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Tegegne D, Gelaw A, Zerefaw G, Ferede G, Gelaw B. Prevalence and associated factors of norovirus infections among patients with diarrhea in the Amhara national regional state, Ethiopia. BMC Infect Dis 2024; 24:1053. [PMID: 39333942 PMCID: PMC11428445 DOI: 10.1186/s12879-024-09988-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 09/23/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Noroviruses (NoVs) are the leading cause of diarrheal disease among all age groups worldwide, with an increased burden in developing countries. As there is no surveillance, epidemiological data is limited in Ethiopia. Hence, this study aimed to investigate the prevalence and associated factors of NoV infection among patients with diarrhea in the Amhara National Regional State, Ethiopia. METHODS A prospective health facility-based cross-sectional study was conducted from May 2021 to November 2021. A total of 550 study participants of all age groups with symptoms of diarrhea were proportionately assigned to the four study areas, area with three health facilities. Study participants were systematically sampled in each health facility. A fecal sample from each case was collected. The RNA was extracted and tested for NoV by one-step RT-PCR. Sociodemographic and other variables were gathered using a pre-tested questionnaire. A descriptive analysis was performed. Both binary and multiple logistic regressions were utilized to identify factors associated with NoV infection. Variables with a p-value < 0.05 in the final model were considered statistically significant. RESULTS Five hundred nineteen out of 550 samples were analyzed (94.4% response rate). The overall prevalence of NoV was 8.9% (46/519). The positivity rates were higher among the elderly (33.3%) and under-5 children (12.5%). Both genogroup I and genogroup II (GII) were identified, with GII being the predominant, at 82.6% (38/46). Of all participants, only 20% reported a history of vomiting. Norovirus infection was more prevalent among participants from Debre Tabor (AOR = 4, 95%CI: 1.2-14) and Bahir Dar areas (AOR = 3.6, 95%CI: 1.04-11) compared to Debre Markos. Additionally, older adults (AOR = 7, 95% CI: 2-24) and under-5 children (AOR = 3.5, 95% CI: 2.8-12) were disproportionately affected compared to adults. The previous history of diarrhea (AOR = 3.6, 95% CI: 1.7-7) was a significant factor contributing to NoV infections. Moreover, the odds of NoV infection were higher among individuals with a high frequency of diarrhea (AOR = 15.3, 95%CI: 7.6-43) and vomiting (AOR = 3.5, 95%CI: 1.5-8). CONCLUSIONS The prevalence of NoV was considerably high, with the predominance of NoV-GII. The positivity rate was higher among the extreme age groups and varied across the study areas. To obtain a comprehensive understanding of the virus`s epidemiology and its genetic diversity, further research is warranted.
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Affiliation(s)
- Dessie Tegegne
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
- Department of Medical Laboratory Sciences, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia.
| | - Aschalew Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Girma Zerefaw
- Department of Molecular Biology, Amhara Public Health Institute, Bahir Dar, Ethiopia
| | - Getachew Ferede
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Baye Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Carlson KB, Dilley A, O'Grady T, Johnson JA, Lopman B, Viscidi E. A narrative review of norovirus epidemiology, biology, and challenges to vaccine development. NPJ Vaccines 2024; 9:94. [PMID: 38811605 PMCID: PMC11137017 DOI: 10.1038/s41541-024-00884-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 05/07/2024] [Indexed: 05/31/2024] Open
Abstract
Norovirus is a leading cause of acute gastroenteritis (AGE) globally. AGE resulting from norovirus causes significant morbidity and mortality in countries of all income levels, particularly among young children and older adults. Prevention of norovirus AGE represents a unique challenge as the virus is genetically diverse with multiple genogroups and genotypes cocirculating globally and causing disease in humans. Variants of the GII.4 genotype are typically the most common genotype, and other genotypes cause varying amounts of disease year-to-year, with GII.2, GII.3, and GII.6 most prevalent in recent years. Noroviruses are primarily transmitted via the fecal-oral route and only a very small number of virions are required for infection, which makes outbreaks of norovirus extremely difficult to control when they occur. Settings like long-term care facilities, daycares, and hospitals are at high risk of outbreaks and can have very high attack rates resulting in substantial costs and disease burden. Severe cases of norovirus AGE are most common in vulnerable patient populations, such as infants, the elderly, and immunocompromised individuals, with available treatments limited to rehydration therapies and supportive care. To date, there are no FDA-approved norovirus vaccines; however, several candidates are currently in development. Given the substantial human and economic burden associated with norovirus AGE, a vaccine to prevent morbidity and mortality and protect vulnerable populations could have a significant impact on global public health.
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Affiliation(s)
| | - Anne Dilley
- Epidemiologic Research & Methods, LLC, Atlanta, GA, USA
| | | | - Jordan A Johnson
- Epidemiologic Research & Methods, LLC, Atlanta, GA, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Ben Lopman
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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Tao L, Zhang X, Wang X, Ding J. Using molecular methods to delineate norovirus outbreaks: a systematic review. Arch Virol 2024; 169:16. [PMID: 38172375 DOI: 10.1007/s00705-023-05953-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
Noroviruses are among the major causative agents of human acute gastroenteritis, and the nature of norovirus outbreaks can differ considerably. The number of single-nucleotide polymorphisms (SNPs) between strains is used to assess their relationships. There is currently no universally accepted cutoff value for clustering strains that define an outbreak or linking the individuals involved. This study was conducted to estimate the threshold value of genomic variations among related strains within norovirus outbreaks. We carried out a literature search in the PubMed and Web of Science databases. SNP rates were defined as the number of SNPs/sequence length (bp) × 100%. The Mann-Whitney U-test was used in comparisons of the distribution of SNP rates for different sequence regions, genogroups (GI and GII), transmission routes, and sequencing methods. A total of 25 articles reporting on 108 norovirus outbreaks were included. In 99.1% of the outbreaks, the SNP rates were below 0.50%, and in 89.8%, the SNP rates were under 0.20%. Outbreak strains showed higher SNP rates when the P2 domain was used for sequence analysis (Z = -2.652, p = 0.008) and when an NGS method was used (Z = -3.686, p < 0.001). Outbreaks caused by different norovirus genotypes showed no significant difference in SNP rates. Compared with person-to-person outbreaks, SNP rates were lower in common-source outbreaks, but no significant difference was found when differences in sequencing methods were taken into consideraton. SNP rates under 0.20% and 0.50% could be considered as the rigorous and relaxed threshold, respectively, of strain similarity within a norovirus outbreak. More data are needed to evaluate differences within and between various norovirus outbreaks.
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Affiliation(s)
- Luqiu Tao
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166, Nanjing, Jiangsu, China
| | - Xinyang Zhang
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166, Nanjing, Jiangsu, China
| | - Xuan Wang
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China
| | - Jie Ding
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China.
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166, Nanjing, Jiangsu, China.
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Sun Z, Niu P, Jin M, Zhang R, Gao Q, Wang H, Ma X, Wang J. Genotyping and traceability analysis of norovirus in Yantai between 2017 and 2019. J Med Virol 2023; 95:e29220. [PMID: 37947460 DOI: 10.1002/jmv.29220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
To investigate the diversity and evolution of noroviruses in Yantai in recent years, this study focused on the coat protein regions of norovirus-positive samples with nucleic acid detection (cycle threshold) values below 30 between 2017 and 2019. A total of 81 sequences were obtained for genotyping. Initially, a high-throughput sequencing approach was established to perform the whole-genome sequencing of multiple typical diarrheal strains. Using bioinformatics software such as BEAST, recombinant variant analysis was performed for each genotype of the norovirus strains, and genetic evolutionary analysis was conducted for the dominant strain GII.4, as well as the rare variant GII.21. The results showed that there were multiple genotypes such as GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.6, GII.13, GII.17, GII.21, and GIX.1 in the positive samples of norovirus from 2017 to 2019. GII.4 is characterized by diverse genotypes, with new changes in antigenic epitopes occurring during the course of the epidemic. This may have led to the emergence of a new pandemic. This suggests a need to strengthen surveillance. The results of this study suggest that attention should be paid to the predominant genotypes prevalent in neighboring countries and regions, and the safety supervision of imported food should be strengthened to aid in the prevention and control of related viruses.
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Affiliation(s)
- Zhenlu Sun
- Yantai Center for Disease Control and Prevention, Yantai, Shandong, China
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Peihua Niu
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Miao Jin
- Department of Viral Diarrhea, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruiqing Zhang
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Qiao Gao
- Yantai Center for Disease Control and Prevention, Yantai, Shandong, China
| | - Hongtao Wang
- Yantai Center for Disease Control and Prevention, Yantai, Shandong, China
| | - Xuejun Ma
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Ji Wang
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
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Tohma K, Ushijima H. [Molecular epidemiology and evolution of human noroviruses]. Uirusu 2023; 73:17-32. [PMID: 39343517 DOI: 10.2222/jsv.73.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Noroviruses are the most common viral cause of acute gastroenteritis after the introduction of rotavirus vaccines. Norovirus infection can cause severe symptoms in vulnerable populations including young children and the elderly. Thus, it is still a leading cause of death from diarrhea in children in developing countries. Recent advancement of genomics platforms facilitated understanding of the epidemiology of norovirus, while the whole picture of norovirus diversity is still undetermined. Currently, there are no approved vaccines for norovirus, but state-of-the-art norovirus cultivation systems could elucidate the antigenic diversity of this fast-evolving virus. In this review, we will summarize the historical and latest findings of norovirus epidemiology, diversity, and evolution.
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Affiliation(s)
- Kentaro Tohma
- Division of Viral Products, US Food and Drug Administration, Maryland, Unites States
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
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Cao R, Ma X, Pan M. Molecular characteristics of norovirus in sporadic and outbreak cases of acute gastroenteritis and in sewage in Sichuan, China. Virol J 2022; 19:180. [DOI: 10.1186/s12985-022-01897-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/09/2022] Open
Abstract
Abstract
Background
Norovirus is highly diverse and constant surveillance is essential for the prevention and control of norovirus gastroenteritis.
Methods
From 2015 to 2019, fecal samples were collected from sporadic cases and outbreaks of acute gastroenteritis reported to Sichuan center for disease control and prevention. Sewage samples were collected from a wastewater treatment plant in Sichuan. All samples were tested for norovirus by real-time reverse transcription polymerase chain reaction. Norovirus-positive clinical samples were sequenced by Sanger sequencing. Sewage samples were sequenced by amplicon and virome sequencing.
Results
A total of 1462 fecal samples were collected and 11 different norovirus genotypes were detected. GII.4 Sydney 2012[P31] and GII.3[P12] were the dominant genotypes in sporadic cases whereas GII.2[P16] and GII.17[P17] were the dominant genotypes in outbreaks. GII.3 was predominant in children 0–6 months of age during spring and summer, while GII.4 was predominant in children older than 6 months and in the autumn. The detection rate of GII.17[P17] increased with age. In sewage, 16 genotypes were detected. GII.3, GII.4, GI.1, and GI.2 were the dominant genotypes.
Conclusion
This study demonstrated that multiple norovirus genotypes co-circulate in Sichuan. It is vital to continuously trace the genetic diversity of norovirus to give a future perspective on surveillance needs and guide vaccine design and policy decisions.
