Complete #genome #sequence of a novel #reassortant #H3N3 #avian #influenza virus (Arch Virol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Arch Virol. 2019 Aug 27. doi: 10.1007/s00705-019-04386-8. [Epub ahead of print]

Complete genome sequence of a novel reassortant H3N3 avian influenza virus.

Le TB1,2, Kim HK3, Le HY1,2, Jeong MC1,2, Kim IK4, Jeong DG5,6, Yoon SW7,8.

Author information: 1 Infectious Disease Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, South Korea. 2 University of Science and Technology (UST), Daejeon, 34113, South Korea. 3 Chungbuk National University, Cheongju, 28644, South Korea. 4 Korea Institute of Environment Ecology, Daejeon, 34016, South Korea. 5 Infectious Disease Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, South Korea. dgjeong@kribb.re.kr. 6 University of Science and Technology (UST), Daejeon, 34113, South Korea. dgjeong@kribb.re.kr. 7 Infectious Disease Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, South Korea. syoon@kribb.re.kr. 8 University of Science and Technology (UST), Daejeon, 34113, South Korea. syoon@kribb.re.kr.

 

Abstract

Aquatic birds are known to be a reservoir for the most common influenza A viruses (IAVs). In the annual surveillance program, we collected the feces of migratory birds for the detection of IAVs in South Korea in November 2016. A novel reassorted H3N3 avian influenza virus (AIV) containing genes from viruses of wild and domestic birds was identified and named A/aquatic bird/South Korea/sw006/2016(H3N3). The polymerase basic 2 (PB2) and non-structural (NS) genes of this isolate are most closely related to those of wild-bird-origin AIV, while the polymerase basic 1 (PB1), polymerase acidic (PA), hemagglutinin (HA), nucleoprotein (NP), neuraminidase (NA), and matrix (M) genes are most closely related to those of domestic-bird-origin AIV. A/aquatic bird/South Korea/sw006/2016 contains PA, NP, M, and NS genes were most closely related to those of AIV subtype H4 and PB2, PB1, and HA genes that are most closely related to those of AIV subtype H3N8, while the NA gene was most closely related to those of subtype H10, which was recently detected in humans in China. These results suggest that novel reassortment of AIV strains occurred due to interaction between wild and domestic birds. Hence, we emphasize the need for continued surveillance of avian influenza virus in bird populations.

PMID: 31456087 DOI: 10.1007/s00705-019-04386-8

Keywords: Avian Influenza; H3N3; H4; H10; H3N8; Wild Birds; S. Korea; Reassortant strain.

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#Economic #Impact of the 2015 #MERS #Outbreak on the Republic of #Korea’s #Tourism-Related #Industries (Health Secur., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Health Secur. 2019 Mar/Apr;17(2):100-108. doi: 10.1089/hs.2018.0115. Epub 2019 Apr 10.

Economic Impact of the 2015 MERS Outbreak on the Republic of Korea’s Tourism-Related Industries.

Joo H1, Maskery BA2, Berro AD3, Rotz LD4, Lee YK5, Brown CM6.

Author information: 1 Heesoo Joo, PhD, is an Economist, Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, Georgia. 2 Brian A. Maskery, PhD, is an Economist, Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, Georgia. 3 Andre D. Berro, MPH, is a Public Health Advisor, Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, Georgia. 4 Lisa D. Rotz, MD, is a Medical Epidemiologist, Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, Georgia. 5 Yeon-Kyeng Lee, PhD, is Division Director, Korea Centers for Disease Control and Prevention, Cheongju-si, Chungcheongbuk-do, Republic of Korea. 6 Clive M. Brown, MD, is Branch Chief, Quarantine and Border Health Services, Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, Georgia.

 

Abstract

The 2015 Middle East respiratory syndrome (MERS) outbreak in the Republic of Korea (ROK) is an example of an infectious disease outbreak initiated by international travelers to a high-income country. This study was conducted to determine the economic impact of the MERS outbreak on the tourism and travel-related service sectors, including accommodation, food and beverage, and transportation, in the ROK. We projected monthly numbers of noncitizen arrivals and indices of services for 3 travel-related service sectors during and after the MERS outbreak (June 2015 to June 2016) using seasonal autoregressive integrated moving average models. Tourism losses were estimated by multiplying the monthly differences between projected and actual numbers of noncitizen arrivals by average tourism expenditure per capita. Estimated tourism losses were allocated to travel-related service sectors to understand the distribution of losses across service sectors. The MERS outbreak was correlated with a reduction of 2.1 million noncitizen visitors corresponding with US$2.6 billion in tourism loss for the ROK. Estimated losses in the accommodation, food and beverage service, and transportation sectors associated with the decrease of noncitizen visitors were US$542 million, US$359 million, and US$106 million, respectively. The losses were demonstrated by lower than expected indices of services for the accommodation and food and beverage service sectors in June and July 2015 and for the transportation sector in June 2015. The results support previous findings that public health emergencies due to traveler-associated outbreaks of infectious diseases can cause significant losses to the broader economies of affected countries.

