Chenglong Xiong

Evolutionary Characteristics of A/Hangzhou/1/2013 and Source of Avian Influenza Virus H7N9 Subtype in China

A patient with an influenza-like illness was first admitted to a hospital in Shanghai on 19 February 2013, and another similar case appeared 8 days later. Both patients died after approximately 2 weeks. The National Health and Family Planning Commission of China officially affirmed the pathogen being a new avian influenza virus (AIV) H7N9 subtype. Up to 20 April, 87 cases in humans were confirmed, 17 of whom died [1]. This study investigated the source of the virus and evolution. We first conducted a homology analysis using MegAlign module of Lasergene7.0 software on an AIV isolate A/ Hangzhou/1/2013 (GenBank accession number KC853766) and found that its hemagglutinin (HA) gene was highly homologous to a strain A/duck/Zhejiang/12/ 2011 (H7N3) (accession number JQ906576) isolated in Hangzhou city (95.8% and 97.9% for nucleotide and derived amino acid sequences), which is likely the provider of HA gene of the H7N9 subtype. The neuraminidase (NA) gene of the AIV isolate A/Hangzhou/1/2013 (GenBank accession number KC853765) was highly homologous with the isolate A/mallard/ Czech Republic/13 438–29K/2010 (H11N9)

Dynamics of spatial clustering of schistosomiasis in the Yangtze River Valley at the end of and following the World Bank Loan Project

The 10-year (1992-2001) World Bank Loan Project (WBLP) contributed greatly to schistosomiasis control in China. However, the re-emergence of schistosomiasis in recent years challenged the long-term progress of the WBLP strategy. In order to gain insight in the long-term progress of the WBLP, the spatial pattern of the epidemic was investigated in the Yangtze River Valley between 1999-2001 and 2007-2008. Two spatial cluster methods were jointly used to identify spatial clusters of cases. The magnitude and number of clusters varied during 1999-2001. It was found that prevalence of schistosomiasis had been greatly reduced and maintained at a low level during 2007-2008, with little change. Besides, spatial clusters most frequently occurred within 16 counties in the Dongting Lake region and within 5 counties in the Poyang Lake region. These findings precisely pointed out the prior places for future public health planning and resource allocation of schistosomiasis.

The complexity of human infected AIV H5N6 isolated from China

BackgroundNovel avian influenza viruses (AIVs) of H7N9, H10N8, and H5N6 are currently circulating in China’s poultry flocks, occasionally infecting human and other mammals. Human infected AIV H5N6 in China during 2014–2015 is believed to be a triple reassortant originated from H6N6 and two clades of H5 viruses. The current report suggests that its reassortment history is more complicated.MethodsGenomes of human infected isolates of AIV H5N6 were searched from the NCBI Influenza Virus Sequence Database and the Global Initiative on Sharing Avian Influenza Data. Sequences shared high identities with each segment of their genomes were obtained through the Basic Local Alignment Search Tool. Alignments were done by mafft-7.037-win32 program; 8 large-scale and then 8 gradually converged phylogenetic trees were constructed by using MEGA5.1/5.2/6.0 Software.ResultsThe events that each segment of the genomes of human infected AIV H5N6 isolates circulated in China had evolved into its current status might have happened before 2013, and so were they then reassorted into the epidemic AIV H5N6. A/Guangzhou/39715/2014(H5N6) and A/Sichuan/26221/2014(H5N6) had their six internal segments (PB2, PB1, PA, NP, NEP, and M) in common, and were reassorted from AIVs H5N1 in the same period and same region as that of HA, while A/Yunnan/0127/2015(H5N6) derived its six internal segments from AIV H9N2 that has been prevalent in Eastern China since 2008.ConclusionsAIV H5N6 isolates established from both human and poultry in China during 2014–2015 were heterogeneous; both AIVs H5N1 and H9N2 were involved in the reassortment of AIV H5N6 in China.

Monitoring schistosomiasis risk in East China over space and time using a Bayesian hierarchical modeling approach

Schistosomiasis remains a major public health problem and causes substantial economic impact in east China, particularly along the Yangtze River Basin. Disease forecasting and surveillance can assist in the development and implementation of more effective intervention measures to control disease. In this study, we applied a Bayesian hierarchical spatio-temporal model to describe trends in schistosomiasis risk in Anhui Province, China, using annual parasitological and environmental data for the period 1997–2010. A computationally efficient approach–Integrated Nested Laplace Approximation–was used for model inference. A zero-inflated, negative binomial model best described the spatio-temporal dynamics of schistosomiasis risk. It predicted that the disease risk would generally be low and stable except for some specific, local areas during the period 2011–2014. High-risk counties were identified in the forecasting maps: three in which the risk remained high, and two in which risk would become high. The results indicated that schistosomiasis risk has been reduced to consistently low levels throughout much of this region of China; however, some counties were identified in which progress in schistosomiasis control was less than satisfactory. Whilst maintaining overall control, specific interventions in the future should focus on these refractive counties as part of a strategy to eliminate schistosomiasis from this region.

