Changing pattern of prevalence and genetic diversity of rotavirus,norovirus, astrovirus,and bocavirus associated with childhood diarrhea in Asian Russia, 2009–2012

This hospital-based surveillance study was carried out in Novosibirsk, Asian Russia from September 2009 to December 2012. Stool samples from 5486 children with diarrhea and from 339 healthy controls were screened for rotavirus, norovirus, astrovirus, and bocavirus by RT-PCR. At least one enteric virus was found in 2075 (37.8%) cases with diarrhea and 8 (2.4%) controls. In the diarrhea cases, rotavirus was the most commonly detected virus (24.9%), followed by norovirus (13.4%), astrovirus (2.8%) and bocavirus (1.1%). Mixed viral infections were identified in 4.3% cases. The prevalence of enteric viruses varied every season. Rotavirus infection was distributed in a typical seasonal pattern with a significant annual increase from November to May, while infections caused by other viruses showed no apparent seasonality. The most common rotavirus was G4P[8] (56%), followed by G1P[8] (20.1%), G3P[8] (5.5%), G9P[8], G2P[4] (each 1.3%), six unusual (1.2%), and five mixed strains (0.5%). Norovirus GII.3 (66.5%) was predominant, followed by GII.4 (27.3%), GII.6 (3.7%), GII.1 (1.6%), and four rare genotypes (totally, 0.9%). Re-infection with noroviruses of different genotypes was observed in four children. The classic human astrovirus belonged to HAstV-1 (82%), HAstV-5 (8%), HAstV-4 (4.7%), HAstV-3 (4%) and HAstV-2 (1.3%). Consecutive episodes of HAstV-1 and HAstV-4 infections were detected in one child with an 8-month interval. Bocavirus strains were genotyped as HBoV2 (56.5%), HBoV1 (38.7%), HBoV4 (3.2%) and HBoV3 (1.6%). In the controls, norovirus strains belonged to GII.4 (n = 4), GII.1, GII.3, and GII.6, and HBoV2 strain were detected. Most of the detected virus isolates were characterized by a partial sequencing of the genomes. The genotype distribution of most common enteric viruses found in the Asian part of Russia did not differ considerably from their distribution in European Russia in 2009–2012.     

2016 - 2018无锡市腹泻病疫情中诺如病毒的分子流行病学特征

目的 鉴定无锡市2016年3月 - 2018年3月急性腹泻病突发疫情中诺如病毒的感染流行情况,并对病原体进行分子特征研究。方法 对疫情上送的暴发急性病例标本,采用荧光PCR初步判定病原体,常规RT - PCR检测诺如病毒RNA聚合酶和衣壳蛋白基因片段,并进行序列测定和分子特征分析。结果 在30起暴发疫情中共有162份标本经荧光PCR检测均为诺如病毒核酸阳性,其中154份标本RT - PCR检测判为GII型诺如病毒,120份标本成功测序。测序结果显示,2016 - 2018年突发疫情中有5种基因型,分别是GII.P16 - GII.2、GII.P17 - GII.17、GII.4_Sydney2012、GII.4_NewOrleans和GI.6,2017年之前以GII.17病毒株流行为主,2017之后新的GII.P16 - GII.2重组株成为无锡市病毒性腹泻疫情中的绝对优势株。结论 诺如病毒是无锡市腹泻病疫情的最常见病原体,其最新的优势流行株是GII.P16 - GII.2重组株,和全国趋势一致。     

2012-2014年湖南省感染性腹泻哨点医院儿童诺如病毒感染及基因型别分析

目的 了解湖南省感染性腹泻哨点医院儿童诺如病毒的感染状况及基因型别。 方法 2012年1月-2014年12月采集湖南省哨点医院腹泻患儿的粪便标本,应用诺如病毒特异性引物进行扩增,选择扩增阳性产物进行基因测序和进化分析。 结果 936份粪便标本RT-PCR检测诺如病毒核酸,阳性100份,阳性率10.68%。对40份诺如病毒核酸阳性标本进行基因序列测定与分析,38份为GⅡ型,其中31份为GⅡ.4型。在31株GⅡ.4型中,Sydney 2012和GII.4 Den Haag 2006b各栓出14株。 结论 2012-2014年湖南省哨点医院儿童腹泻病例中诺如病毒的感染率较高,GⅡ.4是优势株,其中GⅡ.4 sydney 2012和Den Haag 2006b是主要型别。     

