Urban structure and the risk of influenza A (H1N1) outbreaks in municipal districts

Changsha was one of the most affected areas during the 2009 A (H1N1) influenza pandemic in China. Here, we analyze the spatial–temporal dynamics of the 2009 pandemic across Changsha municipal districts, evaluate the relationship between case incidence and the local urban spatial structure and predict high-risk areas of influenza A (H1N1). We obtained epidemiological data on all cases of influenza A (H1N1) reported across municipal districts in Changsha during period May 2009–December 2010 and data on population density and basic geographic characteristics for 239 primary schools, 97 middle schools, 347 universities, 96 malls and markets, 674 business districts and 121 hospitals. Spatial–temporal K functions, proximity models and logistic regression were used to analyze the spatial distribution pattern of influenza A (H1N1) incidence and the association between influenza A (H1N1) cases and spatial risk factors and predict the infection risks. We found that the 2009 influenza A (H1N1) was driven by a transmission wave from the center of the study area to surrounding areas and reported cases increased significantly after September 2009. We also found that the distribution of influenza A (H1N1) cases was associated with population density and the presence of nearest public places, especially universities (OR = 10.166). The final predictive risk map based on the multivariate logistic analysis showed high-risk areas concentrated in the center areas of the study area associated with high population density. Our findings support the identification of spatial risk factors and high-risk areas to guide the prioritization of preventive and mitigation efforts against future influenza pandemics.     

Influenza A （HIN1） transmission by road traffic between cities and towns

Influenza A (H1N1) was spread widely between cities and towns by road traffic and had a major impact on public health in China in 2009. Understanding regulation of its transmission is of great significance with urbanization ongoing and for mitigation of damage by the epidemic. We analyzed influenza A (H1N1) spatiotemporal transmission and risk factors along roads in Changsha, and combined diffusion velocity and floating population size to construct an epidemic diffusion model to simulate its transmission between cities and towns. The results showed that areas along the highways and road intersections had a higher incidence rate than other areas. Expressways and county roads played an important role in the rapid development stage and the epidemic peak, respectively, and intercity bus stations showed a high risk of disease transmission. The model simulates the intensity and center of disease outbreaks in cities and towns, and provides a more complete simulation of the disease spatiotemporal process than other models.     

2009年成都市学校甲型H1N1流感暴发疫情流行特征与控制措施评价

目的:了解2009年成都市学校甲型H1N1流感(简称甲流)暴发疫情流行特征,掌握发病规律,评价控制措施,为今后采取更有效的防控措施提供科学依据。方法:收集整理市、区两级疾控机构处置学校甲流暴发疫情资料,对学校按大、中、小学进行分层随机抽样,并进行流行病学分析。结果:2009年成都市学校甲流暴发疫情时间主要集中在9～10月,中、小学生发病高于大学生,预防性服药(中药)和疫情早期及时停课是有效控制措施。结论:学校甲流暴发疫情控制的关键点在于根据实际情况及时、果断地采取相应防控措施。     

Molecular characterization of H1N1 influenza A viruses from human cases in North America

Subtypes of H1N1 influenza virus can be found in humans in North America, while they are also associated with the infection of swine. Characterization of the genotypes of viral strains in human populations is important to understand the source and distribution of viral strains. Genomic and protein sequences of 10 isolates of the 2009 outbreak of influenza A （H1N1） virus in North America were obtained from GenBank database. To characterize the genotypes of these viruses, phylogenetic trees of genes PB2, PB1, PA, HA, NP, NA, NS and M were constructed by Phylip3.67 program and N-Linked glycosylation sites of HA, NA, PB2, NS1 and M2 proteins were analyzed online by NetNGlyc1.0 program. Phylogenetic analysis indicated that these isolates are virtually identical but may be recombinant viruses because their genomic fragments come from different viruses. The isolates also contain a characteristic lowly pathogenic amino acid motif at their HA cleavage sites （IPSIQSR↓GL）, and an E residue at position 627 of the PB2 protein which shows its high affinity to humans. The homologous model of M proteins showed that the viruses had obtained the ability of anti-amantadine due to the mutation at the drug-sensitive site, while sequence analysis of NA proteins indicated that the viruses are still susceptible to the neuraminidase inhibitor drug （i.e. oseltamivir and zanamivir） because no mutations have been observed. Our results strongly suggested that the viruses responsible for the 2009 outbreaks of influenza A （H1N1） virus have the ability to cross species barriers to infect human and mammalian animals based on molecular analysis. These findings may further facilitate the therapy and prevention of possible transmission from North America to other countries.     

