Epidemiological characteristics and genetic diversity of norovirus infections among outpatient children with diarrhea under 5 years of age in Beijing, China, 2011–2018

Abstract Background Human noroviruses are the leading cause of sporadic cases and outbreaks of viral acute gastroenteritis in all age groups worldwide. Methods Epidemiological data and fecal specimens were collected between January 2011 and December 2018 from 4911 children < 5 years of age with diarrhea in three districts of Beijing. From 2011 to 2013, One-Step Reverse Transcription Polymerase Chain Reaction (RT-PCR) was used to detect noroviruses, and from January 2014 to December 2018, norovirus GI and GII were screened using duplex quantitative real-time RT-PCR (qRT-PCR). One-Step RT-PCR and RT-seminested PCR were performed to amplify the RNA-dependent polymerase and capsid genes of noroviruses in positive sample. Amplified products were sequenced directly; norovirus was typed using the online Norovirus Genotyping Tool v2.0 and phylogenetic analyses were conducted using MEGA-X. Results From 2011 to 2018, noroviruses were detected in 16.5% of specimens from children with diarrhea. The highest prevalence was observed in children aged 12 to 23 months (22.4%, 319/1421), followed by children aged 6 to 11 months (17.6%, 253/1441). The highest prevalence of norovirus infections occurred in autumn followed by winter, spring, and summer. From 2011 to 2018, the most prevalent dual types (genotype and polymerase type) were GII.4 Sydney[P31] (51.6%, 239/463), followed by GII.3[P12] (24.0%, 111/463), GII.4 2006b[P4 2006b] (7.3%, 34/463), GII.2[P16] (5.0%, 23/463), GII.17[P17] (2.6%, 12/463) and GII.6[P7] (2.6%, 12/463). GII.4 2006b[P4 2006b] predominated in 2011 and 2012. GII.4 Sydney[P31] predominated from 2013 to 2018. In total, 15 genotypes, 15 P-types and 19 dual types were detected in this study, reflecting the genetic diversity. Conclusions There were significant epidemiological characteristics and genetic diversity among outpatient children with norovirus infections < 5 years of age in Beijing from 2011 to 2018. These characteristics differ from those of norovirus outbreaks in Beijing. The complete genome sequences of each genotype are needed to better understand norovirus evolutionary mechanisms.

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Genetic Diversity and Epidemiology of Genogroup II Noroviruses in Children with Acute Sporadic Gastroenteritis in Shanghai, China, 2012-2017

10.21203/rs.2.9681/v2 ◽

2019 ◽

Author(s):

Lijuan Lu ◽

Huaqing Zhong ◽

Menghua Xu ◽

Liyun Su ◽

Lingfeng Cao ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Analysis ◽

Acute Gastroenteritis ◽

Dominant Role ◽

Phylogenetic Analyses ◽

Age Groups ◽

Detection Rates ◽

Children Under Five ◽

Under Five ◽

Paediatric Age

Abstract Background Noroviruses (NoVs) are considered an important cause of acute gastroenteritis (AGE) across all age groups, especially in children under five years of age. We investigated the epidemiology of noroviruses in outpatient children from the Children’s Hospital of Fudan University in Shanghai, China. Methods Stool specimens were collected between January 2012 and December 2017 from 1433 children under ﬁve years of age with acute gastroenteritis. All samples were analysed by conventional reverse transcription-polymerase chain reaction (RT-PCR) for genogroup II NoVs amplifying both the RNA-dependent RNA polymerase (RdRp) and partial capsid genes. The Norovirus Genotyping Tool v.2.0 (https://www.rivm.nl/mpf/typingtool/norovirus/) was used for genotyping the strains, and phylogenetic analyses were conducted by MEGA 6.0. Results From 2012 to 2017, GII NoVs were detected in 15.4% (220/1433) of the samples, with the highest detection rate in children aged 7-12 months (19.2%, 143/746). The seasons with the highest prevalence of GII NoVs infection were autumn and winter . Based on genetic analysis of RdRp, GII.Pe (74.5%%, 137/184) was the most predominant RdRp genotype from 2013 to 2017, while GII.P4 played a dominant role in 2012 (55.6%, 21/36). Among the capsid genotypes, the most prevalent NoV genotype from 2012 to 2017 was GII.4 (73.6%, 162/220). On the basis of genetic analysis of RdRp and capsid sequences, the strains were clustered into 19 RdRp/capsid genotypes, and 12 of them were discordant, such as GII.Pe/GII.4-Sydney_2012, GII.P12/GII.3, GII.P7/GII.6, GII.Pe/GII.3, and GII.P16/GII.2. Starting with 2013, GII.Pe/GII.4-Sydney_2012 had completely replaced the pandemic GII.P4-2006b/GII.4-2006b subtype and was detected in children across all age groups. Conclusions The present study shows high detection rates and the genetic diversity of circulating NoV GII genotypes in paediatric AGE samples from Shanghai. The findings emphasize the importance of continuous molecular surveillance of emerging NoV strains.