KEYWORDS: Economic burden of disease; Economic impact; Middle East respiratory syndrome; Outbreak; Tourism; Travel industry

PMID: 30969152 PMCID: PMC6560634 [Available on 2020-04-10] DOI: 10.1089/hs.2018.0115 [Indexed for MEDLINE]

Keywords: MERS-CoV; South Korea; Society.

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#Seroprevalence of #SFTS #Phlebovirus in Domesticated #Deer in South #Korea (Virol Sin., abstract)

[Source: Virologica Sinica, full page: (LINK). Abstract, edited.]

Seroprevalence of Severe Fever with Thrombocytopenia Syndrome Phlebovirus in Domesticated Deer in South Korea

Authors: Min-Ah Yu, Kwang-Min Yu, Su-Jin Park, Young-Il Kim, Norbert John Robles, Young-Jae Si, Eun-Ha Kim, Hyeok-Il Kwon, Hye Won Jeong, Min-Suk Song, Seok-Yong Kim, Young Ki Choi

Research Article / First Online: 25 June 2019

 

Abstract

Severe fever with thrombocytopenia syndrome phlebovirus (SFTSV) has a wide host range. Not only has it been found in humans, but also in many wild and domesticated animals. The infection of breeding deer on farms is a particularly worrisome public health concern due to the large amount of human contact and the diverse use of deer products, including raw blood. To investigate the prevalence of breeding domesticated deer, we examined the SFTSV infection rate on deer farms in South Korea from 2015 to 2017. Of the 215 collected blood samples, 0.9% (2/215) were found to be positive for viral RNA by PCR, and sequence analysis showed the highest homology with the KADGH human isolate. Both SFTSV-specific recombinant N and Gn protein-based ELISAs revealed that 14.0% (30/215) and 7.9% (17/215) of collected blood specimens were positive for SFTSV antibody. These results demonstrate that the breeding farm deer are exposed to SFTSV and could be a potential infection source for humans through direct contact or consumption of byproducts.

Keywords: Severe fever with thrombocytopenia syndrome phlebovirus (SFTSV) – Breeding deer – Seroprevalence – South Korea

 

Notes

Acknowledgements

We thank all involved staffs in the diagnosis of SFTS during this study. We thank veterinarians at Sejeong Farms for collecting the samples. This work was supported by the Ministry of Health & Welfare (government—wide R&D fund project for infectious disease research (HG18C0029).

Author Contributions

M-AY and YKC conceptualized the study. M-AY, KMY, S-JP, Y-IK, NJR, Y-JS, E-HK, and H-IK, conducted the investigation. HWJ, M-SS, S-YK and YKC wrote the paper.

 

Compliance with Ethical Stanadards

Conflict of interest

The authors do not have any competing interests to declare.

Animal and Human Rights Statement

This work was supported by the Ministry of Health & Welfare (government – wide R&D fund project for infectious disease research (HG18C0029). Deer serum samples for the study were collected with the deer owner’s approval, and the experiments were conducted under the guidelines of the Chungbuk National University.

Keywords: SFTS; Phlebovirus; Livestock; Deers; S. Korea.

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#Etiology, characteristics, and #outcomes of community-onset #necrotizing #fasciitis in #Korea: A multicenter study (PLoS One, abstract)

[Source: PLoS One, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Etiology, characteristics, and outcomes of community-onset necrotizing fasciitis in Korea: A multicenter study

Tark Kim, Seong Yeon Park, Yee Gyung Kwak, Jiwon Jung, Min-Chul Kim, Seong-Ho Choi, Shi Nae Yu, Hyo-Lim Hong, Yong Kyun Kim, Se Yoon Park, Eun Hee Song, Ki-Ho Park, Oh Hyun Cho, Sang-Ho Choi , the Korean SSTI Study Group

Published: June 20, 2019 / DOI: https://doi.org/10.1371/journal.pone.0218668

 

Abstract

Background

Necrotizing fasciitis (NF) is a serious skin and soft tissue infection causing high mortality. Investigating region specific epidemiologic factors associated with NF is important for establishing appropriate treatment strategies. This multicenter study was done to provide an update of the microbial etiology, clinical characteristics, and outcomes of NF in Korea.

