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1.
    
Influenza A viruses are one of the most significant viral groups globally with substantial impacts on human, domestic animal and wildlife health. Wild birds are the natural reservoirs for these viruses, and active surveillance within wild bird populations provides critical information about viral evolution forming the basis of risk assessments and countermeasure development. Unfortunately, active surveillance programs are often resource‐intensive, and thus, enhancing programs for increased efficiency is paramount. Machine learning, a branch of artificial intelligence applications, provides statistical learning procedures that can be used to gain novel insights into disease surveillance systems. We use a form of machine learning, gradient boosted trees, to estimate the probability of isolating avian influenza viruses (AIV) from wild bird samples collected during surveillance for AIVs from 2006 to 2011 in the United States. We examined several predictive features including age, sex, bird type, geographic location and matrix gene rRT‐PCR results. Our final model had high predictive power and only included geographic location and rRT‐PCR results as important predictors. The highest predicted viral isolation probability was for samples collected from the north‐central states and the south‐eastern region of Alaska. Lower rRT‐PCR Ct‐values are associated with increased likelihood of AIV isolation, and the model estimated 16% probability of isolating AIV from samples declared negative (i.e., ≥35 Ct‐value) using the rRT‐PCR screening test and standard protocols. Our model can be used to prioritize previously collected samples for isolation and rapidly evaluate AIV surveillance designs to maximize the probability of viral isolation given limited resources and laboratory capacity.  相似文献   

2.
    
Influenza A virus in swine is of significant importance to human and veterinary public health. Environmental sampling techniques that prove practical would enhance surveillance for influenza viruses in swine. The primary objective of this study was to demonstrate the feasibility of bioaerosol and surface sampling for the detection of influenza virus in swine barns with a secondary objective of piloting a mobile application for data collection. Sampling was conducted at a large swine operation between July 2016 and August 2017. Swine oral fluids and surface swabs were collected from multiple rooms. Room‐level air samples were collected using four bioaerosol samplers: a low volume polytetrafluoroethylene (PTFE) filter sampler, the National Institute for Occupational Safety and Health's low volume cyclone sampler, a 2‐stage Andersen impactor and/or one high volume cyclonic sampler. Samples were analysed using quantitative RT‐PCR. Data and results were reported using a mobile data application. Eighty‐nine composite oral fluid samples, 70 surface swabs and 122 bioaerosol samples were analysed. Detection rates for influenza virus RNA in swine barn samples were 71.1% for oral fluids, 70.8% for surface swabs and 71.1% for the PTFE sampler. Analysis revealed a statistically significant relationship between the results of the PTFE sampler and the surface swabs with oral fluid results (p < 0.001 and p < 0.01 respectively). In addition, both the PTFE sampler (p < 0.01) and surface swabs (p = 0.03) significantly correlated with, and predicted oral fluid results. Bioaerosol sampling using PTFE samplers is an effective hands‐off approach for detecting influenza virus activity among swine. Further study is required for the implementation of this approach for surveillance and risk assessment of circulating influenza viruses of swine origin. In addition, mobile data collection stands to be an invaluable tool in the field by allowing secure, real‐time reporting of sample collection and results.  相似文献   

3.
    
The transportation of poultry and related products for international trade contributes to transboundary pathogen spread and disease outbreaks worldwide. To prevent pathogen incursion through poultry products, many countries have regulations about animal health and poultry product quarantine. However, in Japan, animal products have been illegally introduced into the country in baggage and confiscated at the airport. Lately, the number of illegally imported poultry and the incursion risk of transboundary pathogens through poultry products have been increasing. In this study, we isolated avian influenza viruses (AIV s) from raw poultry products illegally imported to Japan by international passengers. Highly (H5N1 and H5N6) and low (H9N2 and H1N2) pathogenic AIV s were isolated from raw chicken and duck products carried by flight passengers. H5 and H9 isolates were phylogenetically closely related to viruses isolated from poultry in China, and haemagglutinin genes of H5N1 and H5N6 isolates belonged to clades 2.3.2.1c and 2.3.4.4, respectively. Experimental infections of H5 and H9 isolates in chickens and ducks demonstrated pathogenicity and tissue tropism to skeletal muscles. To prevent virus incursion by poultry products, it is important to encourage the phased cleaning based on the disease control and eradication and promote the reduction in contamination risk in animal products.  相似文献   

4.
    
