threat.The analysis of molecular evolution of SFTS agent that includes its variants isolated in China, Japan and South Korea was performed in this review. The evolution rate of DBV and the estimated dates of existence of the common ancestor were ascertained, and the possibility of reassortation was demonstrated.The evolutionary rates of DBV genome segments were estimated to be 2.28 × 10-4 nucleotides/site/year for S-segment, 2.42 × 10-4 for M-segment, and 1.19 × 10-4 for L-segment. The positions of positive selection were detected in the viral genome.Phylogenetic analyses showed that virus may be divided into two clades, containing six different genotypes. The structures of phylogenetic trees for S-, M- and L-segments showed that all genotypes originate from the common ancestor.Data of sequence analysis suggest that DBV use several mechanisms to maintain the high level of its genetic diversity. Understanding the phylogenetic factors that determine the virus transmission is important for assessing the epidemiological characteristics of the disease and predicting its possible outbreaks.

Severe fever with thrombocytopenia syndrome virus: emerging novel phlebovirus and their control strategy

An emerging infectious disease first identified in central China in 2009, severe fever with thrombocytopenia syndrome (SFTS) was found to be caused by a novel phlebovirus. Since SFTSV was first identified, epidemics have occurred in several East Asian countries. With the escalating incidence of SFTS and the rapid, worldwide spread of SFTSV vector, it is clear this virus has pandemic potential and presents an impending global public health threat. In this review, we concisely summarize the latest findings regarding SFTSV, including vector and virus transmission, genotype diversity and epidemiology, probable pathogenic mechanism, and clinical presentation of human SFTS. Ticks most likely transmit SFTSV to animals including humans; however, human-to-human transmission has been reported. The majority of arbovirus transmission cycle includes vertebrate hosts, and potential reservoirs include a variety of both domestic and wild animals. Reports of the seroprevalence of SFTSV in both wild and domestic animals raises the probability that domestic animals act as amplifying hosts for the virus. Major clinical manifestation of human SFTS infection is high fever, thrombocytopenia, leukocytopenia, gastrointestinal symptoms, and a high case-fatality rate. Several animal models were developed to further understand the pathogenesis of the virus and aid in the discovery of therapeutics and preventive measures.

Two Different Strains of Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in North and South Osaka by Phylogenetic Analysis of Evolutionary Lineage: Evidence for Independent SFTSV Transmission

Severe fever with thrombocytopenia syndrome (SFTS) is a novel tick-borne infectious disease, therefore, the information on the whole genome of the SFTS virus (SFTSV) is still limited. This study demonstrates a nearly whole genome of the SFTSV identified in Osaka in 2017 and 2018 by next-generation sequencing (NGS). The evolutionary lineage of two genotypes, C5 and J1, was identified in Osaka. The first case in Osaka belongs to suspect reassortment (L:C5, M:C5, S:C4), the other is genotype J1 (L: J1, M: J1, S: J1) according to the classification by a Japanese group. C5 was identified in China, indicating that C5 identified in this study may be transmitted by birds between China and Japan. This study revealed that different SFTSV genotypes were distributed in two local areas, suggesting the separate or focal transmission patterns in Osaka.

Baseline mapping of severe fever with thrombocytopenia syndrome virology, epidemiology and vaccine research and development

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a newly emergent tick-borne bunyavirus first discovered in 2009 in China. SFTSV is a growing public health problem that may become more prominent owing to multiple competent tick-vectors and the expansion of human populations in areas where the vectors are found. Although tick-vectors of SFTSV are found in a wide geographic area, SFTS cases have only been reported from China, South Korea, Vietnam, and Japan. Patients with SFTS often present with high fever, leukopenia, and thrombocytopenia, and in some cases, symptoms can progress to severe outcomes, including hemorrhagic disease. Reported SFTSV case fatality rates range from ~5 to >30% depending on the region surveyed, with more severe disease reported in older individuals. Currently, treatment options for this viral infection remain mostly supportive as there are no licensed vaccines available and research is in the discovery stage. Animal models for SFTSV appear to recapitulate many facets of human disease, although none of the models mirror all clinical manifestations. There are insufficient data available on basic immunologic responses, the immune correlate(s) of protection, and the determinants of severe disease by SFTSV and related viruses. Many aspects of SFTSV virology and epidemiology are not fully understood, including a detailed understanding of the annual numbers of cases and the vertebrate host of the virus, so additional research on this disease is essential towards the development of vaccines and therapeutics.

