Frequent Detection and Genetic Diversity of Human Bocavirus in Urban Sewage Samples

The prevalence and genetic diversity of human bocaviruses (HBoVs) in sewage water samples are largely unknown. In this study, 134 raw sewage samples from 25 wastewater treatment plants (WTPs) in Italy were analyzed by nested PCR and sequencing using species-specific primer pairs and broad-range primer pairs targeting the capsid proteins VP1/VP2. A large number of samples (106, 79.1 %) were positive for HBoV. Out of these, 49 were classified as HBoV species 2, and 27 as species 3. For the remaining 30 samples, sequencing results showed mixed electropherograms. By cloning PCR amplicons and sequencing, we confirmed the copresence of species 2 and 3 in 29 samples and species 2 and 4 in only one sample. A real-time PCR assay was also performed, using a newly designed TaqMan assay, for quantification of HBoVs in sewage water samples. Viral load quantification ranged from 5.51E+03 to 1.84E+05 GC/L (mean value 4.70E+04 GC/L) for bocavirus 2 and from 1.89E+03 to 1.02E+05 GC/L (mean value 2.27E+04 GC/L) for bocavirus 3. The wide distribution of HBoV in sewages suggests that this virus is common in the population, and the most prevalent are the species 2 and 3. HBoV-4 was also found, representing the first detection of this species in Italy. Although there is no indication of waterborne transmission for HBoV, the significant presence in sewage waters suggests that HBoV may spread to other water environments, and therefore, a potential role of water in the HBoV transmission should not be neglected.     

Identification and Genotyping of Human Sapoviruses Collected from Sewage Water in Naples and Palermo, Italy, in 2011

Human sapoviruses were identified in 15 (12.4 %) of 121 inlet sewage samples collected from wastewater treatment plants in Naples and Palermo, Italy, in 2011. All strains, except one GI.1, were genotyped as GI.2 by sequencing a capsid gene fragment. This is the first detection of sapovirus in wastewaters in Italy.     

甾体激素在污水处理厂中的赋存特征和行为归趋

污水处理厂是控制甾体激素环境排放的重要屏障之一,研究不同种类甾体激素在不同工艺污水处理厂中的赋存特征和行为归趋是提高污水处理厂对甾体激素处理效能的重要基础.对无锡市两个污水处理厂各工艺段中22种甾体激素的赋存情况进行8个月的监测,比较了厌氧-缺氧-好氧工艺(A²/O)和倒置A²/O工艺的处理效果.结果表明,甾体激素的进出水总浓度分别为27.7~256.8 ng ·L^-1和5.7~211.0 ng ·L^-1,剩余污泥中激素总含量为36.3~123.6 ng ·g^-1,主要检出雄酮、雄烯二酮、雌酚酮、雌三醇和孕酮.进出水中大多数激素的浓度随降雨量和温度的升高而略有降低的趋势,而冬夏的季节差异未对甾体激素的去除率产生显著影响.污水厂的二、三级处理工艺对激素的去除效果优于一级处理,倒置A²/O和传统A²/O相比对甾体激素的去除并未表现出明显的优势.甾体激素在污水和污泥间的分配系数lg Koc为2~4.5,在厂A中的lg Koc略高于厂B,激素的泥水分配可能影响其处理效果.     

抗生素在城市污水处理系统中的分布及去除

根据目前国内外已有的研究结果,综述了几类主要的抗生素在世界各国城市污水处理厂污水、污泥中的残留浓度及抗生素在城市污水处理系统中的去除途径和去除效果。结果表明,世界各国城市污水处理厂污水、污泥中抗生素的种类和浓度有明显差异:污水中抗生素的浓度与该国抗生素的使用量有关,我国城市污水中四环素类、磺胺类的检出最高浓度达到103¹04ng/L,远高于其他国家;环丙沙星和甲氧苄啶在美国城市污水处理厂出水中检出浓度较高,达到103ng/L。污泥中抗生素残留主要是通过污泥吸附作用,残留浓度受到抗生素在固-液相的分配系数、亲脂性和离子所带电荷影响。自然条件下,水解、光解和传统生物处理工艺对抗生素的去除率低,而高级氧化技术和膜过滤技术对抗生素的去除效率高,可以达到90%以上。     