Three subtypes—H1N1, H1N2 and H3N2—of influenza A viruses of swine (IAV s‐S) are currently endemic in swine worldwide, but there is considerable genotypic diversity among each subtype and limited geographical distribution. Through IAV s‐S monitoring in Vietnam, two H1N2 influenza A viruses were isolated from healthy pigs in Ba Ria‐Vung Tau Province, Southern Vietnam, on 2 December 2016. BLAST and phylogenetic analyses revealed that their HA and NA genes were derived from those of European avian‐like H1N2 IAV s‐S that contained avian‐origin H1 and human‐like N2 genes, and were particularly closely related to those of IAV s‐S circulating in the Netherlands, Germany or Denmark. In addition, the internal genes of these Vietnamese isolates were derived from human A(H1N1)pdm09 viruses, suggesting that the Vietnamese H1N2 IAV s‐S are reassortants between European H1N2 IAV s‐S and human A(H1N1)pdm09v. The appearance of European avian‐like H1N2 IAV s‐S in Vietnam marks their first transmission outside Europe. Our results and statistical analyses of the number of live pigs imported into Vietnam suggest that the European avian‐like H1N2 IAV s‐S may have been introduced into Vietnam with their hosts through international trade. These findings highlight the importance of quarantining imported pigs to impede the introduction of new IAV s‐S.  相似文献   

5.
    
Increased surveillance of influenza A virus (IAV) infections in human and swine populations is mandated by public health and animal health concerns. Antibody assays have proven useful in previous surveillance programmes because antibodies provide a record of prior exposure and the technology is inexpensive. The objective of this research was to compare the performance of influenza serum antibody assays using samples collected from pigs (vaccinated or unvaccinated) inoculated with either A/Swine/OH/511445/2007 γ H1N1 virus or A/Swine/Illinois/02907/2009 Cluster IV H3N2 virus and followed for 42 days. Weekly serum samples were tested for anti‐IAV antibodies using homologous and heterologous haemagglutination‐inhibition (HI) assays, commercial swine influenza H1N1 and H3N2 indirect ELISAs, and a commercial influenza nucleoprotein (NP)‐blocking ELISA. The homologous HIs showed 100% diagnostic sensitivity, but largely failed to detect infection with the heterologous virus. With diagnostic sensitivities of 1.4% and 4.9%, respectively, the H1N1 and H3N2 indirect ELISAs were ineffective at detecting IAV antibodies in swine infected with the contemporary influenza viruses used in the study. At a cut‐off of S/N ≤ 0.60, the sensitivity and specificity of the NP‐blocking ELISA were estimated at 95.5% and 99.6%, respectively. Statistically significant factors which affected S/N results include vaccination status, inoculum (virus subtype), day post‐inoculation and the interactions between those factors (P < 0.0001). Serum antibodies against NP provide an ideal universal diagnostic screening target and could provide a cost‐effective approach for the detection and surveillance of IAV infections in swine populations.  相似文献   

6.
    
Poultry can become infected with avian influenza viruses (AIV) via (in) direct contact with infected wild birds. Free‐range chicken farms in the Netherlands were shown to have a higher risk for introduction of low pathogenic avian influenza (LPAI) virus than indoor chicken farms. Therefore, during outbreaks of highly pathogenic avian influenza (HPAI), free‐range layers are confined indoors as a risk mitigation measure. In this study, we characterized the seasonal patterns of AIV introductions into free‐range layer farms, to determine the high‐risk period. Data from the LPAI serological surveillance programme for the period 2013–2016 were used to first estimate the time of virus introduction into affected farms and then assess seasonal patterns in the risk of introduction. Time of introduction was estimated by fitting a mathematical model to seroprevalence data collected longitudinally from infected farms. For the period 2015–2016, longitudinal follow‐up included monthly collections of eggs for serological testing from a cohort of 261 farms. Information on the time of introduction was then used to estimate the monthly incidence and seasonality by fitting harmonic and Poisson regression models. A significant yearly seasonal risk of introduction that lasted around 4 months (November to February) was identified with the highest risk observed in January. The risk for introduction of LPAI viruses in this period was on average four times significantly higher than the period of low risk around the summer months. Although the data for HPAI infections were limited in the period 2014–2018, a similar risk period for introduction of HPAI viruses was observed. The results of this study can be used to optimize risk‐based surveillance and inform decisions on timing and duration of indoor confinement when HPAI viruses are known to circulate in the wild bird population.  相似文献   

7.
    