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Yu F, Jiang B, Guo X, Hou L, Tian Y, Zhang J, Li Q, Jia L, Yang P, Wang Q, Pang X, Gao Z. Norovirus outbreaks in China, 2000-2018: A systematic review. Rev Med Virol 2022; 32:e2382. [PMID: 35946340 DOI: 10.1002/rmv.2382] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 11/09/2022]
Abstract
To understand epidemiological characteristics of norovirus outbreaks in China from 2000 to 2018 the literature on norovirus outbreaks was identified by searching WANFANG, CNKI, PubMed, and Web of Science databases before 31 December 2018. Statistical analyses were performed using Statistical Product Service Solutions software. RStudio1.4.1717 and ArcGIS trial version were used for plotting bar graphs and maps. A total of 419 norovirus outbreaks were reported in the 394 included articles, which occurred between June 2000 and October 2018, showing an overall increasing trend. The majority of outbreaks occurred in schools (52.28%, 218/417) and kindergartens (55/417, 13.19%). Person-to-person transmission (41.64%, 137/329) was most common, followed by food-borne transmission (75/329, 22.80%) and water-borne transmission (72/329, 21.88%). GII was the most predominant norovirus genogroup, with GII.4, GII.17 and GII.2 being the dominant genotypes in 2007-2013, 2014-2015, 2016-2017, respectively. Increased outbreaks were associated with the prevalence of new variants. Most norovirus outbreaks were reported in the southeast of the country. The number of norovirus outbreaks was positively associated with the per capita gross domestic product and the year-end resident population. Norovirus outbreaks have become an important public health problem in China. It is necessary to establish surveillance in hospitals and nursing homes. Genotyping of noroviruses is important for monitoring the circulating strains and improving the vaccine design, so it should be carried out in more regions.
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Affiliation(s)
- Fan Yu
- China Medical University School of Public Health, Shenyang, China.,Beijing Center for Disease Prevention and Control, Beijing, China
| | - Bo Jiang
- Capital Medical University School of Public Health, Beijing, China
| | - Xinhui Guo
- Fangshan District Center for Disease Prevention and Control, Beijing, China
| | - Liyu Hou
- Capital Medical University School of Public Health, Beijing, China
| | - Yi Tian
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Jiaying Zhang
- Capital Medical University School of Public Health, Beijing, China
| | - Qianqian Li
- Shanghai Institute of Technology, Shanghai, China
| | - Lei Jia
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Peng Yang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Xinghuo Pang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Zhiyong Gao
- China Medical University School of Public Health, Shenyang, China.,Beijing Center for Disease Prevention and Control, Beijing, China
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Emerging norovirus GII.4 Sydney[P31] causing acute gastroenteritis outbreak in children in Japan, during COVID-19, 2021. J Infect Chemother 2022; 28:1347-1351. [PMID: 35661616 DOI: 10.1016/j.jiac.2022.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/19/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022]
Abstract
INTRODUCTION Norovirus (NoV) is the most common agent causing outbreaks and sporadic cases of acute gastroenteritis among all ages, especially children under 5 years old. During the coronavirus disease 2019 (COVID-19) pandemic, NoV infection has decreased drastically in Japan due to school closures and no outbreak related to NoV infection had been reported. METHOD In mid-September 2021, NoV outbreak occurred in kindergarten and nursery schools in Maizuru, Kyoto prefecture, Japan. Twenty-six stool samples collected from patients who were diagnosed of NoV gastroenteritis from the outbreak by an immunochromatographic (IC) kit at a pediatric outpatient clinic in Maizuru city during 3 weeks from September 13 to October 8, 2021 were examined for the presence of NoV GII by reverse transcriptase-polymerase chain reaction (RT-PCR), genome sequencing, and phylogenetic analysis. RESULT All 26 samples were confirmed positive to NoV GII and their genotypes were identified as GII.4 Sydney[P31]. The amino acid substitutions in open reading frame1 (ORF1) and ORF2 genes were found when compared with previously detected sporadic NoV GII.4 Sydney[P31] strains isolated in Japan. The clinical characterization of infected children was described. Most of the children were mild cases and vomiting was the most frequent clinical symptom. CONCLUSION This study reported a recent emergence of NoV GII.4 Sydney[P31] causing acute gastroenteritis outbreak in children in Japan during the COVID-19 pandemic and suggests a need for further monitoring of NoV GII.4 variants.
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He J, Yu Y, Li ZM, Liu ZX, Weng SP, Guo CJ, He JG. Hypoxia triggers the outbreak of infectious spleen and kidney necrosis virus disease through viral hypoxia response elements. Virulence 2022; 13:714-726. [PMID: 35465839 PMCID: PMC9045828 DOI: 10.1080/21505594.2022.2065950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Hypoxia frequently occurs in aquatic environments, especially in aquaculture areas. However, research on the relationship between hypoxic aquatic environments with viral diseases outbreak is limited, and its underlying mechanisms remain elusive. Herein, we demonstrated that hypoxia directly triggers the outbreak of infectious spleen and kidney necrosis virus (ISKNV) disease. Hypoxia or activated hypoxia-inducible factor (HIF) pathway could remarkably increase the levels of viral genomic DNA, titers, and gene expression, indicating that ISKNV can response to hypoxia and HIF pathway. To reveal the mechanism of ISKNV respond to HIF pathway, we identified the viral hypoxia response elements (HREs) in ISKNV genome. Fifteen viral HREs were identified, and four related viral genes responded to the HIF pathway, in which the hre-orf077r promoter remarkably responded to the HIF pathway. The level of orf077r mRNA dramatically increased after the infected cells were treated with dimethyloxalylglycine (DMOG) or the infected cells/fish subjected to hypoxic conditions, and overexpressed orf077r could remarkably increase the ISKNV replication. These finding shows that hypoxic aquatic environments induce the expression of viral genes through the viral HREs to promote ISKNV replication, indicating that viral HREs might be important biomarkers for the evaluation of the sensitivity of aquatic animal viral response to hypoxia stress. Furthermore, the frequencies of viral HREs in 43 species aquatic viral genomes from 16 families were predicted and the results indicate that some aquatic animal viruses, such as Picornavirdea, Dicistronviridae, and Herpesviridae, may have a high risk to outbreak when the aquatic environment encounters hypoxic stress.
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Affiliation(s)
- Jian He
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong, PR China
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, Guangzhou, PR China
| | - Yang Yu
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong, PR China
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, Guangzhou, PR China
| | - Zhi-Min Li
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong, PR China
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, Guangzhou, PR China
| | - Zhi-Xuan Liu
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong, PR China
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, Guangzhou, PR China
| | - Shao-Ping Weng
- Guangdong Province Key Laboratory for Aquatic Economic Animals, and Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, PR China
| | - Chang-Jun Guo
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong, PR China
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, Guangzhou, PR China
- Guangdong Province Key Laboratory for Aquatic Economic Animals, and Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, PR China
| | - Jian-Guo He
- State Key Laboratory for Biocontrol, Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong, PR China
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, Guangzhou, PR China
- Guangdong Province Key Laboratory for Aquatic Economic Animals, and Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, PR China
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Tavakoli M, Tavakkoli-Moghaddam R, Mesbahi R, Ghanavati-Nejad M, Tajally A. Simulation of the COVID-19 patient flow and investigation of the future patient arrival using a time-series prediction model: a real-case study. Med Biol Eng Comput 2022; 60:969-990. [PMID: 35152366 PMCID: PMC8853249 DOI: 10.1007/s11517-022-02525-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/01/2022] [Indexed: 12/12/2022]
Abstract
COVID-19 looks to be the worst pandemic disease in the last decades due to its number of infected people, deaths, and the staggering demand for healthcare services, especially hospitals. The first and most important step is to identify the patient flow through a certain process. For the second step, there is a crucial need for predicting the future patient arrivals for planning especially at the administrative level of a hospital. This study aims to first simulate the patient flow process and then predict the future entry of patients in a hospital as the case study. Also, according to the system status, this study suggests some policies based on different probable scenarios and assesses the outcome of each decision to improve the policies. The simulation model is conducted by Arena.15 software. The seasonal auto-regressive integrated moving average (SARIMA) model is used for patient's arrival prediction within 30 days. Different scenarios are evaluated through a data envelopment analysis (DEA) method. The simulation model runs for predicted patient's arrival for the least efficient scenario and the outputs compare the base run scenario. Results show that the system collapses after 14 days according to the predictions and simulation and the bottleneck of the ICU and CCU departments becomes problematic. Hospitals can use simulation and also prediction tools to avoid the crisis to plan for the future in the pandemic.
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Affiliation(s)
- Mahdieh Tavakoli
- School of Industrial Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | | | - Reza Mesbahi
- School of Industrial Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Mohssen Ghanavati-Nejad
- School of Industrial Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Amirreza Tajally
- School of Industrial Engineering, College of Engineering, University of Tehran, Tehran, Iran
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Ogunsakin RE, Ebenezer O, Ginindza TG. A Bibliometric Analysis of the Literature on Norovirus Disease from 1991-2021. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19052508. [PMID: 35270203 PMCID: PMC8909411 DOI: 10.3390/ijerph19052508] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022]
Abstract
Norovirus (NoV) is one of the oldest recognized diseases and the leading causal pathogen for acute gastroenteritis (AGE) worldwide. Though numerous studies have been reported on NoV disease, limited research has explored the publication trends in this area. As a result, the objective of this work was to fill the void by conducting a bibliometric study in publication trends on NoV studies as well as discovering the hotspots. The Web of Science central assemblage database was hunted for publications from 1991 to 2021 with “norovirus” in the heading. Microsoft Excel 2016, VOSviewer, R Bibliometrix, and Biblioshiny packages were deployed for the statistical analysis of published research articles. A total of 6021 published documents were identified in the Web of Science database for this thirty-year study period (1991–2021). The analyses disclosed that the Journal of Medical Virology was the leading journal in publications on norovirus studies with a total of 215 published articles, the Journal of Virology was the most cited document with 11,185 total citations. The United States of America (USA) has the most significant productivity in norovirus publications and is the leading country with the highest international collaboration. Analysis of top germane authors discovered that X. Jiang (135) and J. Vinje (119) were the two top relevant authors of norovirus publications. The commonly recognized funders were US and EU-based, with the US emerging as a top funder. This study reveals trends in scientific findings and academic collaborations and serves as a leading-edge model to reveal trends in global research in the field of norovirus research. This study points out the progress status and trends on NoV research. It can help researchers in the medical profession obtain a comprehensive understanding of the state of the art of NoV. It also has reference values for the research and application of the NoV visualization methods. Further, the research map on AGE obtained by our analysis is expected to help researchers efficiently and effectively explore the NoV field.
