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

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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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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Molecular Epidemiology and Genetic Diversity of Norovirus in Young Children in Phnom Penh, Cambodia

Journal of Tropical Medicine ◽

10.1155/2016/2707121 ◽

2016 ◽

Vol 2016 ◽

pp. 1-8 ◽

Cited By ~ 3

Author(s):

Kaewkanya Nakjarung ◽

Ladaporn Bodhidatta ◽

Pimmnapar Neesanant ◽

Paphavee Lertsethtakarn ◽

Orntipa Sethabutr ◽

...

Keyword(s):

Genetic Diversity ◽

Young Children ◽

Real Time ◽

Pediatric Hospital ◽

Rt Pcr ◽

Chain Reaction ◽

Phnom Penh ◽

Stool Samples ◽

Polymerase Chain ◽

Predominant Strain

This study investigated the genetic diversity of noroviruses identified from a previous surveillance study conducted at the National Pediatric Hospital in Phnom Penh, Cambodia, from 2004 to 2006. In the previous study, 926 stool samples were collected from children aged 3–60 months with acute diarrhea (cases) and without diarrhea (controls) with reported 6.7% of cases and 3.2% of controls being positive for norovirus. The initial norovirus diagnostic assay was performed with real-time reverse transcription-polymerase chain reaction (real-time RT PCR) which also distinguished between genogroups I and II (GI and GII). Norovirus infection was most commonly detected in children aged 12–23 months in both cases and controls. Norovirus Genotyping Tool and phylogenetic analysis of partial sequences of the 3′ end of the RNA-dependent RNA Polymerase (RdRp) and the capsid domain region were employed to assign genotypes of the norovirus strains. GII.4 was the most predominant capsid genotype detected at 39.5% followed by GII.6 at 14.9%. The GII.4 Hunter 2004 variant was the predominant strain detected. Six RdRP/capsid recombinants including GII.P7/GII.6, GII.P7/GII.14, GII.P7/GII.20, GII.P12/GII.13, GII.P17/GII.16, and GII.P21/GII.3 were also identified. This study of norovirus infection in young children in Cambodia suggests genetic diversity of norovirus as reported worldwide.

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Molecular epidemiology and genetic diversity of norovirus among hospitalized children with acute gastroenteritis in Tianjin, China, 2018–2020

BMC Infectious Diseases ◽

10.1186/s12879-021-06375-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yulian Fang ◽

Zhaoying Dong ◽

Yan Liu ◽

Wei Wang ◽

Mengzhu Hou ◽

...

Keyword(s):