Materials and methods

A retrospective cohort of adult patients with NF was established using patient data from 13 general hospitals between January 2012 and December 2015 in Korea. We evaluated microbial etiology and clinical characteristics to identify risk factors associated with in-hospital mortality; analyses were performed using binary logistic regression models.

Results

A total of 161 patients with NF were included. The most common underlying disease was diabetes mellitus (66 cases, 41.0%). A total of 148 organisms were isolated from 119 (73.9%) patients. Enteric Gram-negative organisms (36 patients) were the most common pathogen, followed by Staphylococcus aureus (30 patients) and streptococci (28 patients). Methicillin-resistant Staphylococcus aureus (MRSA) was identified in 6.2% (10/161) of patients. Of 37 enteric Gram-negative isolates tested, 26 (70.3%) isolates were susceptible to ceftriaxone. The in-hospital mortality rate was 22.4%. Intensive care unit admission, septic shock, and Gram-negative organism infections were significantly associated with in-hospital mortality, and surgery was not a favorable prognostic factor.

Conclusions

As initial empirical antibiotics, glycopeptides against MRSA and broad-spectrum antibiotics against third-generation cephalosporin-resistant organisms should be considered for patients with community-onset NF in Korea.

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Citation: Kim T, Park SY, Kwak YG, Jung J, Kim M-C, Choi S-H, et al. (2019) Etiology, characteristics, and outcomes of community-onset necrotizing fasciitis in Korea: A multicenter study. PLoS ONE 14(6): e0218668. https://doi.org/10.1371/journal.pone.0218668

Editor: Marc O. Siegel, George Washington University, UNITED STATES

Received: December 30, 2018; Accepted: June 6, 2019; Published: June 20, 2019

Copyright: © 2019 Kim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the manuscript and its Supporting Information files.

Funding: TK received the Soonchunhyang University Research Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Necrotizing fasciitis; Staphylococcus aureus; Antibiotics; MRSA; S. Korea.

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Effective #control #measures considering spatial heterogeneity to mitigate the 2016–2017 #avian #influenza epidemic in the Republic of #Korea (PLoS One, abstract)

[Source: PLoS One, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Effective control measures considering spatial heterogeneity to mitigate the 2016–2017 avian influenza epidemic in the Republic of Korea

Jonggul Lee, Youngsuk Ko, Eunok Jung

Published: June 13, 2019 / DOI: https://doi.org/10.1371/journal.pone.0218202

 

Abstract

During the winter of 2016-2017, an epidemic of highly pathogenic avian influenza (HPAI) led to high mortality in poultry and put a serious burden on the poultry industry of the Republic of Korea. Effective control measures considering spatial heterogeneity to mitigate the HPAI epidemic is still a challenging issue. Here we develop a spatial-temporal compartmental model that incorporates the culling rate as a function of the reported farms and farm density in each town. The epidemiological and geographical data of two species, chickens and ducks, from the farms in the sixteen towns in Eumseong-gun and Jincheon-gun are used to find the best-fitted parameters of the metapopulation model. The best culling radius to maximize the final size of the susceptible farms and minimize the total number of culled farms is calculated from the model. The local reproductive number using the next generation method is calculated as an indicator of virus transmission in a given area. Simulation results indicate that this parameter is strongly influenced not only by epidemiological factors such as transmissibility and/or susceptibility of poultry species but also by geographical and demographical factors such as the distribution of poultry farms (or density) and connectivity (or distance) between farms. Based on this result, we suggest the best culling radius with respect to the local reproductive number in a targeted area.

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Citation: Lee J, Ko Y, Jung E (2019) Effective control measures considering spatial heterogeneity to mitigate the 2016–2017 avian influenza epidemic in the Republic of Korea. PLoS ONE 14(6): e0218202. https://doi.org/10.1371/journal.pone.0218202

Editor: Daniel Becker, Montana State University, UNITED STATES

Received: February 13, 2019; Accepted: May 28, 2019; Published: June 13, 2019

Copyright: © 2019 Lee et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: The data that support the findings of this study are publicly available online at www.mafra.go.kr, www.data.go.kr and www.kosis.kr. The authors confirm that the data set used to reach the conclusions drawn in the manuscript are available in the manuscript and Supporting Information files.

