Search

Background: Japanese encephalitis virus (JEV; Flaviridae: Flavivirus) causes Japanese encephalitis (JE), which is the most important arboviral disease in Asia and the western Pacific. Among the five JEV genotypes (GI–IV), GI has dominated traditional epidemic regions in the past 20 years. We investigated the transmission dynamics of JEV GI through genetic analyses. Methods: We generated 18 JEV GI near full length sequences by using multiple sequencing approaches from mosquitoes collected in natural settings or from viral isolates obtained through cell culture. We performed phylogenetic and molecular clock analyses to reconstruct the evolutionary history by integrating our data with 113 publicly available JEV GI sequences. Results: We identified two subtypes of JEV GI (GIa and GIb), with a rate of 5.94 × 10−4 substitutions per site per year (s/s/y). At present, GIa still circulates within a limited region, exhibited no significant growth, the newest strain was discovered in China (Yunnan) in 2017, whereas most JEV strains circulating belong to the GIb clade. During the past 30 years, two large GIb clades have triggered epidemics in eastern Asia: one epidemic occurred in 1992 [95% highest posterior density (HPD) = 1989–1995] and the causative strain circulates mainly in southern China (Yunnan, Shanghai, Guangdong, and Taiwan) (Clade 1); the other epidemic occurred in 1997 (95% HPD = 1994–1999) and the causative strain has increased in circulation in northern and southern China during the past 5 years (Clade 2). An emerging variant of Clade 2 contains two new amino acid markers (NS2a-151V, NS4-169K) that emerged around 2005; this variant has demonstrated exponential growth in northern China. Conclusion: JEV GI stain circulating in Asia have shifted during the past 30 years, spatiotemporal differences were observed among JEV GI subclade. GIa is still circulating within a limited range, exhibite no significant growth. Two large GIb clades have triggered epidemics in eastern Asia, all JEV sequences identified in northern China during the past 5 years were of the new emerging variant of G1b-clade 2. Author summary: Although Japanese encephalitis virus (JEV) genotype I (GI) has circulated in Asia and the western Pacific during the past 30 years, little is known regarding its evolution, geographical distribution, and epidemiology, especially the recent years. To address this knowledge gap, we performed a phylogenetic analysis using all full open reading frame JEV sequences assembled thus far, including 113 viral sequences sampled from eight countries during the past 42 years. We revealed spatiotemporal differences in spread among JEV GI subclades; identified amino acid markers for different clades; made an in-depth study on the evolution of GIb, described the geographical distribution of the recent active GIb clade 2 and identified its emerging variant. [ABSTRACT FROM AUTHOR]

The Tibetan Plateau is the source of most of Asia's major rivers and has been called the Asian Water Tower. Detailed knowledge of its hydrogeology is paramount to enable the understanding of groundwater dynamics, which plays a vital role in headwater areas like the Tibetan Plateau. Nevertheless, due to its remoteness and the harsh environment, there is a lack of field survey data to investigate its hydrogeology. In this study, borehole core lithology analysis, soil thickness measurement, an altitude survey, hydrogeological surveys, and hydrogeophysical surveys (e.g. magnetic resonance sounding – MRS, electrical resistivity tomography – ERT, and transient electromagnetic – TEM) were conducted in the Maqu catchment within the Yellow River source region (YRSR). The hydrogeological surveys reveal that groundwater flows from the west to the east, recharging the Yellow River. The hydraulic conductivity ranges from 0.2 to 12.4 m d -1. The MRS sounding results, i.e. water content and hydraulic conductivity, confirmed the presence of an unconfined aquifer in the flat eastern area. Based on TEM results, the depth of the Yellow River deposits was derived at several places in the flat eastern area, ranging from 50 to 208 m. The soil thickness measurements were done in the western mountainous area of the catchment, where hydrogeophysical and hydrogeological surveys were difficult to be carried out. The results indicate that most soil thicknesses, except on the valley floor, are within 1.2 m in the western mountainous area of the catchment, and the soil thickness decreases as the slope increases. These survey data and results can contribute to integrated hydrological modelling and water cycle analysis to improve a full-picture understanding of the water cycle at the Maqu catchment in the YRSR. The raw dataset is freely available at https://doi.org/10.17026/dans-z6t-zpn7 (Li et al., 2020a), and the dataset containing the processed ERT, MRS, and TEM data is also available at the National Tibetan Plateau Data Center with the link https://doi.org/10.11888/Hydro.tpdc.271221 (Li et al., 2020b). [ABSTRACT FROM AUTHOR]