北京地区诺如病毒分子生物学特点初步研究

目的了解北京地区诺如病毒的分子生物学特点。方法收集北京市2007年1—3月非细菌性胃肠炎暴发和散发病例，采集患者粪便标本，使用逆转录聚合酶链反应（RT—PCR）对粪便标本进行诺如病毒RNA检测，对RT—PCR阳性标本的PCR产物进行克隆测序。结果检测38例粪便标本，共有27例阳性。随机选择其中4例PCR产物进行克隆测序，获得4株诺如病毒序列进行比对分析，结果显示，该4株病毒序列与诺如病毒GⅡ／4型参考株同源性最高，其中与荷兰和日本提交的诺如病毒GⅡ／4型变异株最为接近，同源性分别为97．8％～98．5％和95．2％～95．9％。系统发生树分析表明，该4株诺如病毒与荷兰、日本流行的GⅡ／4型变异株处于同一分支上。结论北京地区存在诺如病毒GⅡ／4型变异株流行，其与2006年荷兰和日本的诺如病毒流行株属同一类GⅡ／4型变异株。     

Novel GII.12 norovirus strain, United States, 2009-2010

In October 2009, a novel GII.12 norovirus strain emerged in the United States and caused 16% of all reported norovirus outbreaks during the winter season. Sequence analysis demonstrated a recombinant virus with a P2 region that was largely conserved compared with previously sequenced GII.12 strains.     

Emergence of unusual G6P[6] rotaviruses in children, Burkina Faso, 2009-2010

To obtain more information about rotavirus (ROTAV) genotypes in Burkina Faso, we characterized 100 ROTAVs isolated from fecal samples of children with acute gastroenteritis in the capital city of Ouagadougou, during December 2009-March 2010. Of note, 13% of the ROTAV-positive samples, including those with mixed infections, were positive for the unusual G6 genotype ROTAV strain. The genotypes identified were G9P[8], G6P[6], G1P[6], G3P[6], G1P[8], and G2P[4]. G9P[8] subgroup (SG)II strains dominated during the beginning of the ROTAV season, but later in the season, other G types associated with P[6] and SGI specificity emerged. This emergence was related to a shift in the overall age of infected children; ROTAV SGII infected younger children and induced more severe symptoms. The finding of a high incidence of G6P[6] strains highlights the need for long-term surveillance of ROTAV strains in Burkina Faso, especially when ROTAV vaccination is being considered in several African countries.     

2017-2019年湖北省病毒性腹泻哨点监测病例中诺如病毒流行及基因特征

  目的  了解湖北省2017-2019年病毒性腹泻哨点监测病例中诺如病毒(norovirus, NV)的流行病学特征和基因型别特征。  方法  收集2017年1月1日-2019年12月30日成人和儿童腹泻患者的粪便标本共1 957份,采用实时荧光RT-PCR法进行NV GI和GII型别鉴定;对NV检测阳性的GII型标本应用RT-PCR扩增开放阅读框(open reading frame, ORF)1/ORF2铰链区,将获得的PCR产物直接测序并进行基因型别和重组分析。  结果  男性和女性腹泻患者中NV阳性检出率差异有统计学意义(χ2 =5.18, P=0.023)。各年龄组腹泻患者间NV阳性检出率差异有统计学意义(χ2 =98.04, P＜0.001),其中1~＜2岁年龄组腹泻患者NV阳性检出率最高,为23.50%。2017-2019年湖北省NV感染呈现2个流行峰,高峰出现在10-12月间,低峰出现在3-4月。NV主要为GII基因型,其中以GII.4、GII.2和GII.3亚型为主。主要的重组型有GII.2[P16]、GII.4[P31]、GII.3[P12]和GII.4[P16]。  结论  2017-2019年湖北地区存在多种基因型NV的感染,并发现不同的重组亚型。加强NV的基因型别监测和重组分析有利于掌握NV的分子流行病学特征,为科学防控提供理论依据。     