甲型H1N1流感在预防控制措施下的传播数学模型构建

从数学应用的角度,研究甲型H1N1流感的传播规律,将人群分为易感人群、病毒潜伏人群、发病人群、退出者人群四类. 分析了甲型H1N1流感在人群间的转化过程;日接触率和"聚集性突然爆发"事件被数学刻画,尝试性地构建了一个在预防控制阶段的传播数学模型.     

Epidemiological and risk analysis of the H7N9 subtype influenza outbreak in China at its early stage

Dozens of human cases infected with H7N9 subtype avian influenza virus (AIV) have been confirmed in China since March, 2013. Distribution data of sexes, ages, professions and regions of the cases were analyzed in this report. The results showed that the elderly cases, especially the male elderly, were significantly more than expected, which is different from human cases of H5N1 avian influenza and human cases of the pandemic H1N1 influenza. The outbreak was rated as a Grade Ⅲ (severe) outbreak, and it would evolve into a Grade IV (very severe) outbreak soon, using a method reported previously. The H7N9 AIV will probably circulate in humans, birds and pigs for years. Moreover, with the driving force of natural selection, the virus will probably evolve into highly pathogenic AIV in birds, and into a deadly pandemic influenza virus in humans. Therefore, the H7N9 outbreak has been assumed severe, and it is likely to become very or extremely severe in the future, highlighting the emergent need of forceful scientific measures to eliminate any infected animal flocks. We also described two possible mild scenarios of the future evolution of the outbreak.     

Spatial epidemiology of networked metapopulation: an overview

An emerging disease is one infectious epidemic caused by a newly transmissible pathogen, which has either appeared for the first time or already existed in human populations, having the capacity to increase rapidly in incidence as well as geographic range. Adapting to human immune system, emerging diseases may trigger large-scale pandemic spreading, such as the transnational spreading of SARS, the global outbreak of A（H1N1）, and the recent potential invasion of avian influenza A（H7N9）. To study the dynamics mediating the transmission of emerging dis- eases, spatial epidemiology of networked metapopulation provides a valuable modeling framework, which takes spatially distributed factors into consideration. This review elaborates the latest progresses on the spatial metapopula- tion dynamics, discusses empirical and theoretical findings that verify the validity of networked metapopulations, and the sketches application in evaluating the effectiveness of disease intervention strategies as well.     

Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia

A highly pathogenic avian influenza virus, H5N1, caused disease outbreaks in poultry in China and seven other east Asian countries between late 2003 and early 2004; the same virus was fatal to humans in Thailand and Vietnam. Here we demonstrate a series of genetic reassortment events traceable to the precursor of the H5N1 viruses that caused the initial human outbreak in Hong Kong in 1997 (refs 2-4) and subsequent avian outbreaks in 2001 and 2002 (refs 5, 6). These events gave rise to a dominant H5N1 genotype (Z) in chickens and ducks that was responsible for the regional outbreak in 2003-04. Our findings indicate that domestic ducks in southern China had a central role in the generation and maintenance of this virus, and that wild birds may have contributed to the increasingly wide spread of the virus in Asia. Our results suggest that H5N1 viruses with pandemic potential have become endemic in the region and are not easily eradicable. These developments pose a threat to public and veterinary health in the region and potentially the world, and suggest that long-term control measures are required.     