Persistent Detection of Cosavirus and Saffold Cardiovirus in Riachuelo River,Argentina

Food and Environmental Virology - Cosaviruses (CoSV) and Saffold cardiovirus (SAFV) are novel members of the Picornaviridae family. The Matanza-Riachuelo river basin covers a total area of 2200 km2...     

First Occurrence of Saffold Virus in Sewage and River Water Samples in Karaj,Iran

Food and Environmental Virology - Saffold virus as a newly discovered virus, which seems to be related to acute gastroenteritis as with other enteric viruses and to human airway diseases in...     

南京8个湖泊超微真核浮游生物遗传多样性的研究

用末端限制性片段长度多态性(terminal restriction fragment length poly morphism,T-RFLP)方法对南京市区8个不同营养水平湖泊的沿岸带和敞水带超微真核浮游生物(0.2～5.0μm)遗传多样性进行了研究,目的是了解不同营养水平湖泊超微真核浮游生物遗传多样性的差异以及影响这种差异的主要因子.T-RFLP结果表明,不同湖泊超微真核浮游生物的T-RFLP指纹图谱存在明显差异,沿岸带和敞水带末端限制性片段T-RFs平均值分别为16.4和15.9,其中营养水平中等的南湖沿岸带T-RFs最多(30个),营养水平较低的百家湖敞水带T-RFs最少(10个),除琵琶湖和莫愁湖外,沿岸带的超微真核浮游生物遗传多样性均比敞水带高.聚类分析表明,除百家湖、前湖、南湖外,其他湖泊沿岸带和敞水带的相似度都比较高.超微真核浮游生物遗传多样性与环境因子的典型对应分析(canonical correspondence analysis,CCA)表明,叶绿素a浓度与超微真核浮游生物群落结构和多样性显著相关(p=0.004).本研究表明,超微真核浮游生物遗传多样性受湖泊营养水平的影响,而且在敞水带和沿岸带存在差异.     

A/O MBR处理生活污水效率与菌群多样性的关系

采用缺氧/好氧膜生物反应器（A/O MBR）工艺处理生活污水,试运行了5种不同的工况以确定最佳工艺参数,利用变性凝胶梯度电泳（DGGE）技术研究缺氧池和好氧池（MBR）中细菌群落结构,分析出水水质与细菌种群多样性的关系.结果表明A/O MBR在水力停留时间（HRT）为12 h,污泥停留时间（SRT）为10 d,硝化液回流比为300%,污泥回流比为100%的条件下,对COD、氨氮、总氮有稳定良好的去除,平均去除率分别为96.4%、99.1%、75.8%;系统运行过程中,缺氧池和好氧池中菌群结构发生较大变化,同一工况下两池菌群的相似性通常大于50%,但缺氧池菌群多样性随工况变换而波动较大,好氧池菌群多样性随运行时间而逐渐丰富;缺氧池菌群多样性指数与反硝化效率成正相关关系.     

鄱阳湖水体细菌群落组成及遗传多样性

利用建立细菌16S rRNA基因文库和限制性内切酶长度多态性(RFLP)分析的方法,对鄱阳湖南、北湖区水体的细菌多样性进行了研究. 结果表明,鄱阳湖水体细菌多样性较高,且南湖区2007年水体的细菌多样性明显高于其2006年水体和北湖区水体. 主要细菌组成分析表明,鄱阳湖水体中的349个阳性克隆代表的167种基因型分别属于十大细菌类群,变形菌门(Proteobacteria)在4个克隆文库中占据了47%～81%,数量极其丰富,尤其是亚型的β-变形菌为优势菌群; 拟杆菌门(Bacteroidetes)和放线菌门(Actinobacteria)也广泛分布,且有2.9%～17.1%的克隆数属于未分类细菌. 研究结果进一步提示鄱阳湖水体有一定程度的富营养化.      