Although Japanese encephalitis virus genotype Ib (JEV GIb) has replaced JEV GIII as the dominant genotype in endemic areas of Asia, no JEV GIb has been isolated from JE cases and natural mosquitoes at the same time in an outbreak of JE. In this study, we conducted virological and molecular biological laboratory tests on JE case samples (serum/cerebrospinal fluid) and locally collected mosquito samples from the 2018 JE outbreak in Ningxia, China. The result of JEV IgM antibody detection showed that 96% (67/70) of the suspected cases were laboratory-confirmed JE cases. Of the mosquitoes collected from local environments, 70% (17400/24900) were Culex tritaeniorhynchus of which 4.6% (16 /348 of the pools tested) were positive for JEV, other mosquitoes were negative. JEVs isolated from both the human cases and C. tritaeniorhynchus specimens belong to JEV GIb and are in the same evolutionary clade according to molecular evolution analyses. JEV GIb was detected simultaneously from specimens of JE cases and mosquito samples collected in nature in this study, suggesting that the JE outbreak that occurred in Ningxia in 2018 was due to infection of JEV GIb. Author summary: Japanese encephalitis virus (JEV) is recognized as an important encephalitis pathogen all over the world. Its genotype is divided into GI-V. In recent years, JEV GIb (a temperate genotype) has gradually replaced GIII as the prevalent strain in JE endemic areas. Although JEV GIb originated from tropical Asia along with JEV GIa, it has rapidly spread for its advantages in wintering and infecting vectors. Although there have been epidemics caused by JEV GI and GIII, there have been no reports of a JE outbreak caused by JEV GIb alone in northeastern Asia. However, a JE outbreak occurred in the Ningxia Hui Autonomous Region in northern China in summer 2018 which was the first outbreak in Ningxia in recent decades. This paper presents a series of laboratory and field studies of this outbreak. The strain isolated from JE cases as well as JEV detected in Culex tritaeniorhynchus collected from local areas in nature all belonged to JEV GIb and were in the same evolutionary clade. This is the first report of a JE outbreak caused by JEV GIb infection in northeastern Asia (latitude 35 ° 14'– 39 ° 23' N, longitude 104 ° 17'– 107 ° 39' E), which used to be a low endemic area of JEV GIII. [ABSTRACT FROM AUTHOR]

Tick-borne encephalitis virus (TBEV) is an emerging pathogen in Europe and North Asia that causes tick-borne encephalitis (TBE). A simple, rapid method for detecting TBEV RNA is needed to control this disease. A reverse-transcription recombinase-aided amplification (RT-RAA) assay was developed. This assay can be completed in one closed tube at 39 °C within 30 minutes. The sensitivity and specificity of RT-RAA were validated using non-infectious synthetic RNA representing a fragment of the NS5 region of the wild-type (WT) TBEV genome and the Senzhang strain. Additionally, 10 batches of tick samples were used to evaluate the performance of the RT-RAA assay. The analytical limit of detection of the assay was 20 copies per reaction of the TBEV synthetic transcript and 3 plaque-forming units (pfu) per reaction of TBEV titers. With the specific assay, no signal due to other arboviruses was observed. Of the 10 batches of tick samples obtained from the Changbai Mountains of China, three were TBEV-positive, which was consistent with the results of the quantitative real-time PCR assay. A rapid, highly sensitive, specific, and easy-to-use method was developed for the detection of the TBEV Far-Eastern subtype. [ABSTRACT FROM AUTHOR]

Japanese encephalitis (JE) is a mosquito-borne disease caused by the Japanese encephalitis virus (JEV). The disease is mainly an epidemic in Asia and has been studied for nearly 90 years. To evaluate the research trends of JE, 3,023 English publications between 1934 and 2020 were retrieved and analyzed from the Web of Science database using indicators for publication, country or territory, citation, journal, author and affiliation, keyword co-occurrence cluster, and strongest citation bursts detection. The results of the bibliometric analysis and the visualization tools show that the number of annual publications on JE has been increasing. JE has been continuously studied in the USA and also many Asian countries, such as Japan, China, India, and South Korea; however, only a few publications have high citations. The main research groups of JE in the last 5 years were in China, Japan, and the UK. The keyword co-occurrence analysis and the strongest citation bursts detection revealed that most studies focused on the pathogenic mechanism of JEV, control of outbreaks, and immunization with JE vaccine. The research maps on JE obtained by our analysis are expected to help researchers effectively explore the disease., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Xu, Zhang, Pan, Wang, Yin, Fu, Li, He, Xu, Wang, Liang, Nie and Wang.)

Zika virus (ZIKV) has been isolated from mosquitoes such as Aedes, Mansonia uniformis, and Culex perfuscus; However, the isolation of ZIKV from Anopheles sinensis and Culex tritaeniorhynchus has not yet been reported. In June and July 2018, 22,985 mosquitoes and 57,500 midges were collected in Jiangxi Province in southeastern China. Among them, six strains of ZIKV were isolated from mosquitoes: four from An. sinensis and two from Cx. tritaeniorhynchus. Molecular genetic analysis showed that the ZIKV isolated from An. sinensis and Cx. tritaeniorhynchus belonged to genotype 2 in the Asian evolutionary branch of ZIKV. In addition, the ZIKV strains isolated from An. sinensis and Cx. tritaeniorhynchus had amino acid substitutions identical to ZIKV strains prevalent in South America since 2015. This study is the first to isolate ZIKV from mosquito specimens collected in the wild of Jiangxi Province, China; This is also the first time that ZIKV has been isolated from An. sinensis and Cx. tritaeniorhynchus. Given that An. sinensis and Cx. tritaeniorhynchus have a very wide geographical distribution in China and even in eastern and southern Asia, the isolation of several strains of ZIKV from these two mosquitoes poses new challenges for the prevention and control of ZIKV infection in the mainland of China and countries and regions with the same distribution of mosquitoes.