2009年加拿大H1N1疫情的ARIMA模型预测与分析

2009年初,世界各地先后发生了甲型H1N1流感.针对加拿大2009年疫情,建立了恰当的ARIMA模型,以实现每日H1N1疫情的预测.经过实证分析,预测的绝对误差在11%以内,总的平均误差是8.39%,该模型成功地对加拿大2009年疫情进行了预测.     

Subtyping of type A influenza by sequencing the variable regions of HA gene specifically amplified with RT-PCR

The outbreak of a novel influenza A （H1N1） virus across the globe poses a threat to human health. It is of paramount importance to develop a rapid, reliable and inexpensive diagnostic procedure. Based on the bioinformatic information from public database, primers specific for influenza A virus surface protein haemagglutinin （HA） of several subtypes （including H1, H2, H3, H5, H7 and H9） were designed. Primer-specific PCR products were subiected to sequencing for accurately distinguishing H1 and H3 subtypes from others. This sequencing-based detection method will not only be applied to rapid detection and simultaneous subtype identification of new influenza A virus H1N1, but also provide the strategies to monitor other new types of influenza virus with explosive potential.     

Subtyping of type A influenza by sequencing the variable regions of HA gene specifically amplified with RT-PCR

The outbreak of a novel influenza A(H1N1) virus across the globe poses a threat to human health.It is of paramount importance to develop a rapid,reliable and inexpensive diagnostic procedure.Based on the bioinformatic information from public database,primers specific for influenza A virus surface protein haemagglutinin(HA) of several subtypes(including H1,H2,H3,H5,H7 and H9) were designed.Primer-specific PCR products were subjected to sequencing for accurately distinguishing H1 and H3 subtypes from others.T...     

Genome evolution of novel influenza A （H1N1 ） viruses in humans

The epidemic situation of A H1N1 flu arose in North America in April 2009, which rapidly expanded to three continents of Europe, Asia and Africa, with the risk ranking up to 5. Until May 13th, the flu virus of A H1N1 had spread into 33 countries and regions, with a laboratory confirmed case number of 5728, including 61 deaths. Based on IRV and EpiFluDB database, 425 parts of A H1N1 flu virus sequence were achieved, followed by sequenced comparison and evolution analysis. The results showed that the current predominant A H1N1 flu virus was a kind of triple reassortment A flu virus： （i） HA, NA, MP, NP and NS originated from swine influenza virus; PB2 and PA originated from bird influenza virus; PB1 originated from human influenza virus. （ii） The origin of swine influenza virus could be subdivided as follows： HA, NP and NS originated from classic swine influenza virus of H1N1 subtype; NA and MP originated from bird origin swine influenza virus of H1N1 subtype. （iii） A H1N1 flu virus experienced no significant mutation during the epidemic spread, accompanied with no reassortment of the virus genome. In the paper, the region of the representative strains for sequence analysis （A/California/04/2009 （H1N1） and A/Mexico/4486/2009 （H1N1）） included USA and Mexico and was relatively wide, which suggested that the analysis results were convincing.     

2009年北京市甲型H1N1流行的气象因子与时空传播风险

 2009年8月初,甲型H1N1逐步在北京市本地人群中大范围传播扩散。实验室检测表明,甲型H1N1阳性病例占流感样病例的比例（从0.0086到0.7035）呈逐步上升趋势。本研究利用相关性统计分析方法,探索了2009年8月3日—11月8日甲型H1N1阳性率和4个气象因子（气温、相对湿度、降水量、风速）之间的关联关系。结果表明,甲型H1N1阳性率与气温的相关系数为-0.9458（P<0.05）,甲型H1N1阳性率与相对湿度的相关系数为-0.4581（P<0.1）,干冷环境下的甲型H1N1阳性率显著偏高。本研究构建了利用气温和相关湿度估算甲型H1N1阳性率的逻辑斯谛模型,反演得到了北京市每个区县每天的甲型H1N1阳性率,分析了北京市甲型H1N1流行的时空传播风险。     