Genetic diversity and evolutionary history of Korean isolates of severe fever with thrombocytopenia syndrome virus from 2013-2016

Severe fever with thrombocytopenia syndrome (SFTS) is caused by SFTS virus (SFTSV). Although SFTS originated in China, it is an emerging infectious disease with prevalence confirmed in Japan, Korea, and Vietnam. The full-length genomes of 51 Korean SFTSV isolates from 2013 to 2016 were sequenced, and the sequences were deposited into a public database (GenBank) and analyzed to elucidate the phylogeny and evolution of the virus. Although most of the Korean SFTSV isolates were closely related to previously reported Japanese isolates, some were closely related to previously reported Chinese isolates. We identified one Korean strain that appears to have resulted from multiple inter-lineage reassortments. Several nucleotide and amino acid variations specific to the Korean isolates were identified. Future studies should focus on how these variations affect virus pathogenicity and evolution.

Genetic and pathogenic diversity of severe fever with thrombocytopenia syndrome virus (SFTSV) in South Korea

To investigate nationwide severe fever with thrombocytopenia syndrome virus (SFTSV) infection status, we isolated SFTSVs from patients with suspected severe fever with thrombocytopenia syndrome (SFTS) in 207 hospitals throughout South Korea between 2013 and April 2017. A total of 116 SFTSVs were isolated from 3137 SFTS-suspected patients, with an overall 21.6% case fatality rate. Genetic characterization revealed that at least 6 genotypes of SFTSVs were co-circulating in South Korea, with multiple reassortments among them. Of these, the genotype B-2 strains were the most prevalent, followed by the A and F genotypes. Clinical and epidemiologic investigations revealed that genotype B strains were associated with the highest case fatality rate, while genotype A caused only one fatality among 10 patients. Further, ferret infection studies demonstrated varying clinical manifestations and case mortality rates with different strains of SFTSV, which suggests this virus could exhibit genotype-dependent pathogenicity.

Seroprevalance of antibodies specific for severe fever with thrombocytopenia syndrome virus and the discovery of asymptomatic infections in Henan Province, China

Background

Severe fever with thrombocytopenia syndrome (SFTS) is a severe emerging disease caused by SFTS virus (SFTSV), and the geographical distribution of SFTS has been increasing throughout China in recent years. To assess SFTSV-specific antibody seroprevalence, a cross-sectional study was conducted for healthy people in high SFTS endemic areas of Henan province in 2016.

Methods

This study used a stratified random sampling method to select 14 natural villages as the investigation sites. From April to May 2016, participants completed a questionnaire survey and serum samples were collected. All serum samples were subjected to ELISA to detect SFTSV-specific IgM and IgG. All IgM-positive samples were further tested by real-time RT-PCR, and isolation of virus from serum was attempted. Any participant who was IgM-positive was followed up with a month later to confirm health status.

Results

In total, 1463 healthy people participated in this study. The average seropositive rates for SFTSV-specific IgG and IgM were 10.46% (153/1463) and 0.82% (12/1463), respectively. IgM was detected in 12 individuals, and SFTSV RNA was detected in six of them. Virus was isolated from five of the six SFTSV RNA-positive individuals, and phylogenetic analyses revealed that all five isolates belonged to SFTSV group A. No IgM-positive participants exhibited any symptoms or other signs of illness at the one-month follow up.

Conclusions

This study identified a relatively high incidence of SFTSV-specific antibody seropositivity in healthy people in Xinyang city. Moreover, our data provide the first evidence for asymptomatic SFTSV infections, which may have significant implications for SFTS outbreak control.