Relative to research focused on inter‐continental viral exchange between Eurasia and North America, less attention has been directed towards understanding the redistribution of influenza A viruses (IAVs) by wild birds between North America and South America. In this study, we genomically characterized 45 viruses isolated from blue‐winged teal (Anas discors) along the Texas and Louisiana Gulf Coast during March of 2012 and 2013, coincident with northward migration of this species from Neotropical wintering areas to breeding grounds in the United States and Canada. No evidence of South American lineage genes was detected in IAVs isolated from blue‐winged teal supporting restricted viral gene flow between the United States and southern South America. However, it is plausible that blue‐winged teal redistribute IAVs between North American breeding grounds and wintering areas throughout the Neotropics, including northern South America, and that viral gene flow is limited by geographical barriers further south (e.g. the Amazon Basin). Surveillance for the introduction of IAVs from Central America and northern South America into the United States may be further optimized through genomic characterization of viruses resulting from coordinated, concurrent sampling efforts targeting blue‐winged teal and sympatric species throughout the Neotropics and along the United States Gulf Coast.  相似文献   

8.
    
Wild dabbling ducks are the main reservoir for avian influenza (AI ) viruses and pose an ongoing threat to commercial poultry flocks. Combining the (i) size of that population, (ii) their flight distances and (iii) their AI prevalence, the density of AI ‐infected dabbling ducks (DID ) was calculated as a risk factor for the introduction of AI viruses into poultry holdings of Emilia‐Romagna region, Northern Italy. Data on 747 poultry holdings and on 39 AI primary outbreaks notified in Emilia‐Romagna between 2000 and 2017 were used to validate that risk factor. A multivariable Bayesian logistic regression was performed to assess whether DID could be associated with the occurrence of AI primary outbreaks. DID value, being an outdoor flock, hobby poultry trading, species reared, length of cycle and flock size were used as explanatory variables. Being an outdoor poultry flock was significantly associated with a higher risk of AI outbreak occurrence. The probability of DID to be a risk factor for AI virus introduction was estimated to be 90%. A DID cut‐off of 0.23 was identified to define high‐risk areas for AI virus introduction. Using this value, the high‐risk area covers 43% of the region. Seventy‐four per cent of the primary AI outbreaks have occurred in that area, containing 39% of the regional poultry holdings. Poultry holdings located in areas with a high DID value should be included in a risk‐based surveillance programme aimed at AI early detection.  相似文献   

9.
    
Migratory waterfowl, including geese and ducks, are indicated as the primary reservoir of avian influenza viruses (AIv) which can be subsequently spread to commercial poultry. The US Department of Agriculture's (USDA) surveillance efforts of waterfowl for AIv have been largely discontinued in the contiguous United States. Consequently, the use of technologies to identify areas of high waterfowl density and detect the presence of AIv in habitat such as wetlands has become imperative. Here we identified two high waterfowl density areas in California using processed NEXt generation RADar (NEXRAD) and collected water samples to test the efficacy of two tangential flow ultrafiltration methods and two nucleic acid based AIv detection assays. Whole‐segment amplification and long‐read sequencing yielded more positive samples than standard M‐segment qPCR methods (57.6% versus 3.0%, p < .0001). We determined that this difference in positivity was due to mismatches in published primers to our samples and that these mismatches would result in failing to detect in the vast majority of currently sequenced AIv genomes in public databases. The whole segment sequences were subsequently used to provide subtype and potential host information of the AIv environmental reservoir. There was no statistically significant difference in sequencing reads recovered from the RexeedTM filtration compared to the unfiltered surface water. This overall approach combining remote sensing, filtration and sequencing provides a novel and potentially more effective, surveillance approach for AIv.  相似文献   

10.
11.
    