Genetic Analysis ◽

Acute Gastroenteritis ◽

Age Groups ◽

Molecular Characteristics ◽

Rt Pcr ◽

Predominant Genotype ◽

Epidemiological Analysis ◽

Version 2.0 ◽

Stool Samples ◽

Polymerase Chain

Abstract Background Norovirus (NoV) is a major cause of viral acute gastroenteritis (AGE) in children worldwide. Epidemiological analysis with respect to the virus strains is limited in China. This study aimed to investigate the prevalence, patterns, and molecular characteristics of NoV infection among children with AGE in China. Methods A total 4848 stool samples were collected from children who were admitted with AGE in Tianjin Children’s Hospital from August 2018 to July 2020. NoV was preliminarily detected using real-time reverse transcription polymerase chain reaction (RT-PCR). Partial sequences of the RNA-dependent RNA polymerase (RdRp) and capsid genes of positive samples were amplified by conventional RT-PCR and then sequenced. The NoV genotype was determined by online Norovirus Typing Tool Version 2.0, and phylogenetic analysis was conducted using MEGA 6.0. Results The prevalence of NoV was 26.4% (1280/4848). NoV was detected in all age groups, with the 7–12 months group having the highest detection rate (655/2014, 32.5%). NoV was detected during most part of the year with higher frequency in winter than other seasons. Based on the genetic analysis of RdRp, GII. Pe was the most predominant genotype detected at 70.7% (381/539) followed by GII.P12 at 25.4% (137/539). GII.4 was the most predominant capsid genotype detected at 65.3% (338/518) followed by GII.3 at 26.8% (139/518). Based on the genetic analysis of RdRp and capsid sequences, the strains were clustered into 10 RdRp–capsid genotypes: GII.Pe-GII.4 Sydney 2012 (65.5%), GII.P12-GII.3 (27.2%), GII.P16-GII.2 (1.8%), GII.P12-GII.2 (0.2%), GII.P17-GII.17 (1.1%), GII.Pe-GII.3 (1.8%), GII.Pe-GII.2 (1.1%), GII.Pe-GII.1 (0.4%), GII.16-GII.4 Sydney 2012 (0.7%), and GII.P7-GII.6 (0.2%). The predominant NoV genotypes changed from GII.Pe-GII.4 Sydney 2012 and GII.P12-GII.3 between August 2018 and July 2019 to GII.Pe-GII.4 Sydney 2012 and GII.P16-GII.2 between August 2019 and July 2020. The patients with GII.Pe-GII.4 Sydney 2012 genotype were more likely to suffer from vomiting symptom than those with GII.P12-GII.3. Conclusions NoV is an important pathogen responsible for viral AGE among children in China. GII.Pe-GII.4 Sydney 2012 and GII.P12-GII.3 were major recombinant genotypes. Knowledge of circulating genotypes and seasonal trends is of great importance for disease prevention and surveillance.

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Limited Genetic Variability Among American Isolates of Grapevine virus E from Vitis spp.

Plant Disease ◽

10.1094/pdis-05-15-0556-re ◽

2016 ◽

Vol 100 (1) ◽

pp. 159-163 ◽

Cited By ~ 4

Author(s):

J. Vargas-Asencio ◽

M. Al Rwahnih ◽

A. Rowhani ◽

F. Celebi-Toprak ◽

J. R. Thompson ◽

...

Keyword(s):

Genetic Diversity ◽

New York ◽

Protein Gene ◽

The United States ◽

Nucleic Acid Binding ◽

Grapevine Virus ◽

Rt Pcr ◽

Viral Cdna ◽

Polymerase Chain ◽

Binding Protein Gene

A survey for the presence of Grapevine virus E (GVE, genus Vitivirus, family Betaflexiviridae) in vineyards in New York and California was conducted using macroarray hybridization or reverse-transcription polymerase chain reaction (RT-PCR) assays. In New York, GVE was detected in 10 of 46 vines of Vitis labrusca, one V. riparia, and one Vitis hybrid. All GVE-infected New York vines were coinfected with Grapevine leafroll-associated virus-3. In California, GVE was detected in 8 of 417 vines of V. vinifera. All GVE-infected California vines were also coinfected by one of the leafroll-associated viruses and other vitiviruses. In order to assess the genetic diversity among GVE isolates, a viral cDNA was amplified by RT-PCR, and a 675-nucleotide region that included the 3′ terminus of the coat protein gene, a short intergenic region, and the 5′ terminus of the putative nucleic acid binding protein gene was sequenced. All 20 GVE isolates sequenced in this study were very closely related, with >98% nucleotide identity to the SA94 isolate from South Africa. These findings confirm the presence of GVE in major grape-growing regions of the United States and indicate a very low level of genetic diversity.

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Epidemiology and genetic diversity of human parechoviruses circulating among children hospitalised with acute gastroenteritis in Pune, Western India: a 5-years study

Epidemiology and Infection ◽

10.1017/s095026881700262x ◽

2017 ◽

Vol 146 (1) ◽

pp. 11-18 ◽

Cited By ~ 12

Author(s):

P. R. PATIL ◽

N. N. GANORKAR ◽

V. GOPALKRISHNA

Keyword(s):