Severe fever with thrombocytopenia syndrome (SFTS) is a severe emerging infectious disease caused by SFTS virus (SFTSV) that was first discovered in rural areas of China. Henan province has had the largest number of SFTS cases in China every year since the disease was discovered, however, seropositivity for SFTSV-specific antibodies in healthy people in this region is still not clear. To address this issue, a cross-sectional survey was performed in high endemic areas from April to May 2016. The results showed that SFTSV seroprevalence was relatively high and possibly increasing. Notably, SFTSV RNA, as well as virus itself, was isolated from specimens obtained from healthy people. This study confirmed there are asymptomatic SFTSV infections in humans, and it is the first to report SFTSV isolation from healthy people.

Patient with severe fever with thrombocytopenia syndrome virus infection and central nervous system disturbance in Dongyang, Zhejiang Province, China, 2017

Background

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging hemorrhagic fever that was first described in China in 2011. We report a patient who died of Severe fever with thrombocytopenia syndrome virus (SFTSV) infection, with a rapidly progressive central nervous system (CNS) disturbance, in Dongyang, Zhejiang Province, China, in 2017.

Case presentation

A 64-year-old man was admitted to hospital after 4 days of fever. SFTSV was detected 1 day after the patient was admitted to hospital. The patient presented with CNS disturbance and died 4 days after admission. Detailed clinical and epidemiological investigations and laboratory tests were conducted. Reduced platelet, white blood cell, lymphocyte, and neutrophil counts, elevated lactate dehydrogenase, creatine kinase, aspartate aminotransferaseand alanine aminotransferase concentrations, and an increased activated partial thromboplastin time were observed. In a phylogenetic analysis, the isolate clustered close to a strain derived from South Korea.

Conclusions: This is the first case of SFTSV infection with CNS disturbance in Dongyang, Zhejiang Province, China. The surveillance of suspected cases of SFTS is important in SFTSV endemic regions.

Susceptibility of spotted doves (Streptopelia chinensis) to experimental infection with the severe fever with thrombocytopenia syndrome phlebovirus

Background

Severe fever with thrombocytopenia syndrome virus (SFTSV), an emerging human pathogen naturally transmitted by ticks, has spread widely since it was first detected in 2010. Although SFTSV-specific antibodies have been detected in wild birds, these natural reservoir and amplifying hosts for the virus have not been well studied.

Methodology/Principle findings

Here we report an experimental infection of spotted doves (Streptopelia chinensis) with two strains of SFTSV, JS2010-14, a Chinese lineage strain, and JS2014-16, a Japanese lineage strain, which represent the main viral genotypes currently circulating in East Asia. In these studies, we have determined that spotted doves are susceptible to SFTSV and the severity of the viremia is dose-dependent. When challenged with 10⁷ and 10⁵ PFU, all doves developed viremia which peaked 3–5 days post infection (dpi). Only a subset (25–62.5%) of the birds developed viremia when challenged at 10³ PFU. Virulence of SFTSV in spotted doves was strain dependent. Infection with 10⁷ PFU of strain JS2014-16 resulted in 12.5% mortality over 6.8 days and mean peak viremia titers of 10^6.9 PFU/mL in experimentally inoculated birds. All doves inoculated with 10⁷ PFU of the JS2010-14 strain survived infection with relatively lower mean viremia titers (10^5.6 PFU/mL at peak) over 6.1 days.

Conclusions/Significance

Our results suggest that spotted doves, one of the most abundant bird species in China, could be a competent amplifying host for SFTSV and play an important role in its ecology. Between the two SFTSV strains, the strain of the Japanese lineage caused mortality, higher viremia titers in infected birds over a longer time period than did the Chinese strain. Our observations shed light on the ecology of SFTSV, which could benefit the implementation of surveillance and control programs.

Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging human pathogen naturally transmitted by ticks. Our recent study has showed that some species of migratory birds, such as swan geese and spotted doves, can be parasitized by Haemaphysalis longicornis, an SFTSV vector, and antibodies against the SFTSV detected in these species. These data demonstrate that migratory birds are infected with SFTSV and may also play a role in the infection of ticks with SFTSV. Other studies have reported that migratory bird routes and the distribution of H. longicornis in East Asia overlap with the geographic distribution of SFTSV. Migratory birds are known to be carriers and transmitters of infectious agents, like the causative agents of influenza, West Nile encephalitis, and Lyme disease. Wild birds often travel long distances carrying various parasites, including ticks, which may be infected with viruses and bacteria. It is therefore reasonable to hypothesize that migratory birds may have played an important role in spreading SFTSV in two potential transmission scenarios: 1) birds are infected with the virus and transmit it back to ticks endemically or in a distal region, or 2) they are carriers of parasitic ticks that are infected with the virus. Here we report an experimental infection of spotted doves (Streptopelia chinensis) with two strains of SFTSV, JS2010-14 from a Chinese lineage and JS2014-16 from a Japanese lineage, which represent the main viral genotypes currently circulating in East Asia. We determined that spotted doves are susceptible to SFTSV and that the severity of the viremia was dose and strain dependent. Infection with the strain of JS2014-16 led to a death rate of 12.5% and higher viremia titers in experimentally inoculated birds while doves inoculated with the JS2010-14 strain survived infection with relatively lower virus titers in the blood. These findings provide novel insights for understanding the rapid spread of the virus in a short time span, in particular the SFTSV strains from the Japanese lineage (genotype E).

Seroprevalence of Severe Fever with Thrombocytopenia Syndrome Phlebovirus in Domesticated Deer in South Korea

Severe fever with thrombocytopenia syndrome phlebovirus (SFTSV) has a wide host range. Not only has it been found in humans, but also in many wild and domesticated animals. The infection of breeding deer on farms is a particularly worrisome public health concern due to the large amount of human contact and the diverse use of deer products, including raw blood. To investigate the prevalence of breeding domesticated deer, we examined the SFTSV infection rate on deer farms in South Korea from 2015 to 2017. Of the 215 collected blood samples, 0.9% (2/215) were found to be positive for viral RNA by PCR, and sequence analysis showed the highest homology with the KADGH human isolate. Both SFTSV-specific recombinant N and Gn protein-based ELISAs revealed that 14.0% (30/215) and 7.9% (17/215) of collected blood specimens were positive for SFTSV antibody. These results demonstrate that the breeding farm deer are exposed to SFTSV and could be a potential infection source for humans through direct contact or consumption of byproducts.

Laboratory detection and molecular phylogenetic analysis of severe fever with thrombocytopenia syndrome virus in Hubei Province, central China

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by the SFTS virus (SFTSV). Hubei Province is a major epidemic area for SFTS in China. In this study, quantitative reverse-transcription polymerase chain reaction (qRT-PCR) and serological testing (IgM) were used simultaneously for laboratory detection of SFTS; however, testing results showed poor consistency between these two methods. Further analysis revealed that time post-onset was the main factor leading to inconsistent results. Thus, qRT-PCR is unable to detect all SFTS cases, and serological testing is essential. Here, 15 strains of SFTSV were successfully isolated from serum samples of acute SFTSV infection and their complete genomes were sequenced and submitted to GenBank. Phylogenetic analysis showed that the 15 SFTS virus strains clustered into four independent genotypes (A, B, D, and E), demonstrating that at least four genotypes of SFTSV have been co-circulating in Hubei Province. Furthermore, four strains of our isolates (HB2014-31, HB2014-35, HB2014-36, and HB2014-37) clustered in genotype E, which was the predominant genotype in Japan and South Korea. In this study, we identified multiple co-prevalent genotypes and confirmed the existence of genotype E viruses circulating in the Dabie Mountains of Hubei, central China. We concluded that SFTSV strains from Hubei exhibit most of the genetic diversity found in China.