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Affiliation(s)
- Ropo E. Ogunsakin
- Discipline of Public Health Medicine, School of Nursing & Public Health, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa;
- Correspondence:
| | - Oluwakemi Ebenezer
- Department of Chemistry, Faculty of Natural Sciences, Mangosuthu University of Technology, Durban 4000, South Africa;
| | - Themba G. Ginindza
- Discipline of Public Health Medicine, School of Nursing & Public Health, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa;
- Cancer & Infectious Diseases Epidemiology Research Unit (CIDERU), College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
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Lu Y, Zhang Z, Xie H, Su W, Wang H, Wang D, Lu J. The Rise in Norovirus-Related Acute Gastroenteritis During the Fight Against the COVID-19 Pandemic in Southern China. Front Public Health 2022; 9:785373. [PMID: 35087785 PMCID: PMC8787315 DOI: 10.3389/fpubh.2021.785373] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/06/2021] [Indexed: 12/22/2022] Open
Abstract
Background: There has been a significant decline in the morbidity of almost all infectious diseases during the COVID-19 pandemic. However, while the incidence of norovirus-related acute gastroenteritis declined in Guangzhou, China during the initial period of the pandemic, incidence increased significantly once the new school year began in September 2020. Methods: Norovirus-related acute gastroenteritis clusters and outbreaks were assessed in Guangzhou from 2015 to 2020. Medians and interquartile ranges were compared between groups using the Mann–Whitney U-test, and attack rates were calculated. Results: While 78,579 cases of infectious diarrhea were reported from 2015 to 2019, with an average of 15,716 cases per year, only 12,065 cases of infectious diarrhea were reported in 2020. The numbers of sporadic cases and outbreaks reported from January to August 2020 were lower than the average numbers reported during the same time period each year from 2015 to 2019 but began to increase in September 2020. The number of cases in each reported cluster ranged from 10 to 70 in 2020, with a total of 1,280 cases and an average attack rate of 5.85%. The median number of reported cases, the cumulative number of cases, and the attack rate were higher than the average number reported each year from 2015 to 2019. The intervention time in 2020 was also higher than the average intervention time reported during 2015–2019. The main norovirus genotypes circulating in Guangzhou during 2015–2020 included genogroup 2 type 2 (GII.2) (n = 79, 26.69%), GII.17 (n = 36, 12.16%), GII.3 (n = 27, 9.12%), GII.6 (n = 8, 2.7%), GII.4 Sydney_2012 (n = 7, 2.36%), and GII.4 (n = 6, 2.03%). Conclusions: Our findings illustrate the importance of maintaining epidemiological surveillance for viral gastroenteritis during the COVID-19 pandemic. Local disease prevention and control institutions need to devote sufficient human resources to control norovirus clusters.
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Affiliation(s)
- Ying Lu
- Department for Infectious Diseases Control and Prevention, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Zhoubin Zhang
- Director's Office, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Huaping Xie
- Department of Virology and Immunology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Wenzhe Su
- Department of Virology and Immunology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Hui Wang
- Department for Infectious Diseases Control and Prevention, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Dahu Wang
- Department for Infectious Diseases Control and Prevention, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Jianyun Lu
- Department for Infectious Diseases Control and Prevention, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
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13
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Calderwood LE, Wikswo ME, Mattison CP, Kambhampati AK, Balachandran N, Vinjé J, Barclay L, Hall AJ, Parashar U, Mirza SA. Norovirus Outbreaks in Long-term Care Facilities in the United States, 2009-2018: A Decade of Surveillance. Clin Infect Dis 2022; 74:113-119. [PMID: 34523674 PMCID: PMC8978331 DOI: 10.1093/cid/ciab808] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND In the United States, norovirus is the leading cause of healthcare-associated gastroenteritis outbreaks. To inform prevention efforts, we describe the epidemiology of norovirus outbreaks in long-term care facilities (LTCFs). METHODS The Centers for Disease Control and Prevention (CDC) collect epidemiologic and laboratory data on norovirus outbreaks from US health departments through the National Outbreak Reporting System (NORS) and CaliciNet. Reports from both systems were merged, and norovirus outbreaks in nursing homes, assisted living, and other LTCFs occurring in 2009-2018 were analyzed. Data from the Centers for Medicare and Medicaid Services and the National Center for Health Statistics were used to estimate state LTCF counts. RESULTS During 2009-2018, 50 states, Washington D.C., and Puerto Rico reported 13 092 norovirus outbreaks and 416 284 outbreak-associated cases in LTCFs. Participation in NORS and CaliciNet increased from 2009 to 2014 and median reporting of LTCF norovirus outbreaks stabilized at 4.1 outbreaks per 100 LTCFs (interquartile range [IQR]: 1.0-7.1) annually since 2014. Most outbreaks were spread via person-to-person transmission (90.4%), and 75% occurred during December-March. Genogroup was reported for 7292 outbreaks with 862 (11.8%) positive for GI and 6370 (87.3%) for GII. Among 4425 GII outbreaks with typing data, 3618 (81.8%) were GII.4. LTCF residents had higher attack rates than staff (median 29.0% vs 10.9%; P < .001). For every 1000 cases, there were 21.6 hospitalizations and 2.3 deaths. CONCLUSIONS LTCFs have a high burden of norovirus outbreaks. Most LTCF norovirus outbreaks occurred during winter months and were spread person-to-person. Outbreak surveillance can inform development of interventions for this vulnerable population, such as vaccines targeting GII.4 norovirus strains.
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Affiliation(s)
- Laura E. Calderwood
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA;,Cherokee Nation Assurance, Arlington, Virginia, USA
| | - Mary E. Wikswo
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Claire P. Mattison
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA;,Cherokee Nation Assurance, Arlington, Virginia, USA
| | - Anita K. Kambhampati
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Neha Balachandran
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA;,Cherokee Nation Assurance, Arlington, Virginia, USA
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Leslie Barclay
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Aron J. Hall
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Umesh Parashar
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sara A. Mirza
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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14
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Sreeramula S, Rahardjo D. Estimating COVID-19 R t in Real-time: An Indonesia health policy perspective. MACHINE LEARNING WITH APPLICATIONS 2021; 6:100136. [PMID: 34939041 PMCID: PMC8378038 DOI: 10.1016/j.mlwa.2021.100136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 02/01/2023] Open
Abstract
COVID-19 (SARS COV2 n-corona virus) is the newfangled virus of the coronavirus family. COVID-19 can cause serious illness with symptoms of fever, cold, cough, and respiratory blockage. COVID-19 is a contagious virus, which originated in Wuhan, China. After one month, WHO declared it as a Pandemic due to its rapid spreading. Presently, Indonesia is also facing a hard time controlling the spread. Hence, it is essential to understand the spread rate in Indonesia and to analyze the strategies to minimize the virus spread. The proposed study can be used to assess variations in virus spread both nationally, and sub-nationally. This allows public health officials and policy-makers to track the progress of the outbreak in near real-time using an epidemiologically valid measure.
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Affiliation(s)
| | - Deny Rahardjo
- Strategic management and innovation lecturer and IT practitioner, Sinarmas Group, Jakarta, Indonesia
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15
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Harrison CJ, Hassan F, Lee B, Boom J, Sahni LC, Johnson C, Dunn J, Payne DC, Wikswo ME, Parashar U, Selvarangan R. Multiplex PCR Pathogen Detection in Acute Gastroenteritis Among Hospitalized US Children Compared With Healthy Controls During 2011-2016 in the Post-Rotavirus Vaccine Era. Open Forum Infect Dis 2021; 8:ofab592. [PMID: 34988246 PMCID: PMC8694200 DOI: 10.1093/ofid/ofab592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/18/2021] [Indexed: 12/02/2022] Open
Abstract
Background Despite vaccine-induced decreases in US rotavirus (RV) disease, acute gastroenteritis (AGE) remains relatively common. We evaluated AGE pathogen distribution in hospitalized US children in the post–RV vaccine era. Methods From December 2011 to June 2016, the New Vaccine Surveillance Network (NVSN) conducted prospective, active, population-based surveillance in hospitalized children with AGE. We tested stools from 2 NVSN sites (Kansas City, Houston) with Luminex x-TAG Gastrointestinal Pathogen Panels (Luminex GPP) and analyzed selected signs and symptoms. Results For 660 pediatric AGE inpatients and 624 age-matched healthy controls (HCs), overall organism detection was 51.2% and 20.6%, respectively (P < .001). Among AGE subjects, GPP polymerase chain reaction detected >1 virus in 39% and >1 bacterium in 14% of specimens. Detection frequencies for AGE subjects vs HCs were norovirus (NoV) 18.5% vs 6.6%, RV 16.1% vs 9.8%, adenovirus 7.7% vs 1.4%, Shigella 4.8% vs 1.0%, Salmonella 3.1% vs 0.1%, and Clostridioides difficile in ≥2-year-olds 4.4% vs 2.4%. More co-detections occurred among AGE patients (37/660, 5.6%) than HCs (14/624, 2.2%; P = .0024). Per logistic regression analysis, ill contacts increased risk for NoV, RV, and Shigella (P < .001). More vomiting episodes occurred with NoV and RV, and more diarrheal episodes with Shigella and Salmonella. Modified Vesikari scores were highest for Shigella and lowest for C. difficile. Conclusions NoV detection was most frequent; however, RV remained important in hospitalized AGE in the post–RV vaccine era. Continued active surveillance is important to document ongoing vaccine effects, pathogen emergence, and baseline disease burden for new vaccines.
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Affiliation(s)
- Christopher J Harrison
- Children's Mercy Kansas City and University of Missouri Kansas City-School of Medicine, Missouri, USA
| | - Ferdaus Hassan
- Children's Mercy Kansas City and University of Missouri Kansas City-School of Medicine, Missouri, USA
| | - Brian Lee
- Children's Mercy Kansas City and University of Missouri Kansas City-School of Medicine, Missouri, USA
| | - Julie Boom
- Texas Children's Hospital, Houston, Texas, USA
| | | | | | - James Dunn
- Texas Children's Hospital, Houston, Texas, USA
| | - Daniel C Payne
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mary E Wikswo
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Umesh Parashar
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City and University of Missouri-Kansas City, School of Medicine, Kansas City, Missouri, USA
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16
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Haddadin Z, Batarseh E, Hamdan L, Stewart LS, Piya B, Rahman H, Spieker AJ, Chappell J, Wikswo ME, Dunn JR, Payne DC, Vinjé J, Hall AJ, Halasa N. Characteristics of GII.4 Norovirus Versus Other Genotypes in Sporadic Pediatric Infections in Davidson County, Tennessee, USA. Clin Infect Dis 2021; 73:e1525-e1531. [PMID: 32667045 PMCID: PMC8492161 DOI: 10.1093/cid/ciaa1001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/10/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Norovirus is a leading cause of epidemic acute gastroenteritis (AGE), with most outbreaks occurring during winter. The majority of outbreaks are caused by GII.4 noroviruses; however, data to support whether this is true for sporadic medically attended AGE are limited. Therefore, we sought to compare the clinical characteristics and seasonality of GII.4 vs non-GII.4 viruses. METHODS Children aged 15 days -17 years with AGE symptoms were recruited from the outpatient, emergency department, and inpatient settings at Vanderbilt Children's Hospital, Davidson County, Nashville, Tennessee, from December 2012 -November 2015. Stool specimens were tested using qRT-PCR for GI and GII noroviruses and subsequently genotyped by sequencing a partial region of the capsid gene. RESULTS A total of 3705 patients were enrolled, and stool specimens were collected and tested from 2885 (78%) enrollees. Overall, 636 (22%) samples were norovirus-positive, of which 567 (89%) were GII. Of the 460 (81%) genotyped GII-positive samples, 233 (51%) were typed as GII.4 and 227 (49%) as non-GII.4. Compared with children with non-GII.4 infections, children with GII.4 infections were younger, more likely to have diarrhea, and more likely to receive oral rehydration fluids. Norovirus was detected year-round and peaked during winter. CONCLUSIONS Approximately 40% of sporadic pediatric norovirus AGE cases were caused by GII.4 norovirus. Children infected with GII.4 had more severe symptoms that required more medical care. Seasonal variations were noticed among different genotypes. These data highlight the importance of continuous norovirus surveillance and provide important information on which strains pediatric norovirus vaccines should protect against.