Special features of the 2009 pandemic swine-origin influenza A H1N1 hemagglutinin and neuraminidase

Since the 2009 pandemic H1N1 swine-origin influenza A virus (09 S-OIV) has reminded the world about the global threat of the ever changing influenza virus,many questions regarding the detailed re-assortment of influenza viruses yet remain unanswered.Influenza A virus is the causative agent of the pandemic flu and contains 2 major antigenic glycoproteins on its surface:(i) hemagglutinin (HA);and (ii) neuraminidase (NA).The structures of the 09 S-OIV HA and NA proteins (09H1 and 09N1) have recently been resolved in our laboratory and provide some clues as to why the 09 S-OIV re-assortment virus is highly infectious with severe consequences in humans.For example,the 09H1 is highly similar to the HA of the 1918 influenza A pandemic virus in overall structure and especially in regards to its 5 defined antibody binding epitopes.For 09N1,its most distinctive feature is the lack of a 150-loop active site cavity,which was previously predicted to be present in all N1 NAs,and we hypothesize that the 150-loop may play a important role in the substrate specificity (α2,3 or α2,6 linked sialic acid receptors) and enzymatic mechanism of influenza NA.Combination of the HA and NA with special characteristics for the 09 S-OIV might contribute to its high increased transmissibility in humans.     

Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets

Highly pathogenic avian H5N1 influenza A viruses occasionally infect humans, but currently do not transmit efficiently among humans. The viral haemagglutinin (HA) protein is a known host-range determinant as it mediates virus binding to host-specific cellular receptors. Here we assess the molecular changes in HA that would allow a virus possessing subtype H5 HA to be transmissible among mammals. We identified a reassortant H5 HA/H1N1 virus-comprising H5 HA (from an H5N1 virus) with four mutations and the remaining seven gene segments from a 2009 pandemic H1N1 virus-that was capable of droplet transmission in a ferret model. The transmissible H5 reassortant virus preferentially recognized human-type receptors, replicated efficiently in ferrets, caused lung lesions and weight loss, but was not highly pathogenic and did not cause mortality. These results indicate that H5 HA can convert to an HA that supports efficient viral transmission in mammals; however, we do not know whether the four mutations in the H5 HA identified here would render a wholly avian H5N1 virus transmissible. The genetic origin of the remaining seven viral gene segments may also critically contribute to transmissibility in mammals. Nevertheless, as H5N1 viruses continue to evolve and infect humans, receptor-binding variants of H5N1 viruses with pandemic potential, including avian-human reassortant viruses as tested here, may emerge. Our findings emphasize the need to prepare for potential pandemics caused by influenza viruses possessing H5 HA, and will help individuals conducting surveillance in regions with circulating H5N1 viruses to recognize key residues that predict the pandemic potential of isolates, which will inform the development, production and distribution of effective countermeasures.     

板蓝根粗提液抑制流感病毒的实验研究

对板蓝根凝聚粗提液的抗流感病毒作用进行了研究。用丙酮脱脂提取板蓝根生药的凝集素，并分别测定各样品的血凝活性，并用45.3mg/mL的样品对流感病毒（A1／京防／97－53H1N1，A1／京防／262／95）进行了体外抑制试验。结果表明：板蓝根凝集素对流感病毒具有显著的直接杀灭作用和预防作用及较好的治疗作用，而且得出抑制流感病毒的效果与板蓝根凝集素血凝活性的高低有关。     

禽流感与防疫

禽流感是一种由A型流感病毒的一种亚型(也称禽流感病毒)引起的禽类(家禽和野禽)和人的传染性疾病,被国际兽疫局定为甲类传染病,了解和认识禽流感的流行与病毒特点、传播途径、主要症状、扑灭措施及疫苗预防,对于控制和防止禽流感的发生,以及为人类健康都有着重大意义。     