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Genetic Diversity and Epidemiology of Genogroup II Noroviruses in Children with Acute Sporadic Gastroenteritis in Shanghai, China, 2012-2017

10.21203/rs.2.9681/v3 ◽

2019 ◽

Author(s):

Lijuan Lu ◽

Huaqing Zhong ◽

Menghua Xu ◽

Liyun Su ◽

Lingfeng Cao ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Analysis ◽

Acute Gastroenteritis ◽

Dominant Role ◽

Phylogenetic Analyses ◽

Age Groups ◽

Detection Rates ◽

Children Under Five ◽

Under Five ◽

Paediatric Age

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Assessment of Social Distancing for Controlling COVID-19 in Korea: An Age-Structured Modeling Approach

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph17207474 ◽

2020 ◽

Vol 17 (20) ◽

pp. 7474

Author(s):

Yongin Choi ◽

James Slghee Kim ◽

Heejin Choi ◽

Hyojung Lee ◽

Chang Hyeong Lee

Keyword(s):

Mathematical Model ◽

Age Groups ◽

Epidemiological Data ◽

The Elderly ◽

Model Parameters ◽

Social Distancing ◽

First Case ◽

Age Structured ◽

Epidemiological Characteristics ◽

The Impact

The outbreak of the novel coronavirus disease 2019 (COVID-19) occurred all over the world between 2019 and 2020. The first case of COVID-19 was reported in December 2019 in Wuhan, China. Since then, there have been more than 21 million incidences and 761 thousand casualties worldwide as of 16 August 2020. One of the epidemiological characteristics of COVID-19 is that its symptoms and fatality rates vary with the ages of the infected individuals. This study aims at assessing the impact of social distancing on the reduction of COVID-19 infected cases by constructing a mathematical model and using epidemiological data of incidences in Korea. We developed an age-structured mathematical model for describing the age-dependent dynamics of the spread of COVID-19 in Korea. We estimated the model parameters and computed the reproduction number using the actual epidemiological data reported from 1 February to 15 June 2020. We then divided the data into seven distinct periods depending on the intensity of social distancing implemented by the Korean government. By using a contact matrix to describe the contact patterns between ages, we investigated the potential effect of social distancing under various scenarios. We discovered that when the intensity of social distancing is reduced, the number of COVID-19 cases increases; the number of incidences among the age groups of people 60 and above increases significantly more than that of the age groups below the age of 60. This significant increase among the elderly groups poses a severe threat to public health because the incidence of severe cases and fatality rates of the elderly group are much higher than those of the younger groups. Therefore, it is necessary to maintain strict social distancing rules to reduce infected cases.

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Genetic stability of equine arteritis virus during horizontal and vertical transmission in an outbreak of equine viral arteritis

Journal of General Virology ◽

10.1099/0022-1317-80-8-1949 ◽

1999 ◽

Vol 80 (8) ◽

pp. 1949-1958 ◽

Cited By ~ 47

Author(s):

Udeni B. R. Balasuriya ◽

Jodi F. Hedges ◽

Steven A. Nadler ◽

William H. McCollum ◽

Peter J. Timoney ◽

...

Keyword(s):