Funding: This work is resulted from the Konkuk University research support program. This paper is supported by the Korea National Research Foundation (NRF) grant funded by the Korean government (MEST) (NRF-2017R1A2B2004651). This paper is also supported by National Institute for Mathematical Sciences (NIMS) grant funded by the Korea government (MSIT) (No. B19610000).

Competing interests: The authors have declared that no competing interests exist.

Keywords: Avian Influenza; Poultry; S. Korea.

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Complete #genome analysis of a #SARS-like #bat #coronavirus identified in the Republic of #Korea (Virus Genes, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Virus Genes. 2019 May 10. doi: 10.1007/s11262-019-01668-w. [Epub ahead of print]

Complete genome analysis of a SARS-like bat coronavirus identified in the Republic of Korea.

Kim Y1,2, Son K1, Kim YS2, Lee SY2, Jheong W1, Oem JK3.

Author information: 1 Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, Republic of Korea. 2 Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea. 3 Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea. jku0623@jbnu.ac.kr.

 

Abstract

Bats have been widely known as natural reservoir hosts of zoonotic diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) caused by coronaviruses (CoVs). In the present study, we investigated the whole genomic sequence of a SARS-like bat CoV (16BO133) and found it to be 29,075 nt in length with a 40.9% G+C content. Phylogenetic analysis using amino acid sequences of the ORF 1ab and the spike gene showed that the bat coronavirus strain 16BO133 was grouped with the Beta-CoV lineage B and was closely related to the JTMC15 strain isolated from Rhinolophus ferrumequinum in China. However, 16BO133 was distinctly located in the phylogenetic topology of the human SARS CoV strain (Tor2). Interestingly, 16BO133 showed complete elimination of ORF8 regions induced by a frame shift of the stop codon in ORF7b. The lowest amino acid identity of 16BO133 was identified at the spike region among various ORFs. The spike region of 16BO133 showed 84.7% and 75.2% amino acid identity with Rf1 (SARS-like bat CoV) and Tor2 (human SARS CoV), respectively. In addition, the S gene of 16BO133 was found to contain the amino acid substitution of two critical residues (N479S and T487 V) associated with human infection. In conclusion, we firstly carried out whole genome characterization of the SARS-like bat coronavirus discovered in the Republic of Korea; however, it presumably has no human infectivity. However, continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by genetic mutation.

KEYWORDS: Bat; Frame shift; SARS-like coronavirus; Whole genome; Zoonotic disease

PMID: 31076983 DOI: 10.1007/s11262-019-01668-w

Keywords: Coronavirus; SARS; Bats; S. Korea.

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Low #risk of #avian #influenza A (#H5N6) #transmission to depopulation #workers in #Korea (Influenza Other Respir Viruses, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Influenza Other Respir Viruses. 2018 May;12(3):412-415. doi: 10.1111/irv.12530. Epub 2018 Jan 5.

Low risk of avian influenza A (H5N6) transmission to depopulation workers in Korea.

Ryu S1,2, Lim JS3, Cowling BJ4, Chun BC2,5.

Author information: 1 Division of Infectious Disease Control, Gyeonggi Provincial Government, Suwon, Korea. 2 Department of Epidemiology and Medical Informatics, Graduate School of Public Health, Korea University, Seoul, Korea. 3 Disease Diagnostic Team, Gyeonggi Province Veterinary Service, Suwon, Korea. 4 WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China. 5 Department of Preventive Medicine, Korea University College of Medicine, Seoul, Korea.

 

Abstract

An outbreak of highly pathogenic avian influenza A (H5N6) virus occurred between November 20, 2016, and March 1, 2017 in poultry farms, in the Gyeonggi Province, Republic of Korea. To identify the risk of transmission of H5N6 to depopulation workers, active and passive surveillance was conducted. Virological testing of respiratory swabs with real-time reverse transcription-polymerase chain reaction was performed for workers who reported respiratory symptoms. Among 4633 depopulation workers, 22 reported respiratory symptoms, but all tested negative for H5N6. Personal protective equipment in addition to antiviral prophylaxis was adequate to limit transmission of H5N6 from poultry to humans.

© 2017 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

KEYWORDS: avian influenza; personal protective equipment; prevention; transmission

PMID: 29236360 PMCID: PMC5907809 DOI: 10.1111/irv.12530 [Indexed for MEDLINE]  Free PMC Article

Keywords: Avian Influenza; H5N6; Poultry; Human; PPE; South Korea.

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