Genetic Diversity ◽

Acute Gastroenteritis ◽

Clinical Manifestations ◽

Western India ◽

Vp1 Gene ◽

Rt Pcr ◽

Chain Reaction ◽

Predominant Genotype ◽

Stool Specimens ◽

Polymerase Chain

SUMMARYHuman parechoviruses (HPeVs) are known to cause various clinical manifestations including acute gastroenteritis. Although HPeV infections and their genotypes have been detected in human patients worldwide, no such reports are available from India to ascertain the association of HPeVs in acute gastroenteritis. The present study was conducted to determine the clinical features and genetic diversity of HPeVs detected in children hospitalised for acute gastroenteritis. Stool specimens (n= 979) collected from children aged ⩽5 years hospitalised for acute gastroenteritis in Pune, western India during January 2006–December 2010 were included. HPeV RNA was detected by reverse transcription-polymerase chain reaction (RT-PCR) (5′UTR) followed by genotyping using VP1 gene-based PCR and phylogenetic analysis. HPeV was detected in 13·9% (136/979) of the cases, co-infections with other enteric viruses were found in 43·4%. HPeV was more frequent in children ⩽1 year age with infections reported throughout the year. A total of 102/136 (75%) HPeV strains were genotyped, which comprised 13 different HPeV genotypes. Of these, HPeV1 was the most predominant genotype detected and phylogenetically clustered with the Harris strain which is rarely reported. The study documents circulation of heterogeneous HPeV genotypes. Two variant strains of HPeV4 and ‘RGD absent’ HPeV5 and 6 strains were also detected. This is the first report of HPeV with diversified genotypes identified in acute gastroenteritis patients from India.

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SARS-CoV-2 neutralizing antibodies: Longevity, breadth, and evasion by emerging viral variants

PLoS Medicine ◽

10.1371/journal.pmed.1003656 ◽

2021 ◽

Vol 18 (7) ◽

pp. e1003656

Author(s):

Fiona Tea ◽

Alberto Ospina Stella ◽

Anupriya Aggarwal ◽

David Ross Darley ◽

Deepti Pilli ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Rt Pcr ◽

Breakthrough Infection ◽

Nucleocapsid Proteins ◽

Viral Neutralization ◽

Polymerase Chain ◽

Serial Samples ◽

High Responders ◽

Neutralization Response ◽

Selection Of

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antibody neutralization response and its evasion by emerging viral variants and variant of concern (VOC) are unknown, but critical to understand reinfection risk and breakthrough infection following vaccination. Antibody immunoreactivity against SARS-CoV-2 antigens and Spike variants, inhibition of Spike-driven virus–cell fusion, and infectious SARS-CoV-2 neutralization were characterized in 807 serial samples from 233 reverse transcription polymerase chain reaction (RT-PCR)–confirmed Coronavirus Disease 2019 (COVID-19) individuals with detailed demographics and followed up to 7 months. A broad and sustained polyantigenic immunoreactivity against SARS-CoV-2 Spike, Membrane, and Nucleocapsid proteins, along with high viral neutralization, was associated with COVID-19 severity. A subgroup of “high responders” maintained high neutralizing responses over time, representing ideal convalescent plasma donors. Antibodies generated against SARS-CoV-2 during the first COVID-19 wave had reduced immunoreactivity and neutralization potency to emerging Spike variants and VOC. Accurate monitoring of SARS-CoV-2 antibody responses would be essential for selection of optimal responders and vaccine monitoring and design.

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Persistence of SARS-CoV-2 RNA in Nasopharynx, Blood, Urine and Stool of Patients with COVID 19: A Hospital-based Longitudinal Study

10.21203/rs.3.rs-218423/v1 ◽

2021 ◽

Author(s):

Farahnaz Joukar ◽

Tofigh Yaghubi Kalurazi ◽

Mahmoud Khoshsorour ◽

Sonbol Taromian ◽

Lida Mahfoozi ◽

...