Genetic Diversity ◽

Vertical Transmission ◽

Genetic Stability ◽

Phylogenetic Analyses ◽

Equine Arteritis Virus ◽

Rt Pcr ◽

Persistently Infected ◽

Equine Viral Arteritis ◽

N Proteins

An imported carrier stallion (A) from Europe was implicated in causing an extensive outbreak of equine viral arteritis (EVA) on a Warmblood breeding farm in Pennsylvania, USA. Strains of equine arteritis virus (EAV) present in the semen of two carrier stallions (A and G) on the farm were compared to those in tissues of foals born during the outbreak, as well as viruses present in the semen of two other stallions that became persistently infected carriers of EAV following infection during the outbreak. The 2822 bp segment encompassing ORFs 2–7 (nt 9807–12628; which encode the GS, GP3, GP4, GL, M and N proteins, respectively) was directly amplified by RT–PCR from semen samples and foal tissues. Nucleotide and phylogenetic analyses confirmed that virus present in the semen of stallion A initiated the outbreak. The genomes of viruses present in most foal tissues (10/11) and serum from an acutely infected mare collected during the outbreak were identical to that of virus present in the lung of the first foal that died of EVA. Virus in the placenta of one foal differed by one nucleotide (99·9% identity) from the predominant outbreak virus. The relative genetic stability of viruses that circulated during the outbreak contrasts markedly with the heterogeneous virus populations variously present in the semen of persistently infected stallions on the farm. These findings are consistent with the hypothesis that the carrier stallion can be a source of genetic diversity of EAV, and that outbreaks of EVA can be initiated by the horizontal aerosol transmission of specific viral variants that occur in the semen of particular carrier stallions.

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Norovirus Epidemiology and Genetic Diversity in Leipzig, Germany during 2013–2017

Viruses ◽

10.3390/v13101961 ◽

2021 ◽

Vol 13 (10) ◽

pp. 1961

Author(s):

Nora Ennuschat ◽

Sabine Härtel ◽

Corinna Pietsch ◽

Uwe G. Liebert

Keyword(s):

Genetic Diversity ◽

Nucleic Acid ◽

Real Time ◽

Older Patients ◽

Vaccine Development ◽

Age Groups ◽

Rt Pcr ◽

Viral Capsids ◽

Stool Samples ◽

Gastrointestinal Complaints

Globally and in all age groups, noroviruses are a main cause of gastroenteritis. To assess their local epidemiology and genetic diversity, stool samples of 7509 inpatients with gastrointestinal complaints from all age groups were analyzed. After detection of norovirus genogroup I and II RNA by real-time RT-PCR, viral capsids were genotyped by partial nucleic acid sequencing. In the case of GII.2 strains, polymerase genotypes were also assessed. Between October 2013 and September 2017, presence of norovirus RNA was shown in 611 samples (8.1%), of which 610 (99.8%) were typed successfully. Norovirus positivity rate was higher in patients aged below five years (14.8%) than in older patients (5.7%). Among the 611 norovirus positive samples, GII.4 (56.6%) strains prevailed, followed by GII.6 (11.3%), GII.3 (11.0%) and GII.2 (9.5%). The most common genogroup I (GGI) genotype was GI.3 (3.6%). In addition, rare genotypes such as GII.13, GII.14 and GII.26 were detected. Interestingly, GII.3 infections were most common in children under the age of five years. Assessment of polymerase genotypes in GII.2 viruses showed a shift from P2 to P16, with higher diversity in P2 sequences. The varying distribution of norovirus genotypes depending on season, age and setting of infection highlights the importance of frequent genotyping as a basis for vaccine development and needful adjustments.

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Survey and Genetic Diversity of Grapevine Leafroll Associated Virus 2 in Algeria

International Journal of Phytopathology ◽

10.33687/phytopath.004.01.1074 ◽

2015 ◽

Vol 4 (1) ◽

pp. 35-42 ◽

Cited By ~ 1

Author(s):

Arezki Lehad ◽

Ilhem Selmi ◽

Meriem Louanchi ◽

Mouni Aitouada ◽

Naima Mahfoudhi

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analyses ◽

Synonymous Site ◽

Rt Pcr ◽

Synonymous Substitutions ◽

Representative Sequence ◽

Polymerase Chain ◽

Das Elisa ◽

Similarity Plot

Vineyards in western and center regions of Algeria were surveyed for the Grapevine leafroll-associated virus 2 (GLRaV-2). Analyses by DAS-ELISA and Reverse Transcription Polymerase Chain Reaction (RT-PCR) reveal 15, 8% prevalence. The genetic diversity of the GLRaV-2 population was studied by phylogenetic analyses of the HSP70h gene region of seven samples sequenced in this study and other sequences downloaded from GenBank. Results reveal segregation of the GLRav-2 population into six distinct groups. An estimation of the ratio of non-synonymous substitutions per non-synonymous site to synonymous substitutions per synonymous site indicated that HSP70h gene evolve under positive selection. Similarity plot constructed with representative sequence from each group confirmed previous results. All Algerian isolates belong to group PN. As far as we know, this is the first characterization of GLRaV-2 isolates from Algeria.