Reassortment events in the evolution of hantaviruses

Hantaviruses (order Bunyavirales, family Hantaviridae), known as important zoonotic human pathogens, possess the capacity to exchange genome segments via genetic reassortment due to their tri-segmented genome. Although not as frequent as in the arthropod-borne bunyaviruses, reports indicating reassortment events in the evolution of hantaviruses have been recently accumulating. The intra- and inter-lineage reassortment between closely related variants has been repeatedly reported for several hantaviruses including the rodent-borne human pathogens such as Sin Nombre virus, Puumala virus, Dobrava-Belgrade virus, or Hantaan virus as well as for the more recently recognized shrew-borne hantaviruses, Imjin and Seewis. Reassortment between more distantly related viruses was rarely found but seems to play a beneficial role in the process of crossing the host species barriers. Besides the findings based on phylogenetic studies of naturally occurring strains, hantavirus reassortants were generated also in in vitro studies. Interestingly, only reassortants with exchanged M segments could be generated suggesting that a high degree of genetic compatibility is required for the S and L segments while the exchange of M segment is better tolerated or is particularly beneficial. Altogether, the numerous reports on hantavirus reassortment, summarized in this review, clearly demonstrate that reassortment events play a significant role in hantavirus evolution and contributed to the currently recognized hantavirus diversity.

Epidemiological and clinical features of laboratory-diagnosed severe fever with thrombocytopenia syndrome in China, 2011-17: a prospective observational study

BACKGROUND

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease with an increasing case number and extensive geographical expansion, raising concerns locally and globally; however, the description of its clinical features needs to be addressed by large studies. We aimed to determine all the clinical features of SFTS in a large population of patients in an endemic area.

METHODS

In this prospective observational study, data were collected on patients admitted to the People's Liberation Army Hospital in Xinyang, Henan Province, China, with laboratory-diagnosed SFTS. Demographic, clinical, laboratory, and treatment data were collected for each patient, and patients were followed up within 2 weeks after discharge or discontinuation of treatment. The association between each demographic, clinical, and laboratory variable with a fatal outcome was assessed. A clinical scoring model was designed for the early prediction of a fatal outcome, and the effect of treatment on outcome was analysed.

FINDINGS

Between April 1, 2011, and Oct 31, 2017, 2096 patients with laboratory-confirmed SFTS were admitted. Mean age at admission was 61·4 years (SD 12·2) and 1239 (59%) patients were female. The case fatality rate (CFR) was 16·2% (95% CI 14·6-17·8). A higher risk was associated with being male (unadjusted odds ratio [OR] 1·45, 95% CI 1·15-1·83; p=0·002), older age (for a 10-year increase, unadjusted OR 1·82, 95% CI 1·62-2·04; p<0·0001), longer delay in admission (for every extra day taken before admission to hospital, unadjusted OR 1·18, 1·12-1·24; p<0·0001), presence of diarrhoea (adjusted OR 1·44, 1·12-1·87; p=0·005) or dyspnoea (adjusted OR 8·35, 5·97-11·69; p<0·0001), and development of haemorrhagic signs (adjusted OR 2·79, 95% CI 2·18-3·57; p<0·0001) or neurological symptoms (adjusted OR 30·26, 21·39-42·81; p<0·0001). Laboratory variables that were associated with death included abnormal concentrations of lactate dehydrogenase, aspartate aminotransferase, and blood urea nitrogen, and abnormal neutrophil percentage, which together with age and neurological symptoms were combined in the clinical scoring system. A total score of more than 8 was the optimal threshold to predict risk of death for patients who were evaluated within 6 days after symptom onset (area under the curve 0·879, 95% CI 0·855-0·902). For all participants, viraemia was a strong predictor of fatal outcome (all p<0·0001). Ribavirin therapy was effective in reducing CFR from 6·25% (15 of 240 participants) to 1·16% (two of 173 participants), but only in patients with a viral load below 1×10⁶ copies per mL (hazard ratio 9·72, 95% CI 1·30-72·87; p=0·027).