Human Enteric Viruses Occurrence in Shellfish from European Markets

Different sources were consulted to obtain information on the occurrence of viruses in bivalve molluscs on the European market. Twenty-six peer-reviewed articles were identified reporting on the molecular detection of viral RNA in 4,260 samples in total. The data obtained will be presented geographically on virus types detected, the origin and treatment of the shellfish, and the detection technique applied. The data demonstrate that viral RNA can be detected in shellfish from polluted areas, in depurated shellfish as well as those for human consumption. The European Rapid Alert System for Food and Feed (RASFF) database was consulted as another source. Twenty-eight notifications were identified on the presence of hepatitis A virus or norovirus in shellfish on the European market. The most recent report of the European laboratory network was referred to, to gain insight into the laboratory capability at present for the analyses of shellfish on the presence of viruses. Approximately 67% of 27 participating laboratories obtained intended results for all samples, consisting of lenticules loaded with 10³ copies norovirus (genogroup I (GGI) and/or genogroup II (GGII)) and/or 1 × 10⁵–8 × 10⁴ copies of hepatitis A virus. From 1993, there has been a continuous development of molecular detection techniques and tools have been described to ensure quality assurance. End product testing will, however, not be achievable. As depuration has been shown not to be effective for the complete elimination of viruses, shellfish should not be in contact with faecal contaminated water in order to minimise the risk of shellfish-transmittable viral diseases.     

Detection of Norovirus GII.17 Kawasaki 2014 in Shellfish,Marine Water and Underwater Sewage Discharges in Italy

Norovirus (NoV) is a major cause of non-bacterial acute gastroenteritis worldwide, and the variants of genotype GII.4 are currently the predominant human strains. Recently, a novel variant of NoV GII.17 (GII.P17_GII.17 NoV), termed Kawasaki 2014, has been reported as the cause of gastroenteritis outbreaks in Asia, replacing the pandemic strain GII.4 Sydney 2012. The GII.17 Kawasaki 2014 variant has also been reported sporadically in patients with gastroenteritis outside of Asia, including Italy. In this study, 384 shellfish samples were subjected to screening for human NoVs using real-time PCR and 259 (67.4%) tested positive for Genogroup II (GII) NoV. Of these, 52 samples, selected as representative of different areas and sampling dates, were further amplified by conventional PCR targeting the capsid gene, using broad-range primers. Forty shellfish samples were characterized by amplicon sequencing as GII.4 (n = 29), GII.2 (n = 4), GII.6 (n = 2), GII.12 (n = 2), and GII.17 (n = 3). Sixty-eight water samples (39 seawater samples from the corresponding shellfish production areas and 29 water samples from nearby underwater sewage discharge points) were also tested using the above broad-range assay: eight NoV-positive samples were characterized as GII.1 (n = 3), GII.2 (n = 1), GII.4 (n = 2), and GII.6 (n = 2). Based on full genome sequences available in public databases, a novel RT-PCR nested assay specific for GII.17 NoVs was designed and used to re-test the characterized shellfish (40) and water (8) samples. In this second screening, the RNA of GII.17 NoV was identified in 17 additional shellfish samples and in one water sample. Upon phylogenetic analysis, these GII.17 NoV isolates were closely related to the novel GII.17 Kawasaki 2014. Interestingly, our findings chronologically matched the emergence of the Kawasaki 2014 variant in the Italian population (early 2015), as reported by hospital-based NoV surveillance. These results, showing GII.17 NoV strains to be widespread in shellfish samples collected in 2015 in Italy, provide indirect evidence that this strain has started circulating in the Italian population. Notably, using a specific assay, we were able to detect many more samples positive for GII.17 NoV, indicating that, in food and water matrices, broad-range assays for NoV may grossly underestimate the prevalence of some, less common, NoVs. The detection of the GII.17 strain Kawasaki 2014 in clinical, water and food samples in Italy highlights the need for more systematic surveillance for future disease control and prevention.     