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Individual-based dengue virus surveillance in Aedes aegypti mosquitoes collected concurrently with suspected patients in Tarlac City, Philippines

10.21203/rs.3.rs-56950/v2 ◽

2020 ◽

Author(s):

Jean Claude Balingit ◽

Thaddeus M. Carvajal ◽

Mariko Saito-Obata ◽

Maribet Gamboa ◽

Amalea Dulcene Nicolasora ◽

...

Keyword(s):

Aedes Aegypti ◽

Dengue Virus ◽

Vector Control ◽

Real Time ◽

Phylogenetic Analyses ◽

Rt Pcr ◽

Pcr Assay ◽

Virus Surveillance ◽

One Step ◽

Mosquito Infection

Abstract Background: Vector control measures are critical in the prevention and reduction of dengue virus (DENV) transmission. In this context, effective vector control is reliant not only on knowledge of mosquito abundance, but also on the timely and accurate detection of mosquito infection. Mosquito-based virus surveillance programs commonly rely on pool-based mosquito testing, but whether individual-based mosquito testing could represent a feasible alternative is not largely studied. Applying an individual-based mosquito testing approach, we conducted a one-month DENV surveillance of adult Aedes aegypti mosquitoes around households of suspected dengue patients during the 2015 dengue peak season in Tarlac City, Philippines to more accurately assess the mosquito infection rate, and to identify the DENV serotypes and genotypes concurrently co-circulating in mosquitoes and patients. Methods: We performed a one-step multiplex real-time RT-PCR assay for the simultaneous detection and serotyping of DENV in patients and in individual female Ae. aegypti mosquito. Additionally, we performed sequencing and phylogenetic analyses to further characterize the detected DENVs in mosquitoes and patients at the genotype level. Results: We collected a total of 583 adult Ae. aegypti mosquitoes, of which we tested 359 female mosquitoes individually for the presence of the DENV. Ten mosquitoes (2.8%) from amongst 359 female mosquitoes were confirmed to be positive for the presence of the DENV. We detected DENV-1, DENV-2, and DENV-4 in the field-collected mosquitoes, which were consistent with the serotypes concurrently infecting patients. Sequencing and phylogenetic analyses of the detected DENVs based on the partial envelope (E) gene revealed three genotypes concurrently present in the sampled mosquitoes and patients during the study period, namely: DENV-1 genotype IV, DENV-2 Cosmopolitan genotype and DENV-4 genotype II. Conclusions: In this study, we demonstrate the utility of a one-step multiplex real-time RT-PCR assay in individual-based DENV surveillance of mosquitoes. Our findings reinforce the importance of detecting and monitoring virus activity in local mosquito populations, which is critical for dengue prevention and control activities.

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Genetic Diversity and Epidemiology of Norovirus in Children with acute sporadic gastroenteritis in Shanghai, China, 2012-2017

10.21203/rs.2.9681/v1 ◽

2019 ◽

Author(s):

Lijuan Lu ◽

Huaqing Zhong ◽

Menghua Xu ◽

Liyun Su ◽

Lingfeng Cao ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Analysis ◽

Acute Gastroenteritis ◽

Dominant Role ◽

Phylogenetic Analyses ◽

Age Groups ◽

Detection Rates ◽

Children Under Five ◽

Under Five ◽

High Detection

Abstract Background Noroviruses are considered the important causes of acute gastroenteritis (AGE) across all age groups especially in children under five years. We investigated the prevalence and molecular epidemiology of norovirus in outpatient children from Children’s Hospital of Fudan University in Shanghai, China. Methods A total of 1433 stool specimens were collected from children under ﬁve years with acute gastroenteritis between January 2012 and December 2017. All the samples were analyzed by conventional reverse transcription-polymerase chain reaction (RT-PCR) for genogroup II targeting both the RNA-dependent RNA polymerase (RdRp) and partial capsid genes. Norovirus Genotyping Tool v.2.0 (https://www.rivm.nl/mpf/typingtool/norovirus/) was used for genotyping strains, and phylogenetic analyses were conducted by MEGA 6.0. Results During 2012 to 2017, NoVs were detected in 15.4% (220/1433) of the samples, with high detection rate in children aged 7-12 months (19.2%, 143/746) and in September (27.7%, 33/119). Based on genetic analysis of RdRp, GII.Pe (74.5%%, 137/184) was the most predominating RdRp genotype from 2013 to 2017 while GII.P4 played a dominant role in 2012 (55.6%, 21/36). The most prevalent NoVs genotype was GII.4 (73.6%, 162/220) during 2012 to 2017 among the capsid genotypes. According to genetic analysis of RdRp and capsid sequences, the strains were clustered into 19 RdRp/capsid genotypes, and 12 of them were discordant RdRp and capsid genotypes, such as GII.Pe/GII.4-Sydney_2012, GII.P12/GII.3, GII.P7/GII.6, GII.Pe/GII.3, GII.P16/GII.2. GII.Pe/GII.4-Sydney_2012 was completely instead of the pandemic of GII.P4-2006b/GII.4-2006b since 2013 and distributed across all age groups in children. Conclusions The present study shows high detection rates and genetic diversity of circulating NoVs genotypes in paediatric AGE samples from Shanghai. The findings emphasize the importance of continuous molecular surveillance of emerging NoVs strains.