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Affiliation(s)
- Zaid Haddadin
- Department of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Einas Batarseh
- Department of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lubna Hamdan
- Department of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Laura S Stewart
- Department of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Bhinnata Piya
- Department of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Herdi Rahman
- Department of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrew J Spieker
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James Chappell
- Department of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mary E Wikswo
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - John R Dunn
- Tennessee Department of Health, Nashville, Tennessee, USA
| | - Daniel C Payne
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jan Vinjé
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Aron J Hall
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Natasha Halasa
- Department of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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17
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Brima Y, Atemkeng M, Tankio Djiokap S, Ebiele J, Tchakounté F. Transfer Learning for the Detection and Diagnosis of Types of Pneumonia including Pneumonia Induced by COVID-19 from Chest X-ray Images. Diagnostics (Basel) 2021; 11:1480. [PMID: 34441414 PMCID: PMC8394302 DOI: 10.3390/diagnostics11081480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 12/23/2022] Open
Abstract
Accurate early diagnosis of COVID-19 viral pneumonia, primarily in asymptomatic people, is essential to reduce the spread of the disease, the burden on healthcare capacity, and the overall death rate. It is essential to design affordable and accessible solutions to distinguish pneumonia caused by COVID-19 from other types of pneumonia. In this work, we propose a reliable approach based on deep transfer learning that requires few computations and converges faster. Experimental results demonstrate that our proposed framework for transfer learning is a potential and effective approach to detect and diagnose types of pneumonia from chest X-ray images with a test accuracy of 94.0%.
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Affiliation(s)
- Yusuf Brima
- African Institute for Mathematical Sciences (AIMS), Kigali P.O. Box 7150, Rwanda;
| | - Marcellin Atemkeng
- Department of Mathematics, Rhodes University, Grahamstown 6140, South Africa
| | - Stive Tankio Djiokap
- Department of Arts, Technology and Heritage, Institute of Fine Arts, University of Dschang, Foumban P.O. Box 31, Cameroon;
| | - Jaures Ebiele
- African Institute for Mathematical Sciences (AIMS), Kigali P.O. Box 7150, Rwanda;
| | - Franklin Tchakounté
- Department of Mathematics and Computer Science, Faculty of Science, University of Ngaoundéré, Ngaoundéré P.O. Box 454, Cameroon;
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18
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Zhang Z, Liu D, Li S, Zhang Z, Hou J, Wang D, Wu Q, Jiang Y, Tian Z. Imported human norovirus in travelers, Shanghai port, China 2018: An epidemiological and whole genome sequencing study. Travel Med Infect Dis 2021; 43:102140. [PMID: 34271206 DOI: 10.1016/j.tmaid.2021.102140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/01/2021] [Accepted: 07/08/2021] [Indexed: 01/04/2023]
Abstract
BACKGROUND Global mobility of the population has accelerated spread of the Human Norovirus (HuNoV), with long-distance travel in enclosed spaces increasing the opportunity for viral outbreaks. However, surveillance of HuNoV transmission is still lacking, especially in cross-border transportation. METHOD From 533 self-reported patients, 83 swab samples (15.6%) tested positive for HuNoV by RT-qPCR. Positive samples were sequenced using next-generation sequencing (NGS). Epidemiological investigation and whole genome analysis were then conducted. RESULTS Most cases occurred in February and March, with large outbreaks involving more than 34 people. A total of 74 HuNoV sequences that could be genotyped were obtained, with near-complete genomes (>7 kb) accounting for most sequences (57/74). A total of 19 different genotypes of viral whole genome sequences were included. The first whole genome sequence of GII.9[P7] was obtained. Rarely reported genotypes including GI.3[P10], GI.3[P13], GII.7[P7], GII.8[P8], and GIX.1[GII.P15] were sequenced and assembled successfully. Four possible sources of virus outbreaks in China were traced. Beyond HuNoV, whole genome sequences of food-borne viruses including Salivirus, Kobuvirus, and Enterovirus were obtained in further assembly. CONCLUSIONS Surveillance of the etiology and epidemiology of HuNoV global spread through travelers will improve pre-travel health advice, empirical treatment, and estimates of vaccine-preventable diseases.
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Affiliation(s)
- Zilong Zhang
- Shanghai International Travel Healthcare Center, Shanghai Customs District PR China, Shanghai, 200335, China
| | - Danlei Liu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai Customs District PR China, Shanghai, 200335, China
| | - Zilei Zhang
- Inspection and Quarantine Technology Communication Department, Shanghai Customs College, Shanghai, China
| | - Jian Hou
- Shanghai International Travel Healthcare Center, Shanghai Customs District PR China, Shanghai, 200335, China
| | - Dapeng Wang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qingping Wu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Yuan Jiang
- Shanghai International Travel Healthcare Center, Shanghai Customs District PR China, Shanghai, 200335, China.
| | - Zhen'gan Tian
- Shanghai International Travel Healthcare Center, Shanghai Customs District PR China, Shanghai, 200335, China.
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19
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Cannon JL, Bonifacio J, Bucardo F, Buesa J, Bruggink L, Chan MCW, Fumian TM, Giri S, Gonzalez MD, Hewitt J, Lin JH, Mans J, Muñoz C, Pan CY, Pang XL, Pietsch C, Rahman M, Sakon N, Selvarangan R, Browne H, Barclay L, Vinjé J. Global Trends in Norovirus Genotype Distribution among Children with Acute Gastroenteritis. Emerg Infect Dis 2021; 27:1438-1445. [PMID: 33900173 PMCID: PMC8084493 DOI: 10.3201/eid2705.204756] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Noroviruses are a leading cause of acute gastroenteritis (AGE) among adults and children worldwide. NoroSurv is a global network for norovirus strain surveillance among children <5 years of age with AGE. Participants in 16 countries across 6 continents used standardized protocols for dual typing (genotype and polymerase type) and uploaded 1,325 dual-typed sequences to the NoroSurv web portal during 2016-2020. More than 50% of submitted sequences were GII.4 Sydney[P16] or GII.4 Sydney[P31] strains. Other common strains included GII.2[P16], GII.3[P12], GII.6[P7], and GI.3[P3] viruses. In total, 22 genotypes and 36 dual types, including GII.3 and GII.20 viruses with rarely reported polymerase types, were detected, reflecting high strain diversity. Surveillance data captured in NoroSurv enables the monitoring of trends in norovirus strains associated childhood AGE throughout the world on a near real-time basis.
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20
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Burke RM, Mattison C, Pindyck T, Dahl RM, Rudd J, Bi D, Curns AT, Parashar U, Hall AJ. Burden of Norovirus in the United States, as Estimated Based on Administrative Data: Updates for Medically Attended Illness and Mortality, 2001-2015. Clin Infect Dis 2021; 73:e1-e8. [PMID: 32291450 PMCID: PMC8112883 DOI: 10.1093/cid/ciaa438] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/13/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Up-to-date estimates of the burden of norovirus, a leading cause of acute gastroenteritis (AGE) in the United States, are needed to assess the potential value of norovirus vaccines in development. We aimed to estimate the rates, annual counts, and healthcare charges of norovirus-associated ambulatory clinic encounters, emergency department (ED) visits, hospitalizations, and deaths in the United States. METHODS We analyzed administrative data on AGE outcomes from 1 July 2001 through 30 June 2015. Data were sourced from IBM MarketScan Commercial and Medicare Supplemental Databases (ambulatory clinic and ED visits), the Healthcare Utilization Project National Inpatient Sample (hospitalizations), and the National Center for Health Statistics multiple-cause-of-mortality data (deaths). Outcome data (ambulatory clinic and ED visits, hospitalizations, or deaths) were summarized by month, age group, and setting. Healthcare charges were estimated based on insurance claims. Monthly counts of cause-unspecified gastroenteritis-associated outcomes were modeled as functions of cause-specified outcomes, and model residuals were analyzed to estimate norovirus-associated outcomes. Healthcare charges were estimated by applying average charges per cause-unspecified gastroenteritis encounter to the estimated number of norovirus encounters. RESULTS We estimate 900 deaths (95% confidence interval [CI], 650-1100), 109 000 hospitalizations (95% CI, 80 000-145 000), 465 000 ED visits (95% CI, 348 000-610 000), and 2.3 million ambulatory clinic encounters (95% CI, 1.7-2.9 million) annually due to norovirus, with an associated $430-$740 million in healthcare charges. CONCLUSIONS Norovirus causes a substantial health burden in the United States each year, and an effective vaccine could have important public health impact.
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Affiliation(s)
- Rachel M. Burke
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Claire Mattison
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Talia Pindyck
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rebecca M. Dahl
- Maximus Federal, contracting agency to the Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jessica Rudd
- Maximus Federal, contracting agency to the Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daoling Bi
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Aaron T Curns
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Umesh Parashar
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Aron J. Hall
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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21
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Steele MK, Wikswo ME, Hall AJ, Koelle K, Handel A, Levy K, Waller LA, Lopman BA. Characterizing Norovirus Transmission from Outbreak Data, United States. Emerg Infect Dis 2021; 26:1818-1825. [PMID: 32687043 PMCID: PMC7392428 DOI: 10.3201/eid2608.191537] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Norovirus is the leading cause of acute gastroenteritis outbreaks in the United States. We estimated the basic (R0) and effective (Re) reproduction numbers for 7,094 norovirus outbreaks reported to the National Outbreak Reporting System (NORS) during 2009–2017 and used regression models to assess whether transmission varied by outbreak setting. The median R0 was 2.75 (interquartile range [IQR] 2.38–3.65), and median Re was 1.29 (IQR 1.12–1.74). Long-term care and assisted living facilities had an R0 of 3.35 (95% CI 3.26–3.45), but R0 did not differ substantially for outbreaks in other settings, except for outbreaks in schools, colleges, and universities, which had an R0 of 2.92 (95% CI 2.82–3.03). Seasonally, R0 was lowest (3.11 [95% CI 2.97–3.25]) in summer and peaked in fall and winter. Overall, we saw little variability in transmission across different outbreaks settings in the United States.