动物源性流感病毒与人流感流行

2009年4月.北美地区发生了人感染H1N1"猪流感"疫情,并且疫情呈现暴发漫延的态势.全世界关注的目光继1997年H5N1禽流感病毒感染人事件首次在中国香港发生,以及2003年以来包括15个国家和地区多起H5N1禽流感病毒感染人事件之后,再次聚焦到动物源性流感病毒上.是否动物流感病毒已经具备了引起人类疫情暴发的能力?是否新的一场大的人流感疫情就要暴发?为什么世界卫生组织又于4月30日为本次"猪流感"更名为"甲型H1N1流感"?对于流感暴发脚步的逼近我们是否做好了准备?本文对历史上人流感疫情暴发情况,动物流感病毒感染人事件的发生情况和流行病学特点,以及人流感疫情发生与动物流感病毒之间的关系等进行了总结与分析,以期更好地了解流感病毒在不同宿主之间的传播,为更加从容地面对这场突如其来的疫情,以及为疫情的预防和控制提供理论指导.为了能够准确反映这次流感的情况和国际对流感及流感病毒的统一命名法则,以及更加清晰并易于理解地表述清楚.我们建议将这次流感称作"北美流感"或"墨西哥流感".     

X-ray structure of NS1 from a highly pathogenic H5N1 influenza virus

The recent emergence of highly pathogenic avian (H5N1) influenza viruses, their epizootic and panzootic nature, and their association with lethal human infections have raised significant global health concerns. Several studies have underlined the importance of non-structural protein NS1 in the increased pathogenicity and virulence of these strains. NS1, which consists of two domains-a double-stranded RNA (dsRNA) binding domain and the effector domain, separated through a linker-is an antagonist of antiviral type-I interferon response in the host. Here we report the X-ray structure of the full-length NS1 from an H5N1 strain (A/Vietnam/1203/2004) that was associated with 60% of human deaths in an outbreak in Vietnam. Compared to the individually determined structures of the RNA binding domain and the effector domain from non-H5N1 strains, the RNA binding domain within H5N1 NS1 exhibits modest structural changes, while the H5N1 effector domain shows significant alteration, particularly in the dimeric interface. Although both domains in the full-length NS1 individually participate in dimeric interactions, an unexpected finding is that these interactions result in the formation of a chain of NS1 molecules instead of distinct dimeric units. Three such chains in the crystal interact with one another extensively to form a tubular organization of similar dimensions to that observed in the cryo-electron microscopy images of NS1 in the presence of dsRNA. The tubular oligomeric organization of NS1, in which residues implicated in dsRNA binding face a 20-A-wide central tunnel, provides a plausible mechanism for how NS1 sequesters varying lengths of dsRNA, to counter cellular antiviral dsRNA response pathways, while simultaneously interacting with other cellular ligands during an infection.     

无血清微载体培养MDCK细胞和甲型流感病毒H1N1的条件优化

 血清微载体培养MDCK细胞,并接种流感病毒H1N1,优化培养条件,为细胞流感疫苗的工艺研发奠定基础.采用不同的细胞接种量在50mL无血清微载体搅拌瓶中培养MDCK细胞,并接种甲型流感病毒H1N1,检测不同pH值和TPCK-胰酶含量的病毒培养液,不同病毒接种量,补加TPCK-胰酶,以及不同收毒时间对血凝效价的影响.以1.0×10⁵mL^-1的MDCK细胞数量接种到无血清微载体上,病毒培养液pH值为7.2~7.4范围内,TPCK-胰酶质量浓度为1.0μg/mL,接种后不补加胰酶,病毒接种量MOI=1.0,并在72h收获,最高血凝效价达到512.由此获得了在无血清为载体上培养MDCK细胞和甲型流感病毒H1N1的适宜条件.