Molecular epidemiology of noroviruses detected in Nepalese children with acute diarrhea between 2005 and 2011: Increase and predominance of minor genotype GII.13

Noroviruses, an important cause of acute gastroenteritis, possess a highly divergent genome which was classified into five genogroups and dozens of genotypes. However, changes in genotype distribution over time were poorly understood, particularly in developing countries. We therefore conducted a molecular epidemiological study which characterized the norovirus strains detected in 4437 Nepalese children with acute diarrhea between November 2005 and January 2011 to gain insight into how their genotypes changed over time. Of the 356 samples positive for noroviruses, 277 (78%) were successfully genotyped into 22 capsid genotypes; GII.4 (n = 113), GII.3 (n = 38) and GII.13 (n = 37) were the majority. Interestingly, GII.13 accounted for only 1.7% (4/230) between 2005 and 2008 (period 1) but increased substantially to 26.2% (33/126) between 2009 and 2011 (period 2). Phylogenetic analysis of the VP1 nucleotide sequences of 35 GII.13 strains indicated that they clustered into two lineages named NPL2008 and NPL2009 to which two period 1 strains and 33 period 2 strains belonged, respectively. Lineage NPL2009 contained GII.13 strains that were detected in a large-scale gastroenteritis outbreak in Germany in 2012. Both Nepalese and German VP1 sequences carried two substitutions, H378N and V394Q, in the putative histo-blood group antigen (HBGA)-binding sites. As to the polymerase genotypes of Nepalese strains, the period 1 strains possessed GII.Pm, but the period 2 strains possessed GII.P13, GII.P16, and GII.P21. Together with recent reports on the predominance of GII.P13/GII.13 and GII.P16/GII.13 in India and GII.P16/GII.13 in European countries, this study predicts that genotype GII.13 which was previously regarded as a minor genotype has a potential to become an epidemiologically important genotype.     

Occurrence of Norovirus GII.4 Sydney Variant-related Outbreaks in Korea

Human noroviruses are major causative agents of food and waterborne outbreaks of nonbacterial acute gastroenteritis. In this study, we report the epidemiological features of three outbreak cases of norovirus in Korea, and we describe the clinical symptoms and distribution of the causative genotypes. The incidence rates of the three outbreaks were 16.24% (326/2,007), 4.1% (27/656), and 16.8% (36/214), respectively. The patients in these three outbreaks were affected by acute gastroenteritis. These schools were provided unheated food from the same manufacturing company. Two genotypes (GII.3 and GII.4) of the norovirus were detected in these cases. Among them, major causative strains of GII.4 (Hu-jeju-47-2007KR-like) were identified in patients, food handlers, and groundwater from the manufacturing company of the unheated food. In the GII.4 (Hu-jeju-47-2007KR-like) strain of the norovirus, the nucleotide sequences were identical and identified as the GII.4 Sydney variant. Our data suggests that the combined epidemiological and laboratory results were closely related, and the causative pathogen was the GII.4 Sydney variant strain from contaminated groundwater.     

2015年-2017年湖州诺如病毒感染的流行特征研究

目的研究湖州地区诺如病毒(NoV)的流行病学模式和遗传特征。方法2015年1月-2017年12月,收集急性胃肠炎患者的粪便标本,进行实时RT-PCR(qPCR)检测NoV。RT-PCR用于基因组扩增和序列测定。病毒基因型别使用在线NoV分型工具(http://www.rivm.nl/mpf/norovirus/typingtool)分型。结果NoV感染的总体流行率为23.7%(414/1757)。在414个NoV阳性标本中,393个被鉴定为NoV GⅡ,11个属于NoV GⅠ,10个是NoV GⅠ和GⅡ共同感染。共235份标本成功测序,这3年的主要流行型别是GⅡ.Pe-GⅡ.4 Sydney2012和GⅡ.P17-GⅡ.17,2017年还出现新的流行优势株GⅡ.P16-GⅡ.2。全年均检测到NoV感染,流行高峰发生在每年的冬春期间。结论在2014年10月GⅡ.17首次在湖州出现后,稳步取代了以前流行的GⅡ.4 Sydney 2012菌株。但在2016年GⅡ.4 Sydney 2012又回到主导地位,2017年出现新的流行优势株GⅡ.P16-GⅡ.2。     