关帝山森林土壤真菌群落结构与遗传多样性特征

土壤微生物群落驱动土壤碳、氮、磷、硫生物地球化学循环,在维持土壤碳汇和生态系统功能等方面发挥重要的作用.分析环境与空间因素在寒温性针叶林土壤微生物群落构建中的作用,可以为区域森林生态系统管理措施的制定提供理论依据.本文利用Illumina高通量测序技术分析了关帝山庞泉沟自然保护区华北落叶松(Larix principis-rupprechtii)林、青杄(Picea wilsonii)林、油松(Pinus tabulaeformis)林以及桦树(Betula spp.)林这4种林型的5个土壤真菌群落(Lp MC1、Lp MC2、Pw MC、Pt MC和BMC)的结构.同时测定林下土壤环境因子及林下植被多样性,分析真菌群落的结构与植被和土壤环境因子的相关性.结果表明:(1)5个样地中共有7个真菌门和33个优势真菌属;(2)冗余分析结果表明:土壤pH、温度、含水率、全氮含量、NH+4含量、全碳含量、蔗糖酶活性、脲酶活性、林下植被优势度和均匀度与土壤真菌群落结构显著相关;(3)聚类分析和PCA分析结果表明,森林植被类型、土壤环境因子和林下植被对土壤真菌群落结构影响显著.(4)空间变量(PCNM)分析结果表明,在局域尺度(local scale)上扩散限制对研究区域真菌群落构建的影响不显著.本研究区森林土壤真菌群落结构主要受到环境选择(土壤pH、温度、含水率、全氮含量、NH+4含量、全碳含量、蔗糖酶活性、脲酶活性、林下植被优势度和均匀度、森林类型)的显著影响.     

太湖不同湖区真核微型浮游生物基因多样性的研究

用DGGE(denatured gradient gel electrophoresis)和构建18S rDNA克隆文库2种方法对太湖不同湖区的真核微型浮游生物(0.8～20μm)多样性及组成结构进行了研究.DGGE结果表明,不同湖区真核微型浮游生物的DGGE指纹图谱存在明显差异,其中营养水平较低的东太湖和贡湖DGGE条带数最多,分别为23和24,香农多样性指数分别为3.135和3.178,而营养水平较高的梅梁湾和五里湖最少,均为18,香农多样性指数为2.890,表明营养水平较低湖区的多样性高于营养水平较高的湖区.克隆测序结果表明太湖中真核微型浮游生物种类车富,占优势的主要是一些鞭毛藻、异养鞭毛虫、纤毛虫和真菌,而营养水平不同的梅梁湾、湖心、东太湖中真核微型浮游生物组成明显不同.在营养水平较高的梅梁湾,28.6%的OUT(operational taxonomicunit)属于异养鞭毛虫,另外隐藻、金藻分别占22.9%和14.3%;在湖心,金藻的比例最大,占25.7%,另外比较多的是异养鞭毛虫和隐藻,分别为20.0%和14.3%;而营养水平较低的东太湖各类纤毛虫所占比份最大,为26.8%,异养鞭毛虫较少,仅占4.9%,另外真菌含量较高,占12.2%.     