Keyword(s):

Longitudinal Study ◽

Rt Pcr ◽

Chain Reaction ◽

Northern Iran ◽

Virus Persistence ◽

Viral Shedding ◽

Maximum Duration ◽

Hygienic Measures ◽

Stool Samples ◽

Polymerase Chain

Abstract Background: This study was conducted to determine the persistence of SARS-CoV-2 RNA in the nasopharynx, blood, urine and stool of patients with COVID-19.Methods: In this hospital based longitudinal study, 100 confirmed COVID-19 cases were recruited, between March and August 2020 in Guilan province (Northern Iran). Nasopharynx, blood, urine and stool samples were obtained from each patient at the time of hospital admission, discharge, followed by one week after discharge and every 2 weeks until all samples were negative for SARS-CoV-2 RNA by reverse transcription polymerase chain reaction (RT-PCR). Survival analysis was used to identify the duration of virus persistence over time.Results: Positive blood, urine, stool RT-PCR were detected in 24%, 7% and 6% of patient respectively. The median duration of virus persistence in blood, urine and stool were 7 days (95% CI: 6.07–7.93), 6 days (95% CI: 4.16–8.41) and 13 days, 95% CI: 6.96–19.4), respectively. The maximum duration of virus persistent in blood, urine and stool were 17, 11 and 42 days from admission, respectively. Conclusions: According our results, until obtaining definite evidence of the duration of infective viral shedding, prolonged isolation duration at least 25 days from admission to hospital and strict hygienic measures for about one month were recommended.

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Genetic Diversity Among Viruses Associated with Sugarcane Mosaic Disease in Tucumán, Argentina

Phytopathology ◽

10.1094/phyto-99-1-0038 ◽

2009 ◽

Vol 99 (1) ◽

pp. 38-49 ◽

Cited By ~ 19

Author(s):

M. F. Perera ◽

M. P. Filippone ◽

C. J. Ramallo ◽

M. I. Cuenya ◽

M. L. García ◽

...

Keyword(s):

Genetic Diversity ◽

Mosaic Virus ◽

Fragment Length Polymorphism ◽

Rflp Analysis ◽

Mosaic Disease ◽

Rt Pcr ◽

Rflp Profile ◽

Pcr Rflp ◽

Polymerase Chain ◽

Sugarcane Mosaic Disease

Sugarcane leaves with mosaic symptoms were collected in 2006–07 in Tucumán (Argentina) and analyzed by reverse-transcriptase polymerase chain reaction (RT-PCR) restriction fragment length polymorphism (RFLP) and sequencing of a fragment of the Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV) coat protein (CP) genes. SCMV was detected in 96.6% of samples, with 41% showing the RFLP profile consistent with strain E. The remaining samples produced eight different profiles that did not match other known strains. SCMV distribution seemed to be more related to sugarcane genotype than to geographical origin, and sequence analyses of CP genes showed a greater genetic diversity compared with other studies. SrMV was detected in 63.2% of samples and most of these were also infected by SCMV, indicating that, unlike other countries and other Argentinean provinces, where high levels of co-infection are infrequent, co-existence is common in Tucumán. RFLP analysis showed the presence of SrMV strains M (68%) and I (14%), while co-infection between M and H strains was present in 18% of samples. Other SCMV subgroup members and the Sugarcane streak mosaic virus (SCSMV) were not detected. Our results also showed that sequencing is currently the only reliable method to assess SCMV and SrMV genetic diversity, because RT-PCR-RFLP may not be sufficiently discriminating.

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Detection of Anti-Nucleocapsid Antibody in COVID-19 Patients in Bangladesh Is not Correlated with Previous Dengue Infection

Pathogens ◽

10.3390/pathogens10060637 ◽

2021 ◽

Vol 10 (6) ◽

pp. 637

Author(s):

Simon D. Lytton ◽

Mahmuda Yeasmin ◽

Asish Kumar Ghosh ◽

Md. Rakibul Hassan Bulbul ◽

Md. Maruf Ahmed Molla ◽

...