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Genetic Diversity of Sapoviruses among Inpatients in Germany, 2008−2018

Viruses ◽

10.3390/v11080726 ◽

2019 ◽

Vol 11 (8) ◽

pp. 726 ◽

Cited By ~ 5

Author(s):

Mann ◽

Pietsch ◽

Liebert

Keyword(s):

Genetic Diversity ◽

Age Groups ◽

Structural Protein ◽

Rt Pcr ◽

Sporadic Cases ◽

Stool Samples ◽

Gastrointestinal Complaints ◽

Polymerase Chain ◽

Infants And Young Children ◽

Selection Of

Sapovirus enteric disease affects people of all ages across the globe, in both sporadic cases and outbreak settings. Sapovirus is seldom assessed in Germany and its epidemiology in the country is essentially unknown. Thus, sapovirus occurrence and genetic diversity were studied by real-time reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing of major viral structural protein (VP1) gene in two different sets of stool samples: 1) a selection of 342 diarrheal stools collected from inpatient children during 2008−2009, and 2) 5555 stool samples collected during 2010–2018 from inpatients of all age groups with gastrointestinal complaints. Results showed year-round circulation of sapoviruses, with peaks during cooler months. In total, 30 samples (8.8%) of the first and 112 samples of the second set of samples (2.0%) were sapovirus positive. Capsid gene sequencing was successful in 134/142 samples (94.4%) and showed circulation of all known human pathogenic genogroups. Genotype GI.1 predominated (31.8%), followed by GII.1 (16.7%), GII.3 (14.5%), GI.2 (13.8%) and GV.1 (12.3%). Additionally, minor circulation of GI.3, GI.6, GII.2, GII.4, GII.6 and GIV.1 was shown. Consequently, sapovirus diagnostics need broadly reactive RT-PCR protocols and should particularly be considered in infants and young children. Further studies from other sampling sites are essential to extend our knowledge on sapovirus epidemiology in Germany.

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Isolation and Characterization of Bovine RVA from Northeast China, 2017–2020

Life ◽

10.3390/life11121389 ◽

2021 ◽

Vol 11 (12) ◽

pp. 1389

Author(s):

Xi Cheng ◽

Wei Wu ◽

Fei Teng ◽

Yue Yan ◽

Guiwei Li ◽

...

Keyword(s):

Genetic Diversity ◽

Amino Acid ◽

Northeast China ◽

Epidemiological Data ◽

Amino Acid Identity ◽

Amino Acid Sequences ◽

Acid Identity ◽

Bovine Rotavirus ◽

Isolation And Characterization ◽

Epidemiological Characteristics

Group A rotaviruses (RVAs) are major enteric pathogens causing infections in calves. To investigate the epidemiological characteristics and genetic diversity of bovine rotavirus (BRV), 233 fecal samples were collected from calves with diarrhea in northeast China. The samples were analyzed for sequences encoding the inner capsid protein VP6 (subgroup) and the outer capsid proteins VP7 and VP4 (G and P type, respectively) using RT-PCR. Ten of the 233 samples (4.3%) were identified as BRV positive and were used for virus isolation and sequence analysis, revealing that all strains analyzed were of the G6P[1] genotype. The isolates exhibited high VP6 sequence identity to the USA cow RVA NCDV strain (>99% amino acid identity) and were further shown to be closely related to Japanese cow RVA BRV101 and Israelian human RVA G6P[1] strains, with >99% amino acid identity to VP7 and VP4 proteins, respectively. Comparative analyses of genome-predicted amino acid sequences between the isolates and the NCDV strains indicated that the antigenicity and infectivity of the strains isolated had changed. In this study, BRV genotypes and the genetic diversity among vaccinated cattle herds were monitored to provide epidemiological data and references for early diagnosis, allowing for early detection of new, potentially pathogenic RVA strains.

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