A detailed veterinary and laboratory investigation revealed an unusual case of concurrent avian avulavirus type 1 (AAvV‐1, formerly called avian paramyxovirus type 1) and low pathogenicity avian influenza (LPAI) virus infections of chickens during March 2010 in a mixed poultry and livestock farm in Great Britain. Respiratory signs and daily mortality of 5–6 birds in a broiler flock 8‐weeks of age prompted submission of two carcasses to an Animal and Plant Health Agency (APHA) regional laboratory. Infectious bronchitis virus infection was suspected initially and virus isolation in SPF embryonated fowls’ eggs was attempted at APHA‐Weybridge. Avirulent AAvV‐1 was detected in the first sampling. Both in vitro nucleotide sequencing of the fusion gene and in vivo pathotyping by intracerebral pathogenicity index revealed an avirulent AAvV‐1 not definitively ascribed to licensed vaccine. Upon initial detection of the AAvV‐1 virus, statutory restrictions were placed on the farm, an official veterinary visit was performed and further samples were submitted to APHA‐Weybridge for official statutory disease investigation. An H2N3 LPAI virus was subsequently isolated from tissue samples and swabs submitted from the follow‐up statutory investigation. The subtype was confirmed by haemagglutination inhibition test (HAIT) and neuraminidase inhibition (NI) tests on egg‐amplified virus. As neither virus was notifiable according to the internationally recognized EU and OIE standards, and/or definitions of disease, statutory farm restrictions were lifted. Veterinary investigations identified the broiler flock to be free‐range, next to a river and duck pen, reinforcing the suspicion of wild bird origin for both viruses which may have been co‐circulating in ducks. It could not, however, be established as to whether there were separate introductions of the two viruses or whether there had been a single co‐introduction of the viruses. The described case highlights the value of integrated surveillance and laboratory approaches, including veterinary field investigations, international standards and definitions of notifiable avian disease, validated RRT‐PCR assays, and virus isolation in achieving rapid and accurate diagnostic results.  相似文献   

12.
Ambient water temperature is a key factor controlling the distribution and impact of disease in fish populations, and optimum temperature ranges have been characterised for the establishment of a number important aquatic diseases exotic to the UK. This study presents a simple regression method to approximate daily average surface water temperature in lakes of 0.5–15 ha in size across the UK using 5 km2 gridded daily average air temperatures provided by the UK Meteorological Office. A Geographic information system (GIS) is used to present thematic maps of relative risk scores established for each grid cell based on the mean number of days per year that water temperature satisfied optimal criteria for the establishment of two economically important pathogens of cyprinid fish (koi herpesvirus (KHV) and spring viraemia of carp virus (SVCV)) and the distribution and density of fish populations susceptible to these viruses. High‐density susceptible populations broadly overlap the areas where the temperature profiles are optimal for KHV (central and south‐east England); however, few fish populations occur in areas where temperature profiles are most likely to result in the establishment of spring viremia of carp (SVC) (namely northern England and Scotland). The highest grid‐cell risk scores for KHV and SVC were 7 and 6, respectively, out of a maximum score of 14. The proportion of grid cells containing susceptible populations with risk scores of 5 or more was 37% and 5% for KHV and SVC, respectively. This work demonstrates a risk‐based approach to inform surveillance for exotic pathogens in aquatic animal health management, allowing efficient use of resources directed towards higher risk animals and geographic areas for early disease detection. The methodology could be used to examine the change in distribution of high‐risk areas for both exotic and endemic fish diseases under different climate change scenarios.  相似文献   

13.
目的 分析腹腔感染病人腹腔引流液中病原菌布及其耐药性。方法 收集2012年1月至2014年12月大连医科大学附属第一医院收治的310例腹腔感染病人的腹腔引流液标本,对其进行细菌鉴定及耐药分析,分析病原菌分布与细菌耐药性变化。结果 腹腔引流液标本分离出病原菌578株,其中革兰阴性菌377株(65.2%),革兰阳性菌156株(27.0%),真菌45株(7.8%);3年总分离数量最高的前5位病原菌为大肠埃希菌(19.6%)、肺炎克雷伯菌(11.4%)、鲍曼不动杆菌(10.2%)、屎肠球菌(8.1%)、铜绿假单胞菌(7.3%);屎肠球菌对多数被测药物的耐药率高于粪肠球菌,对氨苄青霉素、环丙沙星、左氧氟沙星、红霉素耐药率均>80%,葡萄球菌对复方新诺明、氯霉素的敏感率>90.0%,3年均未发现耐万古霉素及利奈唑胺的革兰阳性菌;肠杆菌科细菌中产超广谱β内酰胺酶的检出率>55.0%,对碳青霉烯类药物、阿米卡星、β-内酰胺类联合酶抑制剂敏感率较高,对三代头孢菌素耐药严重,碳青霉烯类耐药的肠杆菌科细菌的检出率呈逐年上升趋势;鲍曼不动杆菌除对米诺环素(11.9%)、头孢哌酮/舒巴坦(37.3%)耐药率较低外,对其他测试药物耐药率均>60.0%,其中对碳青霉烯类药物耐药率>70.0%,对头孢曲松、头孢噻肟耐药率>80.0%,对庆大霉素耐药率>90.0%,而铜绿假单胞菌对碳青霉烯类药物、头孢他啶、头孢吡肟、哌拉西林/他唑巴坦、阿米卡星的耐药率低于鲍曼不动杆菌。结论 腹腔感染病人腹腔引流液病原菌以肠杆菌科为主,非发酵菌所占比例亦较高,部分细菌耐药率有逐年升高趋势,应严密监测以指导合理使用抗菌药物。  相似文献   