Relative Abundance of Human Bocaviruses in Urban Sewage in Greater Cairo,Egypt

Human bocavirus (HBoV) is predominantly found in the respiratory tract infections and in the stool of patients with gastroenteritis symptoms. However, data on the prevalence of HBoV genotypes in environmental samples are limited. Here we addressed the prevalence of HBoV in sewage collected from three different wastewater treatment plants in Egypt. HBoV-1, HBoV-2, and HBoV-3 were detected, whereas none of the samples were positive for HBoV-4. The median concentration of HBoV in influent samples was 8.5 × 10³ GC/l for HBoV-1, 3.0 × 10⁴ GC/l for HBoV-2, and 2.5 × 10⁴ GC/l for HBoV-3. The concentration was reduced but not completely removed in the effluent samples. The median concentration in the outlet samples was 2.9 × 10³ GC/l for HBoV-1, 4.1 × 10³ GC/l for HBoV-2, and 2.1 × 10³ GC/l for HBoV-3. Moreover, no seasonality pattern of HBoVs was found. The high incidence of HBoV in sewage samples provided an evidence of its circulation in the local population. Although the role of HBoV in respiratory or gastro-intestinal infections still remains to be fully elucidated, the risk of infection via contaminated water should be taken into consideration.     

Molecular Detection of Human Salivirus in Italy Through Monitoring of Urban Sewages

Food and Environmental Virology - Salivirus (SalV) is a newly discovered virus associated to acute gastroenteritis in humans. In Italy, its prevalence and genetic diversity is unknown. To reduce...     

Human Bocavirus: Detection,Quantification and Molecular Characterization in Sewage and Surface Waters in Uruguay

Human bocavirus (HBoV) infections are related to respiratory and gastroenteric diseases. The aim of this study was to investigate the presence of HBoV in both sewage and surface waters in Uruguay. Sixty-eight sewage samples from the cities of Salto, Paysandú, Bella Unión, Fray Bentos, Treinta y Tres and Melo and 36 surface water samples from the cities of Salto, Florida and Santa Lucía were studied. HBoV was screened by multiplex qPCR for the detection of the four subtypes, followed by monoplex qPCRs for the independent quantification of each subtype. A qualitative PCR followed by DNA sequencing and phylogenetic analysis was carried out for molecular characterization of HBoV strains. HBoV was present in a high frequency (69%) in sewage and only one positive sample (3%) was found in surface water. Concerning sewage samples, HBoV1 was detected in 11 (23%) out of the 47 positives samples, with a mean concentration of 8.2 × 10⁴ genomic copies/Liter (gc/L), HBoV3 was detected in 35 (74%) of the positive samples with a mean concentration of 4.1 × 10⁶ gc/L and subtypes 2 and/or 4 were detected in 39 (83%) of the positive samples with a mean concentration of 7.8 × 10⁶ gc/L. After the phylogenetic analysis performed by a Bayesian approach, the four HBoV subtypes were confirmed. This is the first study determining a high frequency of HBoV and the presence of the four HBoV subtypes in aquatic matrices in Latin America, mainly in sewage. Although HBoV was scarcely detected in surface water, a waterborne transmission is likely to occur if people enter in contact with polluted surface waters for recreational activities such as fishing or swimming since an elevated frequency of HBoV was detected in raw sewage which is usually directly discharged into surface waters.     

The First Detection of Human Bocavirus Species 2 and 3 in Raw Sewage and Mussels in South Africa

Human bocavirus (HBoV) has a global distribution and is associated with respiratory and enteric infections, particularly in the paediatric population. In this study, raw sewage and mussel samples were analysed for the presence of HBoV using nested PCR with primers targeting the VP1/VP2 junction. Amplification and sequencing of the 382 bp region followed by phylogenetic analysis indicated the presence of HBoV 2 in mussel samples and HBoV 3 in sewage samples. This is the first report describing the presence of enteric-associated HBoV in environmental samples from South Africa and in mussel samples from the African continent. The results signify the need for further studies examining the potential risk of foodborne transmission of HBoV and highlight the importance of continued screening to determine the prevalence and epidemiology of HBoV in South Africa.     

Infectious Pepper Mild Mottle Virus and Human Adenoviruses as Viral Indices in Sewage and Water Samples

Food and Environmental Virology - The objective of this study was to compare human adenoviruses (HAdVs) genome and infectivity, polyomaviruses (JC and BK) genome (JCPyVs) and (BKPyVs), Pepper Mild...