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22
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Reyes Y, González F, Gutierrez L, Blandon P, Centeno E, Zepeda O, Toval-Ruíz C, Lindesmith LC, Baric RS, Vielot N, Diez-Valcarce M, Vinjé J, Svensson L, Becker-Dreps S, Nordgren J, Bucardo F. Secretor status strongly influences the incidence of symptomatic norovirus infection in a genotype-dependent manner in a Nicaraguan birth cohort. J Infect Dis 2021; 225:105-115. [PMID: 34129046 DOI: 10.1093/infdis/jiab316] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The role of histo-blood group on the burden and severity of norovirus gastroenteritis in young infants has not been well documented. METHODS Norovirus gastroenteritis was assessed in 443 Nicaraguan children followed from birth until 3 years of age. Stool samples were tested for norovirus by RT-qPCR and histo-blood group antigens (HBGA) were determined by phenotyping of saliva and blood. Hazards ratios (95% CI) and predictors of norovirus AGE outcome stratified by HBGA were estimated using Cox proportional hazards models. RESULTS Of 1,353 AGE episodes experienced by children, 229 (17%) tested positive for norovirus with an overall incidence of 21.9/100 child-years. Secretor children were infected as early as 2 months old and had a higher incidence of norovirus GII compared to non-secretor children (15.4 vs 4.1/100 child-years, P = 0.006). Furthermore, all GII.4 AGE episodes occurred in secretor children. Children infected with GI (adjusted OR=0.09, 95% CI 0.02-0.33) or non-GII.4 viruses (adjusted OR=0.2, 95% CI: 0.07-0.6) were less likely to have severe AGE compared to GII.4 infected children. CONCLUSION Secretor status in children strongly influences the incidence of symptomatic norovirus infection in a genogroup or genotype-dependent manner and provides evidence that clinical severity in children depends on norovirus genotypes.
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Affiliation(s)
- Yaoska Reyes
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua - León, León, Nicaragua.,Division of Molecular Medicine and Virology, Linköping University, Linköping, Sweden
| | - Fredman González
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Lester Gutierrez
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Patricia Blandon
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Edwing Centeno
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Omar Zepeda
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Christian Toval-Ruíz
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Lisa C Lindesmith
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nadja Vielot
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Marta Diez-Valcarce
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA, United States of America.,Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Jan Vinjé
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA, United States of America
| | - Lennart Svensson
- Division of Molecular Medicine and Virology, Linköping University, Linköping, Sweden.,Division of Medicine, Karolinska Institute, Sweden
| | - Sylvia Becker-Dreps
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Johan Nordgren
- Division of Molecular Medicine and Virology, Linköping University, Linköping, Sweden
| | - Filemón Bucardo
- Department of Microbiology and Parasitology, National Autonomous University of Nicaragua - León, León, Nicaragua
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Du J, Gu Q, Liu Y, Li Q, Guo T, Liu Y. The endemic GII.4 norovirus-like-particle induced-antibody lacks of cross-reactivity against the epidemic GII.17 strain. J Med Virol 2021; 93:3974-3979. [PMID: 32869863 PMCID: PMC8246737 DOI: 10.1002/jmv.26474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/02/2020] [Accepted: 08/20/2020] [Indexed: 12/26/2022]
Abstract
Norovirus-like particle (VLP) vaccine is promising against human norovirus infection. Unfortunately, genetic diversity of norovirus hindered the development of this vaccine. In this study, the immunogenicity of norovirus VLPs induced by the endemic GII.4 and the epidemic GII.17 genotypes, and the cross-reactivity between them as well as GI.1 and GII.3 VLPs were evaluated in mice by using serum IgG and histo-blood group antigen (HBGA) blocking antibodies as index. Results showed well immunogenicity of both GII.4 and GII.17 VLPs in mice. Serum IgG GMT (Geometric Mean Titer) were 3.63 (GII.4) and 3.88 (GII.17) respectively, and sustained to the 15th week. The HBGA blocking antibodies were 130 (GII.4) and 360 (GII.17) respectively at the end of the 4th week. Additionally, there was a dramatically statistical difference found in the cross-reactivity within genogroup (GII.3, GII.4 and GII.17) (p < .001), and also showed similar difference between genogroups (GI.1 vs. GII.3, GII.4 and GII.17) (p < .001). Summarized the pPICZa pichi pichia expression system showed a potential to be the alternative for expression of norovirus VLPs in secretion form, and the little cross-reactivity found between the endemic strain and the epidemic strain provides an evident for the consideration of selecting candidates of norovirus vaccine strains.
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Affiliation(s)
- Jialiang Du
- Division of Enteric Viral VaccinesNational Institutes for Food and Drug ControlBeijingChina
| | - Qiong Gu
- Division of Enteric Viral VaccinesNational Institutes for Food and Drug ControlBeijingChina
- National Vaccine and Serum InstituteBeijingChina
| | - Yan Liu
- Division of Enteric Viral VaccinesNational Institutes for Food and Drug ControlBeijingChina
| | - Qiming Li
- National Vaccine and Serum InstituteBeijingChina
| | - Tai Guo
- Division of Enteric Viral VaccinesNational Institutes for Food and Drug ControlBeijingChina
| | - Yueyue Liu
- Division of Enteric Viral VaccinesNational Institutes for Food and Drug ControlBeijingChina
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24
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Fu J, Ai J, Bao C, Zhang J, Wu Q, Zhu L, Hu J, Xing Z. Evolution of the GII.3[P12] Norovirus from 2010 to 2019 in Jiangsu, China. Gut Pathog 2021; 13:34. [PMID: 34039425 PMCID: PMC8149921 DOI: 10.1186/s13099-021-00430-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/12/2021] [Indexed: 12/28/2022] Open
Abstract
Objectives Norovirus genotype GII.3[P12] strains have been an important pathogen for sporadic gastroenteritis infection. In previous studies of GII.3[P12], the number of specimens and time span are relatively small, which is difficult to truly reflect the infection and evolution of this type of norovirus. Here we report a molecular epidemiological study of the NoVs prevalent in Jiangsu between 2010 and 2019 to investigate the evolution of the GII.3[P12] strains in China. Methods In this study 60 GII.3[P12] norovirus strains were sequenced and analyzed for evolution, recombination, and selection pressure using bioanalysis software. Results The GII.3[P12] strains were continuously detected during the study period, which showed a high constituent ratio in males, in winter and among children aged 0–11 months, respectively. A time-scaled evolutionary tree showed that both GII.P12 RdRp and GII.3 VP1 sequences were grouped into three major clusters (Cluster I–III). Most GII.3[P12] strains were mainly located in sub-cluster (SC) II of Cluster III. A SimPlot analysis identified GII.3[P12] strain to be as an ORF1-intragenic recombinant of GII.4[P12] and GII.3[P21]. The RdRp genes of the GII.3[P12] showed a higher mean substitution rate than those of all GII.P12, while the VP1 genes of the GII.3[P12] showed a lower mean substitution rate than those of all GII.3. Alignment of the GII.3 capsid sequences revealed that three HBGA binding sites of all known GII.3 strains remained conserved, while several amino acid mutations in the predicted antibody binding sites were detected. The mutation at 385 was within predicted antibody binding regions, close to host attachment factor binding sites. Positive and negative selection sites were estimated. Two common positively selected sites (sites 385 and 406) were located on the surface of the protruding domain. Moreover, an amino acid substitution (aa204) was estimated to be near the active site of the RdRp protein. Conclusions We conducted a comprehensive analysis on the epidemic and evolution of GII.3[P12] noroviruses and the results suggested that evolution was possibly driven by intergenic recombination and mutations in some key amino acid sites. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-021-00430-8.
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Affiliation(s)
- Jianguang Fu
- Medical School and the Jiangsu Provincial Key Laboratory of Medicine, Nanjing University, 22 Hankou Road, Gulou District, Nanjing, 210093, China.,Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jing Ai
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Changjun Bao
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.
| | - Jun Zhang
- Suzhou Center for Disease Control and Prevention, Suzhou, China
| | - Qingbin Wu
- Soochow University Affiliated Children's Hospital, Suzhou, China
| | - Liguo Zhu
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jianli Hu
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Zheng Xing
- College of Veterinary Medicine, Department of Veterinary Biomedical Sciences, University of Minnesota At Twin Cities, Saint Paul, MN, 55108, USA.
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25
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Kuda T, Nishizawa M, Toshima D, Matsushima K, Yoshida S, Takahashi H, Kimura B, Yamagishi T. Antioxidant and anti-norovirus properties of aqueous acetic acid macromolecular extracts of edible brown macroalgae. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.110942] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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26
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Jin M, Wu S, Kong X, Xie H, Fu J, He Y, Feng W, Liu N, Li J, Rainey JJ, Hall AJ, Vinjé J, Duan Z. Norovirus Outbreak Surveillance, China, 2016-2018. Emerg Infect Dis 2021; 26:437-445. [PMID: 32091361 PMCID: PMC7045832 DOI: 10.3201/eid2603.191183] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
CaliciNet China, a network of provincial, county, and city laboratories coordinated by the Chinese Centers for Disease Control and Prevention, was launched in October 2016 to monitor the epidemiology and genotype distribution of norovirus outbreaks in China. During October 2016–September 2018, a total of 556 norovirus outbreaks were reported, and positive fecal samples from 470 (84.5%) outbreaks were genotyped. Most of these outbreaks were associated with person-to-person transmission (95.1%), occurred in childcare centers or schools (78.2%), and were reported during November–March of each year (63.5%). During the 2-year study period, 81.2% of all norovirus outbreaks were typed as GII.2[P16]. In China, most norovirus outbreaks are reported by childcare centers or schools; GII.2[P16] is the predominant genotype. Ongoing surveillance by CaliciNet China will provide information about the evolving norovirus genotype distribution and outbreak characteristics important for the development of effective interventions, including vaccines.
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27
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Burke RM, Mattison CP, Marsh Z, Shioda K, Donald J, Salas SB, Naleway AL, Biggs C, Schmidt MA, Hall AJ. Norovirus and Other Viral Causes of Medically Attended Acute Gastroenteritis Across the Age Spectrum: Results from the Medically Attended Acute Gastroenteritis Study in the United States. Clin Infect Dis 2021; 73:e913-e920. [PMID: 34398953 DOI: 10.1093/cid/ciab033] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Acute gastroenteritis (AGE) causes a substantial burden in the United States, but its etiology frequently remains undetermined. Active surveillance within an integrated healthcare delivery system was used to estimate the prevalence and incidence of medically attended norovirus, rotavirus, sapovirus, and astrovirus. METHODS Active surveillance was conducted among all enrolled members of Kaiser Permanente Northwest during July 2014-June 2016. An age-stratified, representative sample of AGE-associated medical encounters were recruited to provide a stool specimen to be tested for norovirus, rotavirus, sapovirus, and astrovirus. Medically attended AGE (MAAGE) encounters for a patient occurring within 30 days were grouped into 1 episode, and all-cause MAAGE incidence was calculated. Pathogen- and healthcare setting-specific incidence estimates were calculated using age-stratified bootstrapping. RESULTS The overall incidence of MAAGE was 40.6 episodes per 1000 person-years (PY), with most episodes requiring no more than outpatient care. Norovirus was the most frequently detected pathogen, with an incidence of 5.5 medically attended episodes per 1000 PY. Incidence of norovirus MAAGE was highest among children aged < 5 years (20.4 episodes per 1000 PY), followed by adults aged ≥ 65 years (4.5 episodes per 1000 PY). Other study pathogens showed similar patterns by age, but lower overall incidence (sapovirus: 2.4 per 1000 PY; astrovirus: 1.3 per 1000 PY; rotavirus: 0.5 per 1000 PY). CONCLUSIONS Viral enteropathogens, particularly norovirus, are important contributors to MAAGE, especially among children < 5 years of age. The present findings underline the importance of judicious antibiotics use for pediatric AGE and suggest that an effective norovirus vaccine could substantially reduce MAAGE.