Phylogenetic analyses of Norovirus strains detected in Uruguay reveal the circulation of the novel GII.P7/GII.6 recombinant variant

Noroviruses (NoV) are one of the major etiological agent of acute gastroenteritis (AGE) outbreaks worldwide. Distinct NoV genotypes have been associated with different transmission patterns and disease severity in humans. Therefore, it is important to identify genetically different NoV genotypes circulating in a particular region. However, genotyping has become a challenge due to recombination events occurring mainly nearby ORF1/ORF2 junction of NoV genome, leading to distinct genotypes with polymerase and capsid regions derived from parenteral strains. Taking this into account, ORF1/ORF2 sequences were obtained from NoV strains collected from patients with AGE in Uruguay. This study reveals in silico evidences of recombination events taking place in four out of six strains analyzed for which its polymerase gene and its capsid region correspond to GII.P7 and to GII.6 genotype, respectively. These results also reveal the circulation of a GII.P7/GII.6 recombinant variant in the natural populations of NoV strains in the northwestern region of Uruguay. As far as we know this is the first report about the circulation of a NoV GII.P7/GII.6 recombinant variant in the Americas.     

A decade of G3P[8] and G9P[8] rotaviruses in Brazil: Epidemiology and evolutionary analyses

This study aims to estimate the frequency of group A rotaviruses (RVA) infection with genotypes G3P[8] and G9P[8] in children that suffered from diarrheal disease (DD) between 2001 and 2011 in different Brazilian regions. In addition, the genetic diversity of G3P[8] and G9P[8] RVA strains recovered from vaccinated and non-vaccinated children was assessed. Laboratory-based RVA surveillance included 15,115 cases of DD, and RVA was detected by enzyme immune-assay and/or polyacrylamide gel electrophoresis in 3357 (22%) samples. RVA was genotyped by the semi-nested RT-PCR and among RVA-positive samples, 100 (2.9%) were G3 (63 G3P[8], 32 G3P not typed [NT], and 5 G3P[6]) and 378 (16.2%) were G9 (318 G9P[8], 59 G9P[NT], and 1 G9P[6]). From the G3 and G9 positive samples, 16 and 12, respectively, were obtained from children aged 4–48 months vaccinated with the monovalent vaccine (Rotarix®, RV1). Phylogenetic analyses of the VP7 and VP8¹ encoding genes were performed for 26 G3P[8] and 48 G9P[8] strains. VP8¹ phylogenetic analysis revealed that all strains analyzed belonged to P[8] lineage III, whereas RV1 belongs to P[8]-I lineage. VP7 analysis revealed that all G3 and G9 strains belonged to G3-lineage III and G9-lineage III. The comparison of the VP7 and VP8¹ antigenic epitopes regions of Brazilian strains with RV1 strain revealed several amino acid changes. However, no particular differences among Brazilian strains detected before and after vaccine introduction were observed, or among strains detected from vaccinated and non-vaccinated children. Complete genome characterization of four G3P[8] and seven G9P[8] strains revealed a typical conserved human Wa-like genomic constellation. Changes in the genetic diversity of G3P[8] and G9P[8] RVA detected from 2001 to 2011 in Brazil seemed not be related to RV1 introduction in Brazil.     