INTERPRETATION

The changing epidemiological features and high CFR of SFTS underscore the necessity of continued surveillance. Early prediction of fatal outcome can be attained by monitoring of clinical and laboratory data. Ribavirin should be applied early, with best results achieved before the viral load reaches 1 × 10⁶ copies per mL.

FUNDING

National Natural Science Foundation of China.

Current status of Severe Fever with Thrombocytopenia Syndrome vaccine development

Severe Fever with Thrombocytopenia Syndrome (SFTS) is a new emerging tick-borne disease caused by the phlebovirus, SFTS virus (SFTSV). The virus was discovered in central China in 2009 and has since been identified in both Japan and South Korea. Significant progress has been made on the molecular biology of the virus, and this has been used to develop diagnostic assays and reagents. Less progress has been made on the epidemiology, maintenance and transmission, clinical manifestations, immunological responses, and treatment regimens. A number of animal models have been investigated but, to date, none recapitulate all the clinical manifestations seen in humans. Vaccine development is at an early discovery phase.

Replication capacity and adaptability of a severe fever with thrombocytopenia syndrome virus at different temperatures

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging disease caused by the SFTS virus (SFTSV). Although fever and thrombocytopenia are the typical manifestations of SFTS, a specific SFTS case with no fever was observed in Zhejiang, China. In this report, we aimed to explore the probable reason for the absence of fever by analyzing the genetic characteristics and temperature sensitivity (ts) of the SFTSV strain ZJ2013-06, which was isolated from the specific case. Phylogenetically, different clusters of SFTSV strains circulated in Zhejiang. ZJ2013-06 was farthest from ZJ2014-02, an isolate belonging to a Chinese dominant cluster, and nearest to the coastal strain NB24/CHN/2013. Ts tests, performed on Vero cells at 37°C and 39°C, indicated that ZJ2013-06 had restricted replication at 39°C. Its viral loads were substantially reduced at 39°C compared with that at 37°C (approximately 100-fold reduction) and were significantly lower than that of ZJ2014-02 at 39°C (P < 0.01). By adaptive culture at 39°C, the induced strain ZJ2013-06-P7 was obtained. Owing to a reverse mutation (S1616), ZJ2013-06-P7 lost the ts of the original strain, displaying similar replication processes with NB24/CHN/2013. The results indicated that the amino acid residue 1616 was related to the ts characteristics of ZJ2013-06. Our study revealed that ZJ2013-06 was temperature-sensitive and may be related to the absence of fever in our case.

Molecular genomic characterization of tick- and human-derived severe fever with thrombocytopenia syndrome virus isolates from South Korea

BACKGROUND

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne viral disease caused by the SFTS virus (SFTSV) from Bunyaviridae that is endemic in East Asia. However, the genetic and evolutionary characteristics shared between tick- and human-derived Korean SFTSV strains are still limited.

METHODOLOGY/PRINCIPAL FINDINGS

In this study we identify, for the first time, the genome sequence of a tick (Haemaphysalis longicornis)-derived Korean SFTSV strain (designated as KAGWT) and compare this virus with recent human SFTSV isolates to identify the genetic variations and relationships among SFTSV strains. The genome of the KAGWT strain is consistent with the described genome of other members of the genus Phlebovirus with 6,368 nucleotides (nt), 3,378 nt, and 1,746 nt in the Large (L), Medium (M) and Small (S) segments, respectively. Compared with other completely sequenced human-derived Korean SFTSV strains, the KAGWT strain had highest sequence identities at the nucleotide and deduced amino acid level in each segment with the KAGWH3 strain which was isolated from SFTS patient within the same region, although there is one unique amino acid substitution in the Gn protein (A66S). Phylogenetic analyses of complete genome sequences revealed that at least four different genotypes of SFTSV are co-circulating in South Korea, and that the tick- and human-derived Korean SFTSV strains (genotype B) are closely related to one another. Although we could not detect reassortant, which are commonly observed in segmented viruses, further large-scale surveillance and detailed genomic analysis studies are needed to better understand the molecular epidemiology, genetic diversity, and evolution of SFTSV.