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Affiliation(s)
- Rachel M Burke
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA
| | - Claire P Mattison
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee,USA
| | - Zachary Marsh
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee,USA
| | - Kayoko Shioda
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee,USA
| | - Judy Donald
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon,USA
| | - S Bianca Salas
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon,USA
| | - Allison L Naleway
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon,USA
| | - Christianne Biggs
- Public Health Division of the Oregon Health Authority, Portland, Oregon,USA
| | - Mark A Schmidt
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon,USA
| | - Aron J Hall
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA
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28
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Yen CS, Huang YC, Chen CJ, Shie SS, Yang SL, Huang CG, Tsao KC, Chiu CH, Hsieh YC, Kuo CY, Arthur Huang KY, Lin TY. Detection of norovirus and rotavirus among inpatients with acute gastroenteritis in a medical center in northern Taiwan, 2013–2018. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2020; 53:955-962. [DOI: 10.1016/j.jmii.2020.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/10/2020] [Accepted: 06/26/2020] [Indexed: 12/14/2022]
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29
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Mattioli MC, Benedict KM, Murphy J, Kahler A, Kline KE, Longenberger A, Mitchell PK, Watkins S, Berger P, Shanks OC, Barrett CE, Barclay L, Hall AJ, Hill V, Weltman A. Identifying septic pollution exposure routes during a waterborne norovirus outbreak - A new application for human-associated microbial source tracking qPCR. J Microbiol Methods 2020; 180:106091. [PMID: 33137355 DOI: 10.1016/j.mimet.2020.106091] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/13/2020] [Accepted: 10/27/2020] [Indexed: 11/18/2022]
Abstract
In June 2017, the Pennsylvania Department of Health (PADOH) was notified of multiple norovirus outbreaks associated with 179 ill individuals who attended separate events held at an outdoor venue and campground over a month period. Epidemiologic investigations were unable to identify a single exposure route and therefore unable to determine whether there was a persistent contamination source to target for exposure mitigation. Norovirus was detected in a fresh recreational water designated swimming area and a drinking water well. A hydrogeological site evaluation suggested a nearby septic leach field as a potential contamination source via ground water infiltration. Geological characterization revealed a steep dip of the bedrock beneath the septic leach field toward the well, providing a viral transport pathway in a geologic medium not previously documented as high risk for viral ground water contamination. The human-associated microbial source tracking (MST) genetic marker, HF183, was used as a microbial tracer to demonstrate the hydrogeological connection between the malfunctioning septic system, drinking water well, and recreational water area. Based on environmental investigation findings, venue management and local public health officials implemented a series of outbreak prevention strategies including discontinuing the use of the contaminated well, issuing a permit for a new drinking water well, increasing portable toilet and handwashing station availability, and promoting proper hand hygiene. Despite the outbreaks at the venue and evidence of ground water contamination impacting nearby recreational water and the drinking water well, no new norovirus cases were reported during a large event one week after implementing prevention practices. This investigation highlights a new application for human-associated MST methods to trace hydrological connections between multiple fecal pollutant exposure routes in an outbreak scenario. In turn, pollutant source information can be used to develop effective intervention practices to mitigate exposure and prevent future outbreaks associated with human fecal contaminated waters.
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Affiliation(s)
- Mia C Mattioli
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, USA.
| | - Katharine M Benedict
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, USA
| | - Jennifer Murphy
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, USA
| | - Amy Kahler
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, USA
| | - Kelly E Kline
- Pennsylvania Department of Health, Division of Infectious Disease Epidemiology, USA
| | - Allison Longenberger
- Pennsylvania Department of Health, Division of Infectious Disease Epidemiology, USA
| | - Patrick K Mitchell
- Pennsylvania Department of Health, Division of Infectious Disease Epidemiology, USA; Epidemic Intelligence Service, Division of Scientific Education and Professional Development, Center for Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sharon Watkins
- Pennsylvania Department of Health, Division of Infectious Disease Epidemiology, USA
| | - Philip Berger
- U.S. Environmental Protection Agency, Office of Ground Water and Drinking Water, Washington, DC, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Catherine E Barrett
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, USA
| | - Leslie Barclay
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, USA
| | - Aron J Hall
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, USA
| | - Vincent Hill
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, USA
| | - Andre Weltman
- Pennsylvania Department of Health, Division of Infectious Disease Epidemiology, USA
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Abstract
Several outbreak prediction models for COVID-19 are being used by officials around the world to make informed decisions and enforce relevant control measures. Among the standard models for COVID-19 global pandemic prediction, simple epidemiological and statistical models have received more attention by authorities, and these models are popular in the media. Due to a high level of uncertainty and lack of essential data, standard models have shown low accuracy for long-term prediction. Although the literature includes several attempts to address this issue, the essential generalization and robustness abilities of existing models need to be improved. This paper presents a comparative analysis of machine learning and soft computing models to predict the COVID-19 outbreak as an alternative to susceptible–infected–recovered (SIR) and susceptible-exposed-infectious-removed (SEIR) models. Among a wide range of machine learning models investigated, two models showed promising results (i.e., multi-layered perceptron, MLP; and adaptive network-based fuzzy inference system, ANFIS). Based on the results reported here, and due to the highly complex nature of the COVID-19 outbreak and variation in its behavior across nations, this study suggests machine learning as an effective tool to model the outbreak. This paper provides an initial benchmarking to demonstrate the potential of machine learning for future research. This paper further suggests that a genuine novelty in outbreak prediction can be realized by integrating machine learning and SEIR models.
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31
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Enhanced Gaussian process regression-based forecasting model for COVID-19 outbreak and significance of IoT for its detection. APPL INTELL 2020; 51:1492-1512. [PMID: 34764576 PMCID: PMC7785924 DOI: 10.1007/s10489-020-01889-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Virus based epidemic is one of the speedy and widely spread infectious disease which can affect the economy of the country as well as it is life-threatening too. So, there is a need to forecast the epidemic lifespan, which can help us in taking preventive measures and remedial action on time. These preventive measures and corrective action may consist of closing schools, closing malls, closing theaters, sealing of borders, suspension of public services, and suspension of traveling. Resuming such restrictions is depends upon the outbreak momentum and its decay rate. The accurate forecasting of the epidemic lifespan is one of the enormously essential and challenging tasks. It is a challenging task because the lack of knowledge about the novel virus-based diseases and its consequences with complicated societal-governmental factors can influence the widespread of this newly born disease. At this stage, any forecasting can play a vital role, and it will be reliable too. As we know, the novel virus-based diseases are in a growing phase, and we also do not have real-time data samples. Thus, the biggest challenge is to find out the machine learning-based best forecasting model, which could offer better forecasting with the limited training samples. In this paper, the Multi-Task Gaussian Process (MTGP) regression model with enhanced predictions of novel coronavirus (COVID-19) outbreak is proposed. The purpose of the proposed MTGP regression model is to predict the COVID-19 outbreak worldwide. It will help the countries in planning their preventive measures to reduce the overall impact of the speedy and widely spread infectious disease. The result of the proposed model has been compared with the other prediction model to find out its suitability and correctness. In subsequent analysis, the significance of IoT based devices in COVID-19 detection and prevention has been discussed.
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Mallory ML, Lindesmith LC, Brewer-Jensen PD, Graham RL, Baric RS. Bile Facilitates Human Norovirus Interactions with Diverse Histoblood Group Antigens, Compensating for Capsid Microvariation Observed in 2016-2017 GII.2 Strains. Viruses 2020; 12:E989. [PMID: 32899556 PMCID: PMC7552067 DOI: 10.3390/v12090989] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/01/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023] Open
Abstract
Human norovirus (HuNoV) is the leading cause of global infectious acute gastroenteritis, causing ~20% of reported diarrheal episodes. Typically, GII.4 strains cause 50-70% of yearly outbreaks, and pandemic waves of disease approximately every 2-7 years due to rapid evolution. Importantly, GII.4 dominance is occasionally challenged by the sudden emergence of other GII strains, most recently by GII.2 strains which peaked in 2016-2017, dramatically increasing from 1% to 20% of total HuNoV outbreaks. To determine if viral capsid evolution may account for the sudden rise in GII.2 outbreaks, Virus Like Particles (VLPs) of two 2016-2017 GII.2 strains were compared by antigenic and histo blood group antigen (HBGA) binding profiles to the prototypic 1976 GII.2 Snow Mountain Virus (SMV) strain. Despite >50 years of GII.2 strain persistence in human populations, limited sequence diversity and antigenic differences were identified between strains. However, capsid microvariation did affect HBGA binding patterns, with contemporary strains demonstrating decreased avidity for type A saliva. Furthermore, bile salts increased GII.2 VLP avidity for HBGAs, but did not alter antigenicity. These data indicate that large changes in antigenicity or receptor binding are unlikely to explain GII.2 emergence, in contrast to the pandemic GII.4 strains, and indicate that host factors such as waning or remodeling of serum or mucosal immunity likely contributed to the surge in GII.2 prevalence.
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Affiliation(s)
| | | | | | | | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA; (M.L.M.); (L.C.L.); (P.D.B.-J.); (R.L.G.)
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Abstract
PURPOSE OF REVIEW The majority of norovirus outbreaks in the United States occur in healthcare facilities. With the growing population of immunocompromised hosts who are in frequent contact with healthcare facilities, norovirus is not only a threat to hospitals and nursing homes but also to these individuals. This review summarizes the impact of norovirus infection on healthcare facilities and immunocompromised hosts. RECENT FINDINGS The natural history of norovirus infection in immunocompromised individuals remains poorly understood. Although host immune responses play a critical role in reducing duration of viral shedding and viral load in norovirus-infected individuals, why some immunocompromised patients spontaneously recover while others develop a chronic and protracted course of illness remains unclear. Norovirus outbreaks occur in healthcare facilities because the virus is highly contagious, resistant to disinfection and efficiently transmitted. The use of real-time metagenomic next-generation sequencing and phylogenetic analyses has provided valuable information on transmission patterns in complex hospital-associated norovirus outbreaks. The development of human intestinal enteroid cultures enables the determination of effectiveness of disinfectants against human noroviruses, circumventing the validity questions with surrogate virus models due to differences in susceptibility to inactivation and disinfectants. SUMMARY Metagenomics next-generation sequencing can enhance our understanding of norovirus transmission and lead to more timely mitigation strategies to curb norovirus outbreaks in healthcare facilities. With new in-vitro cultivation methods for human noroviruses, candidate vaccines and effective antivirals could be available in the near future.
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34
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COVID-19 Pandemic Prediction for Hungary; A Hybrid Machine Learning Approach. MATHEMATICS 2020. [DOI: 10.3390/math8060890] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Several epidemiological models are being used around the world to project the number of infected individuals and the mortality rates of the COVID-19 outbreak. Advancing accurate prediction models is of utmost importance to take proper actions. Due to the lack of essential data and uncertainty, the epidemiological models have been challenged regarding the delivery of higher accuracy for long-term prediction. As an alternative to the susceptible-infected-resistant (SIR)-based models, this study proposes a hybrid machine learning approach to predict the COVID-19, and we exemplify its potential using data from Hungary. The hybrid machine learning methods of adaptive network-based fuzzy inference system (ANFIS) and multi-layered perceptron-imperialist competitive algorithm (MLP-ICA) are proposed to predict time series of infected individuals and mortality rate. The models predict that by late May, the outbreak and the total morality will drop substantially. The validation is performed for 9 days with promising results, which confirms the model accuracy. It is expected that the model maintains its accuracy as long as no significant interruption occurs. This paper provides an initial benchmarking to demonstrate the potential of machine learning for future research.