Healthcare-associated Viral Gastroenteritis among Children in a Large Pediatric Hospital, United Kingdom

Viruses are the major pathogens of community-acquired (CA) acute gastroenteritis (AGE) in children, but their role in healthcare-associated (HA) AGE is poorly understood. Children with AGE hospitalized at Alder Hey Children’s Hospital, Liverpool, UK, were enrolled over a 2-year period. AGE was classified as HA if diarrhea developed >48 hours after admission. Rotavirus, norovirus, adenovirus 40/41, astrovirus, and sapovirus were detected by PCR. A total of 225 children with HA-AGE and 351 with CA-AGE were enrolled in the study. HA viral gastroenteritis constituted one fifth of the diarrheal diseases among hospitalized children and commonly occurred in critical care areas. We detected >1 virus in 120 (53%) of HA-AGE cases; rotavirus (31%), norovirus (16%), and adenovirus 40/41 (15%) were the predominant viruses identified. Molecular evidence indicated rotaviruses and noroviruses were frequently introduced into the hospital from the community. Rotavirus vaccines could substantially reduce the incidence of HA-AGE in children.     

Efficacy of an intramuscular bivalent norovirus GI.1/GII.4 virus-like particle vaccine candidate in healthy US adults

BackgroundWe performed this first-in-human efficacy trial of Takeda’s bivalent norovirus vaccine candidate (TAK-214) against moderate or severe acute gastroenteritis (AGE) in healthy adults.MethodsThis double-blind, randomized, placebo-controlled phase 2b trial was conducted over two winter seasons in 18–49 year-old US Navy recruits. Participants were randomized (1:1) to receive intramuscular injections of saline placebo (N = 2,357) or TAK-214 [15 μg GI.1 and 50 μg GII.4c VLPs, 0.5 mg Al(OH)₃] (N = 2,355), and monitored for 45 days post-vaccination for AGE. Norovirus genotypes were identified by RT-PCR and sequencing of stool/vomitus samples. Sera from AGE cases were used to assess immune responses as genotype-specific histo-blood group antigen (HBGA)-blocking antibodies.FindingsWith low rates of homotypic norovirus AGE detected the statistical analysis was proactively modified to account for AGE due to any norovirus genotype. Of the 48 norovirus AGE cases of “any severity”, 29 in placebo and 19 in vaccinees, causative genotypes were GI.1 (n = 1), G1.7a (n = 1), GII.2 (n = 39) and GII.4 (n = 7). Applying predefined definitions of moderate or severe AGE gave 26 vs. 10 cases due to any norovirus genotype in placebo vs. vaccine groups, a vaccine efficacy (VE) of 61.8% (95.01% CI, 20.8 to 81.6; p = 0.0097). Five vs. one moderate or severe cases due to vaccine GI.1/GII.4 homotypic genotypes in placebo vs. vaccine arms gave a primary endpoint vaccine efficacy of 80.0% (99.99% CI, −1318.1 to 99.7; p = 0.142). Levels of GI.1 and GII.4 HBGA-blocking antibodies were increased in vaccinees and in some placebo AGE cases infected with GII.2, indicating cross-reactivity in the immune responses to different genotypes.InterpretationDespite limited cases of homotypic norovirus AGE meaning the primary endpoint was not fully evaluable, we showed TAK-214 provided statistically significant efficacy against “any moderate/severe norovirus AGE” principally caused by the heterotypic GII.2 genotype, demonstrating induction of cross-genotype protection.     

2006年上海监测点婴幼儿腹泻标本中诺如病毒基因分析

[目的]了解2006年上海监测点婴幼儿病毒性腹泻散发病例中诺如病毒基因型别及核酸变异情况。[方法]应用一步法RT-PCR扩增89份病毒性腹泻标本中诺如病毒核酸,测序后应用基因分析软件包对核酸序列进行分析。[结果]12条核酸序列经测序和比对均属于诺如病毒GII基因组,其中3条核酸测序序列与2006年德国公布的序列同源性相近;其余9条核酸测序序列与2004年中国、2004、2005年日本、2006年荷兰公布的序列同源性相近。[结论]2006年上海地区婴幼儿中存在诺如病毒GII基因组散发病例,并以GII4基因型为主。