Effects of oral florfenicol and azithromycin on gut microbiota and adipogenesis in mice

Certain antibiotics detected in urine are associated with childhood obesity. In the current experimental study, we investigated two representative antibiotics detected in urine, florfenicol and azithromycin, for their early effects on adipogenesis, gut microbiota, short-chain fatty acids (SCFAs), and bile acids in mice. Thirty C57BL/6 mice aged four weeks were randomly divided into three groups (florfenicol, azithromycin and control). The two experimental groups were administered florfenicol or azithromycin at 5 mg/kg/day for four weeks. Body weight was measured weekly. The composition of the gut microbiota, body fat, SCFAs, and bile acids in colon contents were measured at the end of the experiment. The composition of the gut microbiota was determined by sequencing the bacterial 16S rRNA gene. The concentration of SCFAs and bile acids was determined using gas chromatography and liquid chromatography coupled to tandem mass spectrometry, respectively. The composition of the gut microbiota indicated that the two antibiotics altered the gut microbiota composition and decreased its richness and diversity. At the phylum level, the ratio of Firmicutes/Bacteroidetes increased significantly in the antibiotic groups. At the genus level, there were declines in Christensenella, Gordonibacter and Anaerotruncus in the florfenicol group, in Lactobacillus in the azithromycin group, and in Alistipes, Desulfovibrio, Parasutterella and Rikenella in both the antibiotic groups. The decrease in Rikenella in the azithromycin group was particularly noticeable. The concentration of SCFAs and secondary bile acids decreased in the colon, but the concentration of primary bile acids increased. These findings indicated that florfenicol and azithromycin increased adipogenesis and altered gut microbiota composition, SCFA production, and bile acid metabolism, suggesting that exposure to antibiotics might be one risk factor for childhood obesity. More studies are needed to investigate the specific mechanisms.

Sandwich mapping of schistosomiasis risk in Anhui Province, China

Schistosomiasis mapping using data obtained from parasitological surveys is frequently used in planning and evaluation of disease control strategies. The available geostatistical approaches are, however, subject to the assumption of stationarity, a stochastic process whose joint probability distribution does not change when shifted in time. As this is impractical for large areas, we introduce here the sandwich method, the basic idea of which is to divide the study area (with its attributes) into homogeneous subareas and estimate the values for the reporting units using spatial stratified sampling. The sandwich method was applied to map the county-level prevalence of schistosomiasis japonica in Anhui Province, China based on parasitological data collected from sample villages and land use data. We first mapped the county-level prevalence using the sandwich method, then compared our findings with block Kriging. The sandwich estimates ranged from 0.17 to 0.21% with a lower level of uncertainty, while the Kriging estimates varied from 0 to 0.97% with a higher level of uncertainty, indicating that the former is more smoothed and stable compared to latter. Aside from various forms of reporting units, the sandwich method has the particular merit of simple model assumption coupled with full utilization of sample data. It performs well when a disease presents stratified heterogeneity over space.

Global spatial risk pattern of highly pathogenic avian influenza H5N1 virus in wild birds: A knowledge-fusion based approach

Highly pathogenic avian influenza (HPAI) H5N1 viruses have continuously circulated throughout much of the world since 2003, resulting in huge economic losses and major public health problems. Wild birds have played an important role in the spread of H5N1 HPAI. To understand its spatial distribution, H5N1 HPAI have been studied by many disciplines from different perspectives, but only one kind of disciplinary knowledge was involved, which has provided limited progress in understanding. Combining risk information from different disciplines based on knowledge fusion can provide more accurate and detailed information. In this study, local k function, phylogenetic tree analysis, and logistic spatial autoregressive models were used to explore the global spatial pattern of H5N1 HPAI based on outbreak data in wild birds, genetic sequences, and risk factors, respectively. On this basis, Dempster-Shafer (D-S) evidence theory was further applied to study the spatial distribution of H5N1 HPAI. We found D-S evidence theory was more robust and reliable than the other three methods, providing technical and methodological support for application to the research of other diseases. The shortest distance to wild bird migration routes, roads and railways, elevation, the normalized difference vegetation index (NDVI), land use and land cover (LULC) and infant mortality rates (IMR) were significantly associated with the occurrence of H5N1 HPAI. The high-risk areas were mainly located in Northern and Central Europe, the eastern Mediterranean, and East and Southeast Asia. High-risk clusters were closely related to the social, economic and ecological environment of the region. Locations where the potential transmission risk remains high should be prioritized for control efforts.