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35
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Karmarkar E, Jain S, Higa J, Fontenot J, Bertolucci R, Huynh T, Hammer G, Brodkin A, Thao M, Brousseau B, Hopkins D, Kelly E, Sheffield M, Henley S, Whittaker H, Herrick RL, Pan CY, Chen A, Kim J, Schaumleffel L, Khwaja Z, Epson E, Chai SJ, Wadford D, Vugia D, Lewis L. Outbreak of Norovirus Illness Among Wildfire Evacuation Shelter Populations - Butte and Glenn Counties, California, November 2018. MMWR. MORBIDITY AND MORTALITY WEEKLY REPORT 2020; 69:613-617. [PMID: 32437337 PMCID: PMC7357343 DOI: 10.15585/mmwr.mm6920a1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Camp Fire, California's deadliest wildfire, began November 8, 2018, and was extinguished November 25 (1). Approximately 1,100 evacuees from the fire sought emergency shelter. On November 10, acute gastroenteritis (AGE) was reported in two evacuation shelters; norovirus illness was suspected, because it is commonly detected in shelter-associated AGE outbreaks. Norovirus is highly contagious and resistant to several disinfectants. Butte County Public Health Department (BCPHD), assisted by the California Department of Public Health (CDPH), initiated active surveillance to identify cases, confirm the etiology, and assess shelter infection prevention and control (IPC) practices to guide recommendations. During November 8-30, a total of 292 patients with AGE were identified among nine evacuation shelters; norovirus was detected in 16 of 17 unique patient stool specimens. Shelter IPC assessments revealed gaps in illness surveillance, isolation practices, cleaning, disinfection, and handwashing. CDPH and BCPHD collaborated with partner agencies to implement AGE screening, institute isolation protocols and 24-hour cleaning services, and promote proper hand hygiene. During disasters with limited resources, damaged infrastructure, and involvement of multiple organizations, establishing shelter disease surveillance and IPC is difficult. However, prioritizing effective surveillance and IPC at shelter activation is necessary to prevent, identify, and contain outbreaks.
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Surveillance of the 'bud event of norovirus-associated gastroenteritis' in schools: does it work in the prevention of norovirus infection outbreaks in Shanghai? Epidemiol Infect 2020; 148:e104. [PMID: 32381124 PMCID: PMC7315464 DOI: 10.1017/s0950268820000965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Outbreaks of norovirus-associated gastroenteritis have been reported in schools in recent decades in China. For early warning and response to infectious disease outbreaks, the Shanghai Infectious Diseases Bud Event Surveillance System (IDBESS) was established in 2016. Bud event is a term used for the early sign of a potential infectious disease outbreak in public settings when the first few cases appear. This study aimed to describe the epidemiological characteristics of Norovirus-associated gastroenteritis bud events from June 2016 to December 2017 and to understand factors influencing the severity of events. Data were extracted from the IDBESS, supplemented by field investigations and school absence surveillance. In total, 189 bud events of Norovirus-associated gastroenteritis were reported in schools and kindergartens, affecting 3827 individuals and 52.38% happened in primary schools. The attack rate of Norovirus-associated gastroenteritis was 3.82% on average in students in the affected schools. In each event, case numbers varied between 5 and 148, with a median of 16. The duration of bud events lasted for 2 days on average. School absence happened in 47.93% (1797/3749) of affected students and the average duration of absence was 3.07 days. It was found that a longer delay before reporting was associated with a longer-lasting duration of bud event (OR = 2.25, 95% CI: 1.65, 3.07). In conclusion, ascribed to the sensitive threshold for alerting and the timely field investigation, the surveillance of bud events of Norovirus-associated gastroenteritis is effective in the control of Norovirus infection among preschool children and students in Shanghai.
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Mitra S, Nayak MK, Majumdar A, Sinha A, Chatterjee S, Deb A, Chawla-Sarkar M, Dutta S. Development and evaluation of a multiplex conventional reverse-transcription polymerase chain reaction assay for detection of common viral pathogens causing acute gastroenteritis. Diagn Microbiol Infect Dis 2020; 97:115061. [PMID: 32585545 DOI: 10.1016/j.diagmicrobio.2020.115061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/27/2020] [Accepted: 04/12/2020] [Indexed: 12/11/2022]
Abstract
Timely identification of etiological agents of enteric infections is necessary to reduce the burden of infantile diarrheal mortality. Nucleic acid amplification-based detection methods offer a quick, reliable way for diagnosis of microbes in clinical specimens. This study was undertaken to evaluate an easy-to-use, cost-effective multiplex conventional reverse-transcription polymerase chain reaction (RT-PCR) assay developed at the Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases virology laboratory to identify 4 common enteric viruses (rotavirus, norovirus, adenovirus, astrovirus) in stool samples from patients who were being evaluated for acute diarrhea. On comparison with a commercially available real-time PCR method, significant agreement in sensitivity and specificity was observed. Though the turnaround time for RT-PCR was 6-8 h compared to 5-6 h for real-time PCR, the real-time PCR has high test cost (approximately 28 USD/2000 INR) for Fast-Track Diagnostics kit-based quantitative RT-PCR versus 6 USD or 400 INR for conventional multiplex RT-PCR/sample. Thus, the conventional RT-PCR method is expected to be adaptable at local hospitals and health cares in resource-poor settings.
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Affiliation(s)
- Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | | | - Agniva Majumdar
- Regional Virus Research and Diagnostic Lab (VRDL), ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Avisek Sinha
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Soumyadipta Chatterjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Alok Deb
- Division of Epidemiology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India.
| | - Shanta Dutta
- Regional Virus Research and Diagnostic Lab (VRDL), ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
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Epidemiologic characteristics of outbreaks of three norovirus genotypes (GII.2, GII.17 and GII.4 Sydney) in Guangzhou, China, from 2012 to 2018. Epidemiol Infect 2020; 147:e207. [PMID: 31364544 PMCID: PMC6624865 DOI: 10.1017/s0950268819000992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To compare the epidemiologic features (e.g. settings and transmission mode) and patient clinical characteristics associated with outbreaks of different norovirus (Nov) strains, we retrospectively analysed data of Nov outbreaks occurring in Guangzhou, China from 2012 to 2018. The results suggested that outbreaks of Nov GII.2, GII.17 and GII.4 Sydney exhibited different outbreak settings, transmission modes and symptoms. GII.2 outbreaks mainly occurred in kindergartens, elementary and high schools and were transmitted mainly through person-to-person contact. By contrast, GII.4 Sydney outbreaks frequently occurred in colleges and were primarily associated with foodborne transmission. Cases from GII.2 and GII.17 outbreaks reported vomiting more frequently than those from outbreaks associated with GII.4 Sydney.
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Fu J, Bao C, Huo X, Hu J, Shi C, Lin Q, Zhang J, Ai J, Xing Z. Increasing Recombinant Strains Emerged in Norovirus Outbreaks in Jiangsu, China: 2015-2018. Sci Rep 2019; 9:20012. [PMID: 31882797 PMCID: PMC6934623 DOI: 10.1038/s41598-019-56544-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 12/02/2019] [Indexed: 11/19/2022] Open
Abstract
From January 2015 to December 2018, 213 norovirus outbreaks with 3,951 patients were reported in Jiangsu, China. Based on viral RdRp and VP1 genes, eight genotypes, GII.2[P16] (144, 67.6%), GII.3[P12] (21, 9.9%), GII.6[P7] (5, 2.3%), GII.14[P7] (4, 1.9%), GII.4 Sydney[P31] (3, 1.4%), GII.1[P33] (1, 0.5%), GII.2[P2] (3, 1.4%), and GII.17[P17] (16, 7.5%) were identified throughout the study period. These genotypes were further regrouped as GII.R (Recombinant) and GII.Non-R (Non-recombinant) strains. In this report we showed that GII.R strains were responsible for at least 178 (83.6%) of 213 norovirus-positive outbreaks with a peak in 2017 and 2018. Most norovirus outbreaks occurred in primary schools and 94 of 109 (86.2%) outbreaks in primary schools were caused by GII.R, while GII.Non-R and GII.NT (not typed) strains accounted for 6 (5.5%) and 9 (8.3%) norovirus outbreaks, respectively. The SimPlot analysis showed recombination breakpoints near the ORF1/2 junction for all six recombinant strains. The recombination breakpoints were detected at positions varying from nucleotides 5009 to 5111, localized in the ORF1 region for four strains (GII.2[P16], GII.3[P12], GII.6[P7], and GII.14[P7]) and in the ORF2 region for the other (GII.4 Sydney[P31] and GII.1[P33]). We identified four clusters, Cluster I through IV, in the GII.P7 RdRp gene by phylogenetic analysis and the GII.14[P7] variants reported here belonged to Cluster IV in the RdRp tree. The HBGA binding site of all known GII.14 strains remained conserved with several point mutations found in the predicted conformational epitopes. In conclusion, gastroenteritis outbreaks caused by noroviruses increased rapidly in the last years and these viruses were classified into eight genotypes. Emerging recombinant noroviral strains have become a major concern and challenge to public health.
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Affiliation(s)
- Jianguang Fu
- Medical School and the Jiangsu Provincial Key Laboratory of Medicine, Nanjing University, Nanjing, China.,Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Changjun Bao
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xiang Huo
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jianli Hu
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Chao Shi
- Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Qin Lin
- Changzhou Center for Disease Control and Prevention, Changzhou, China
| | - Jun Zhang
- Yangzhou Center for Disease Control and Prevention, Yangzhou, China
| | - Jing Ai
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.
| | - Zheng Xing
- Medical School and the Jiangsu Provincial Key Laboratory of Medicine, Nanjing University, Nanjing, China. .,College of Veterinary Medicine, Department of Veterinary Biomedical Sciences, University of Minnesota at Twin Cities, Saint Paul, Minnesota, 55108, USA.