Keyword(s):

Dengue Infection ◽

Antibody Responses ◽

Viral Rna ◽

Structural Protein ◽

Rt Pcr ◽

Chain Reaction ◽

N Protein ◽

Polymerase Chain ◽

Normal Controls ◽

Post Onset

Background: The assessment of antibody responses to severe acute respiratory syndrome coronavirus-2 is potentially confounded by exposures to flaviviruses. The aims of the present research were to determine whether anti-dengue antibodies affect the viral load and the detection of anti-coronavirus nucleocapsid (N)-protein antibodies in coronavirus infectious disease 2019 (COVID-19) in Bangladesh. Methods: Viral RNA was evaluated in swab specimens from 115 COVID-19 patients by real-time reverse transcription polymerase chain reaction (rT-PCR). The anti-N-protein antibodies, anti-dengue virus E-protein antibodies and the dengue non-structural protein-1 were determined in serum from 115 COVID-19 patients, 30 acute dengue fever pre-COVID-19 pandemic and nine normal controls by ELISA. Results: The concentrations of viral RNA in the nasopharyngeal; Ct median (95% CI); 22 (21.9–23.3) was significantly higher than viral RNA concentrations in oropharyngeal swabs; and 29 (27–30.5) p < 0.0001. Viral RNA concentrations were not correlated with-dengue IgG levels. The anti-nucleocapsid antibodies were IgA 27% positive and IgG 35% positive at days 1 to 8 post-onset of COVID-19 symptoms versus IgA 0% and IgG 0% in dengue patients, p < 0.0001. The levels of anti- nucleocapsid IgA or IgG versus the levels of anti-dengue IgM or IgG revealed no significant correlations. Conclusions: Viral RNA and anti-nucleocapsid antibodies were detected in COVID-19 patients from dengue-endemic regions of Bangladesh, independently of the dengue IgG levels.

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ENTEROPATHOGENIC ESCHERICHIA COLI STRAINSFROM DIARRHOEIC STOOLSAMPLES OF CHILDREN BELOW 5 YEARS OF AGE IN DAMATURU, YOBE STATE, NIGERIA

African Journal of Science and Nature ◽

10.46881/ajsn.v8i0.162 ◽

2020 ◽

Vol 8 ◽

pp. 19

Author(s):

Anotu Mopelola Deji-Agboola ◽

Mohammed Ali ◽

Olubunmi Adetokunbo Osinupebi ◽

Stephen Olaosebikan Makanjuola

Keyword(s):

Escherichia Coli ◽

Polymerase Chain Reaction Method ◽

Enteropathogenic Escherichia Coli ◽

Hygiene Practices ◽

Cause Of Deaths ◽

Stool Samples ◽

Polymerase Chain ◽

Susceptibility Tests ◽

Predominant Strain ◽

Infants And Young Children

Enteropathogenic Escherichia coli (EPEC) is an important cause of deaths mostly in infants and young children with diarrhoea worldwide. This study investigated Enteropathogenic Escherichia coli strains in diarrhoeic stool samples of children below 5 years of age in Damaturu, Yobe State, Nigeria. Microscopy, culture and antibiotic susceptibility tests were carried out on stool specimens obtained from children with diarrhoea. All isolated Escherichia coli were investigated for virulence eae and eaf genes of EPEC strains using Polymerase Chain Reaction method. Information on risk factors of diarrhoea was obtained using the questionnaire. Out of 307 children, 154 (50.2%) were male and 153 (49.8%) female, majority 107 (34.9%) were 3 years old. A total of 175 (57.0%) Escherichia coli were isolated, 19 (10.9%) were identified to be enteropathogenic Escherichia coli of these, 17 (89.5%) were atypical (carries eae genes) while only 2 (10.5%) were typical (harbours eaf genes). Multidrug resistance was observed in some of the isolates, the EPEC were resistant to Reflacin (47.4%), Ciprofloxacin (36.8%), Augmentin (36.8%), Septrin (36.8%). The major factor that predispose children to diarrhoea are poor hygiene practices. Escherichia coli was the most prevalent bacterial causing diarrhoea and atypical EPEC is the predominant strain circulating among these children.

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