CONCLUSIONS/SIGNIFICANCE

Full-length sequence analysis revealed a clear association between the genetic origins of tick- and human-derived SFTSV strains. While the most prevalent Korean SFTSV is genotype B, at least four different genotypes of SFTSV strains are co-circulating in South Korea. These findings provide information regarding the molecular epidemiology, genetic diversity, and evolution of SFTSV in East Asia.

Increased Prevalence of Severe Fever with Thrombocytopenia Syndrome in Eastern China Clustered with Multiple Genotypes and Reasserted Virus during 2010-2015

Severe fever with thrombocytopenia syndrome (SFTS) is a novel tick-borne viral disease with high mortality. Since January 2010, we have conducted an epidemiological surveillance and etiological study of SFTS in Jiangsu and Anhui provinces. From January 2010 through December 2015, a total of 286 SFTS cases were confirmed in Jiangsu and Anhui provinces with a case fatality rate of 16.1%. The majority of confirmed SFTS cases were distributed in the border area of Jiangsu and Anhui provinces. Our findings suggest that the SFTS prevalence rate rose since 2010 and reached its highest in 2015. Phylogenetic analysis demonstrated that the majority of the SFTSV strains (83.6%) from Jiangsu and Anhui provinces belonged to genotypes A and D. Notably, we identified three strains of SFTSV clustered into the genotype E. This is the first report of the genotype E SFTSV strains in mainland of China. A reassortment between genotype A and D was found in the central region of the endemic areas, where three SFTSV genotypes (A, C and D) were co-circulating.

Current status of severe fever with thrombocytopenia syndrome in China

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by SFTS virus (SFTSV). SFTSV is associated with a high mortality rate and has been reported in China, South Korea and Japan. SFTSV undergoes rapid changes owing to evolution, gene mutations, and reassortment between different strains of SFTSV. In this review, we summarize the recent cases and general properties of SFTS, focusing on the epidemiology, genetic diversity, clinical features, and diagnostics of SFTSV in China. From 2010 to October 2016, SFTS cases were reported in 23 provinces of China, with increased numbers yearly. Infection and death cases are mainly found in central China, where the Haemaphysalis longicornis ticks are spread. The national average mortality rate of SFTS infection was 5.3%, with higher risk to elder people. The main epidemic period was from May to July, with a peak in May. Thus, SFTS reminds a significant public health problem, and development of prophylactic vaccines and effective antiviral drugs will be highly needed.

Novel sub-lineages, recombinants and reassortants of severe fever with thrombocytopenia syndrome virus

Severe fever with thrombocytopenia syndrome virus (SFTSV) has been continuously circulating in Eastern Asia in recent years, without the availability of effective vaccines or antiviral drugs, posing a serious threat to public health, particularly in the central-eastern provinces of China. In this study, we isolated and sequenced four new SFTSV strains from Shandong Province identified in 2015. Phylogenetic analysis, with all publicly available L, M and S gene segments, revealed that the four newly described SFTSV strains belonged to genotype C3. In addition, our phylogenetic analyses also identified two potentially novel sub-lineages of SFTSV, tentatively named C6 and J4. Our comprehensive analysis revealed twenty recombination events in fourteen SFTSV genomes and recombination events were found in the S gene segment for the first time. A total of twenty-six strains were probable SFTSV reassortants, including sixteen which were previously unidentified. We further characterised the genetic constellation of these putative reassortants and classified them into twelve different reassortment forms. Our study revealed multiple evolutionary forces acting on SFTSV, responsible for the increasing genetic diversity of this agent, which could potentially alter the antigenicity and pathogenicity of the virus. This calls for an urgent need for intensified surveillance and the development of vaccines and antiviral drugs against this high-consequence pathogen.