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40
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Lindesmith LC, McDaniel JR, Changela A, Verardi R, Kerr SA, Costantini V, Brewer-Jensen PD, Mallory ML, Voss WN, Boutz DR, Blazeck JJ, Ippolito GC, Vinje J, Kwong PD, Georgiou G, Baric RS. Sera Antibody Repertoire Analyses Reveal Mechanisms of Broad and Pandemic Strain Neutralizing Responses after Human Norovirus Vaccination. Immunity 2019; 50:1530-1541.e8. [PMID: 31216462 PMCID: PMC6591005 DOI: 10.1016/j.immuni.2019.05.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/15/2019] [Accepted: 05/15/2019] [Indexed: 12/13/2022]
Abstract
Rapidly evolving RNA viruses, such as the GII.4 strain of human norovirus (HuNoV), and their vaccines elicit complex serological responses associated with previous exposure. Specific correlates of protection, moreover, remain poorly understood. Here, we report the GII.4-serological antibody repertoire—pre- and post-vaccination—and select several antibody clonotypes for epitope and structural analysis. The humoral response was dominated by GII.4-specific antibodies that blocked ancestral strains or by antibodies that bound to divergent genotypes and did not block viral-entry-ligand interactions. However, one antibody, A1431, showed broad blockade toward tested GII.4 strains and neutralized the pandemic GII.P16-GII.4 Sydney strain. Structural mapping revealed conserved epitopes, which were occluded on the virion or partially exposed, allowing for broad blockade with neutralizing activity. Overall, our results provide high-resolution molecular information on humoral immune responses after HuNoV vaccination and demonstrate that infection-derived and vaccine-elicited antibodies can exhibit broad blockade and neutralization against this prevalent human pathogen. Serum vaccine response is dominated by a small number of abundant antibody clonotypes Vaccine-boosted antibodies predominantly target conserved norovirus epitopes Identified cross-genogroup and strain-specific epitopes Discovered a pandemic-genotype neutralizing antibody recognizing a conserved epitope
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Affiliation(s)
- Lisa C Lindesmith
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan R McDaniel
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Anita Changela
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott A Kerr
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Veronica Costantini
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Paul D Brewer-Jensen
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - William N Voss
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel R Boutz
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - John J Blazeck
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jan Vinje
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA.
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41
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Emerging Novel GII.P16 Noroviruses Associated with Multiple Capsid Genotypes. Viruses 2019; 11:v11060535. [PMID: 31181749 PMCID: PMC6631344 DOI: 10.3390/v11060535] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/31/2019] [Accepted: 06/05/2019] [Indexed: 02/01/2023] Open
Abstract
Noroviruses evolve by antigenic drift and recombination, which occurs most frequently at the junction between the non-structural and structural protein coding genomic regions. In 2015, a novel GII.P16-GII.4 Sydney recombinant strain emerged, replacing the predominance of GII.Pe-GII.4 Sydney among US outbreaks. Distinct from GII.P16 polymerases detected since 2010, this novel GII.P16 was subsequently detected among GII.1, GII.2, GII.3, GII.10 and GII.12 viruses, prompting an investigation on the unique characteristics of these viruses. Norovirus positive samples (n = 1807) were dual-typed, of which a subset (n = 124) was sequenced to yield near-complete genomes. CaliciNet and National Outbreak Reporting System (NORS) records were matched to link outbreak characteristics and case outcomes to molecular data and GenBank was mined for contextualization. Recombination with the novel GII.P16 polymerase extended GII.4 Sydney predominance and increased the number of GII.2 outbreaks in the US. Introduction of the novel GII.P16 noroviruses occurred without unique amino acid changes in VP1, more severe case outcomes, or differences in affected population. However, unique changes were found among NS1/2, NS4 and VP2 proteins, which have immune antagonistic functions, and the RdRp. Multiple polymerase-capsid combinations were detected among GII viruses including 11 involving GII.P16. Molecular surveillance of protein sequences from norovirus genomes can inform the functional importance of amino acid changes in emerging recombinant viruses and aid in vaccine and antiviral formulation.
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42
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Haynes J, Perry V, Benson E, Meeks A, Watts G, Watkins H, Braun R. In Depth Breadth Analyses of Human Blockade Responses to Norovirus and Response to Vaccination. Viruses 2019; 11:v11050392. [PMID: 31035476 PMCID: PMC6563306 DOI: 10.3390/v11050392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/12/2019] [Accepted: 04/23/2019] [Indexed: 12/19/2022] Open
Abstract
To evaluate and understand the efficacy of vaccine candidates, supportive immunological measures are needed. Critical attributes for a norovirus vaccine are the strength and breadth of antibody responses against the many different genotypes. In the absence of suitable neutralization assays to test samples from vaccine clinical trials, blockade assays offer a method that can measure functional antibodies specific for many of the different norovirus strains. This paper describes development and optimization of blockade assays for an extended panel of 20 different norovirus strains that can provide robust and reliable data needed for vaccine assessment. The blockade assays were used to test a panel of human clinical samples taken before and after vaccination with the Takeda TAK-214 norovirus vaccine. Great variability was evident in the repertoire of blocking antibody responses prevaccination and postvaccination among individuals. Following vaccination with TAK-214, blocking antibody levels were enhanced across a wide spectrum of different genotypes. The results indicate that adults may have multiple exposures to norovirus and that the magnitude and breadth of the complex preexisting antibody response can be boosted and expanded by vaccination.
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Affiliation(s)
- Joel Haynes
- Vaccines Discovery Research, Takeda Pharmaceuticals, Cambridge, MA 02139, USA.
| | - Virginia Perry
- Vaccines Discovery Research, Takeda Pharmaceuticals, Cambridge, MA 02139, USA.
| | - Evelyn Benson
- Vaccines Discovery Research, Takeda Pharmaceuticals, Cambridge, MA 02139, USA.
| | - Alisa Meeks
- Vaccines Discovery Research, Takeda Pharmaceuticals, Cambridge, MA 02139, USA.
| | - Gayle Watts
- Vaccines Discovery Research, Takeda Pharmaceuticals, Cambridge, MA 02139, USA.
| | - Heather Watkins
- Vaccines Discovery Research, Takeda Pharmaceuticals, Cambridge, MA 02139, USA.
| | - Ralph Braun
- Vaccines Discovery Research, Takeda Pharmaceuticals, Cambridge, MA 02139, USA.
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43
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Near-Complete Genome Sequence of a Human Norovirus GII.P7-GII.6 Strain Detected in a Maryland Patient in 2018. Microbiol Resour Announc 2019; 8:8/16/e00191-19. [PMID: 31000549 PMCID: PMC6473143 DOI: 10.1128/mra.00191-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genomic recombination is a crucial mechanism used to generate genetic variation in human noroviruses. Recombinant variants have been increasingly identified and have contributed to sporadic cases and epidemic outbreaks of acute gastroenteritis globally. We report the near-complete genome of a novel recombinant norovirus GII.P7-GII.6 strain detected in an adult with norovirus gastroenteritis in the United States in 2018.
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44
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GII.4 Human Norovirus: Surveying the Antigenic Landscape. Viruses 2019; 11:v11020177. [PMID: 30791623 PMCID: PMC6410000 DOI: 10.3390/v11020177] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/22/2022] Open
Abstract
Human norovirus is the leading cause of viral acute onset gastroenteritis disease burden, with 685 million infections reported annually. Vulnerable populations, such as children under the age of 5 years, the immunocompromised, and the elderly show a need for inducible immunity, as symptomatic dehydration and malnutrition can be lethal. Extensive antigenic diversity between genotypes and within the GII.4 genotype present major challenges for the development of a broadly protective vaccine. Efforts have been devoted to characterizing antibody-binding interactions with dynamic human norovirus viral-like particles, which recognize distinct antigenic sites on the capsid. Neutralizing antibody functions recognizing these sites have been validated in both surrogate (ligand blockade of binding) and in vitro virus propagation systems. In this review, we focus on GII.4 capsid protein epitopes as defined by monoclonal antibody binding. As additional antibody epitopes are defined, antigenic sites emerge on the human norovirus capsid, revealing the antigenic landscape of GII.4 viruses. These data may provide a road map for the design of candidate vaccine immunogens that induce cross-protective immunity and the development of therapeutic antibodies and drugs.
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45
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Tamminen K, Malm M, Vesikari T, Blazevic V. Immunological Cross-Reactivity of an Ancestral and the Most Recent Pandemic Norovirus GII.4 Variant. Viruses 2019; 11:v11020091. [PMID: 30678195 PMCID: PMC6410201 DOI: 10.3390/v11020091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/11/2019] [Accepted: 01/18/2019] [Indexed: 01/06/2023] Open
Abstract
Norovirus (NoV) genotype GII.4 is responsible for the majority of NoV infections causing pandemics every few years. A NoV virus-like particle (VLP)-based vaccine should optimally cover the high antigenic variation within the GII.4 genotype. We compared the immune responses generated by VLPs of the ancestral GII.4 1999 strain (GII.4 1995/96 US variant) and the most recent GII.4 Sydney 2012 pandemic strains in mice. No significant differences were observed in the type-specific responses but GII.4 1999 VLPs were more potent in inducing high-avidity antibodies with better cross-reactivity. GII.4 1999 immune sera blocked binding of GII.4 2006 and GII.4 2012 VLPs to the putative receptors in a surrogate neutralization assay, whereas GII.4 2012 immune sera only had low blocking activity against GII.4 2006 VLPs. Amino acid substitution in the NERK motif (amino acids 310, 316, 484, and 493, respectively), altering the access to conserved blocking epitope F, moderately improved the cross-blocking responses against mutated GII.4 2012 VLPs (D310N). NoV GII.4 1999 VLPs, uptaken and processed by antigen-presenting cells, induced stronger interferon gamma (IFN-γ) production from mice splenocytes than GII.4 2012 VLPs. These results support the use of GII.4 1999 VLPs as a major component of a NoV vaccine.
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Affiliation(s)
- Kirsi Tamminen
- Vaccine Research Center, Faculty of Medicine and Health Technology, Tampere University, Biokatu 10, FI-33520 Tampere, Finland.
| | - Maria Malm
- Vaccine Research Center, Faculty of Medicine and Health Technology, Tampere University, Biokatu 10, FI-33520 Tampere, Finland.
| | - Timo Vesikari
- Vaccine Research Center, Faculty of Medicine and Health Technology, Tampere University, Biokatu 10, FI-33520 Tampere, Finland.
| | - Vesna Blazevic
- Vaccine Research Center, Faculty of Medicine and Health Technology, Tampere University, Biokatu 10, FI-33520 Tampere, Finland.
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46
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Hallowell BD, Parashar UD, Hall AJ. Epidemiologic challenges in norovirus vaccine development. Hum Vaccin Immunother 2018; 15:1279-1283. [PMID: 30481104 PMCID: PMC6663132 DOI: 10.1080/21645515.2018.1553594] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 11/24/2018] [Indexed: 10/27/2022] Open
Abstract
Norovirus is the leading cause of acute gastroenteritis (AGE) worldwide. In the United States norovirus is estimated to cause 19-21 million illnesses, 1.7-1.9 million outpatient visits, 56,000-71,000 hospitalizations, and 570-800 deaths annually. Through direct costs and loss of productivity, norovirus disease cost the US economy more than $5.5 billion annually. Due to the lack of available therapies to treat norovirus infections and their highly infectious nature, preventing norovirus illness through vaccination is an appealing strategy. Currently, several norovirus vaccines are in development, including five vaccines in preclinical trials, an oral monovalent vaccine (Vaxart, Inc.) that recently completed a phase IB clinical trial, and a bivalent intramuscular vaccine (Takeda Pharmaceutical Company Limited) in a phase IIB clinical trial. However, no norovirus vaccines are currently available on the market. In this commentary we aim to describe some of the barriers faced in norovirus vaccine development, particularly focusing on vaccine effectiveness and defining the target population.
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Affiliation(s)
- Benjamin D. Hallowell
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Centers for Disease Control and Prevention, Epidemic Intelligence Service, Atlanta, GA, USA
| | - Umesh D. Parashar
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Aron J. Hall
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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