Avian influenza viruses (AIVs) H9N2 are in the course of reassorting into novel AIVs

中文概要目的分析H9N2 禽流感病毒通过基因重配形成H7N9 和H10N8 人间禽流感病毒的进程,探讨作为供体 的禽流感病毒H9N2 在当前中国的主要分布及其 内部6 个基因节段的进化关系。创新点人间禽流感病毒H7N9 和H10N8 共起源于H9N2 禽流感病毒早已成为共识,但共起源的时间节 点、作为供体的禽流感病毒H9N2 在当前中国的 分布及其内部6 个基因节段的进化关系鲜有论 及。2014 年,H5N6 禽流感被多次报道造成人类 感染。研究表明,H5N6 禽流感具有复杂的重配 来源,H9N2 正是其一,加之H7N9 第五波流行 的严峻形势,亟需明确H9N2 禽流感病毒通过基 因重配形成新亚型的能力以及它在我国的当前 主要分布。方法从流感病毒公共数据库下载基因序列,评估查找 适当的碱基替代模型,通过进化树查看与H7N9、 H10N8 及H5N6 具有高度相似性的H9N2 病毒的 分布地区以及它们在内部6 个基因节段上的进化 关系,同时通过碱基替代速率的计算追溯最近共 同祖先(tMRCA)及其分歧时间。结论人间禽流感病毒H7N9 与H10N8 均在2012 年之 前形成,短期内通过碱基替代与基因重配形成了 两种可感染人类的禽流感病毒,证实了H9N2 通 过重配形成新亚型的高效性。作为重配供体的 H9N2 至今仍广布于华东、华南及东南亚。其内 部基因节段的重配复杂,发生在亚型内部的重配 以及通过重配形成新的病毒亚型的风险都很高, 需在禽畜中加强流感病毒的流行动态监测,特别 是那些一向被忽视的编码内部蛋白的基因组节 段。

Human infections and co-infections with helminths in a rural population in Guichi, Anhui Province, China.

Helminth infections are believed to be common in tropical and subtropical countries. A cross-sectional study was carried out in two villages located in Guichi District in Anhui Province, the Peoples Republic of China, where multiparasitism was investigated using parasitological tests. The data collected were fitted to Bayesian multi-level models to profile risk factors for helminth infections. The prevalence of Schistosoma (S.) japonicum, Ascaris (A.) lumbricoides and Trichuris (T.) trichiura were 0.43% (range: 0-0.87% at the village level), 2.28% (range: 1.69-2.88%), and 0.21% (range: 0-0.42%), respectively. No hookworm infection was found. With regard to multiparasitism, only a 33-year-old female was found to be co-infected with S. japonicum and A. lumbricoides. Multiparasitism was unexpectedly rare in the study area, which contrasts with results from other studies carried out elsewhere in the country. The long-term usage of albendazole for individuals serologically positive for schistosomiasis may be the main reason, but this needs to be confirmed by future studies.

Notorious Novel Avian Influenza Viruses H10N8 and H7N9 in China in 2013 Co-originated from H9N2

In 2013, two new avian influenza viruses (AIVs) H7N9 and H10N8 emerged in China caused worldwide concerns. Previous studies have studied their originations independently; this study is the first time to investigate their co-originating characteristics. Gene segments of assorted subtype influenza A viruses, as well as H10N8 and H7N9, were collected from public database. 26 With the help of series software, small and large-scale phylogenetic trees, mean evolutionary rates, and divergence years were obtained successionally. The results demonstrated the two AIVs co-originated from H9N2, and shared a spectrum of mutations in common on many key sites related to pathogenic, tropism and epidemiological characteristics. For a long time, H9N2 viruses had been circulated in eastern and southern China; poultry was the stable and lasting maintenance reservoir. High carrying rate of AIVs H9N2 in poultry had an extremely high risk of co-infections with other influenza viruses, which increased the risk of virus reassortment. It implied that novel AIVs reassortants based on H9N2 might appear and prevail at any time in China; therefore, surveillance of H9N2 AIVs should be given a high priority.