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The H5N8 highly pathogenic avian influenza viruses (HPAIVs) belonging to clade 2.3.4.4 spread from Eastern China to Korea in 2014 and caused outbreaks in domestic poultry until 2016. To understand how H5N8 HPAIVs spread at host species level in Korea during 2014–2016, a Bayesian phylogenetic analysis was used for ancestral state reconstruction and estimation of the host transition dynamics between wild waterfowl, domestic ducks and chickens. Our data support that H5N8 HPAIV most likely transmitted from wild waterfowl to domestic ducks, and then maintained in domestic ducks followed by dispersal of HPAIV from domestic ducks to chickens, suggesting domestic duck population plays a central role in the maintenance, amplification and spread of wild HPAIV to terrestrial poultry in Korea.  相似文献   

16.
目的建立四价流感病毒亚单位疫苗制备方法。 方法将4株毒种分别接种于9~11日龄的健康鸡胚尿囊腔中,在33~35 ℃培养箱培养48~72 h后,冷胚处理,收获尿囊液,经澄清、病毒灭活、裂解和纯化,除菌过滤制成单价疫苗原液;利用聚丙烯酰胺凝胶电泳(SDS-PAGE)方法,分析有效成分及纯度。将收获的4种单价疫苗原液进行混配,制成四价流感病毒亚单位疫苗。最终按《中华人民共和国药典》2015年版对成品疫苗进行全面检定。 结果成功制备出四价流感病毒亚单位疫苗,其有效成分血凝素含量占总蛋白比例为91.4%。4种疫苗株血凝素含量分别为H1N1:30 μg/ml、H3N2:34 μg/ml、B1:36 μg/ml、B2:30 μg/ml,对成品的检定完全合格。 结论本研究所制备的四价流感亚单位疫苗符合生产和检定规程要求。  相似文献   

17.
    
Influenza D is a newly described virus of cattle, pigs and small ruminants first detected in North America during 2011. Cattle have been shown to be the main viral reservoir and mounting evidence indicates that infection with influenza D may contribute to the development of bovine respiratory disease. The virus has been detected across the United States, Europe and Asia. To date, influenza D has not been reported in the UK. During the winter and spring of 2017/2018, we performed molecular testing of cattle submitted for post‐mortem examination where respiratory disease signs were present. We detected influenza D virus in 8.7% of cases, often as the sole viral agent and always in conjunction with bacterial co‐infection with one or more agents. Viral RNA was present in both the upper and lower respiratory tract and pathological changes in lung tissues were observed alongside signs of concurrent bacterial infections. Sequencing of one UK isolate revealed that it is similar to viruses from the Republic of Ireland and Italy.  相似文献   

18.
19.
In October 2009, highly pathogenic avian influenza virus (HPAIV) was isolated for the first time in poultry in Spain. Sequencing analysis revealed that it was an H7N7 HPAIV. The progenitors of H7 HPAIV strains involved in recent European poultry outbreaks were simultaneously circulating in wild birds. The infected Spanish farm is located close to a reservoir abundant in wild birds. Epidemiological investigation found no links to other poultry holdings and those located in the control area were negative for AIV. Previous spatial risk analyses had identified the area where the infected holding is located to beat high relative risk for the introduction and presence of H5N1 HPAIV by wild birds. We suggest a risk‐based surveillance scheme that targets smaller geographical units but maintains the number of wild birds being sampled, as early detection of potentially pathogenic AIV is crucial in preventing spread to poultry.  相似文献   

20.
This is a continuation of our studies previously published in this journal to use data analysis to explore why the reassortment of genetic segments from different host species and from different subtypes of influenza A viruses occurred frequently, which was considered the main reason for the generation of new strains. Of eleven proteins from influenza A virus, we have studied seven proteins in our previous studies. To get a full picture, 2352 polymerase basic proteins 1 from influenza A viruses were analysed. The results showed that the variations between host species/subtypes are smaller than those within host species/subtype. In combination with the results obtained from hemagglutinin, neuraminidase, nucleoprotein, matrix proteins 1 and 2, polymerase acidic protein and polymerase basic proteins 1 and 2, the results suggested that the predisposition to reassortment of genetic segments of influenza A virus from different host species and subtypes was mainly because of the small variations between the virus isolates.  相似文献   

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