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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Inevitable #isolation and the change of #stress markers in #hemodialysis patients during the 2015 #MERS-CoV #outbreak in #Korea (Sci Rep., abstract)

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

Sci Rep. 2019 Apr 5;9(1):5676. doi: 10.1038/s41598-019-41964-x.

Inevitable isolation and the change of stress markers in hemodialysis patients during the 2015 MERS-CoV outbreak in Korea.

Kim YG1, Moon H1, Kim SY1, Lee YH1, Jeong DW1, Kim K1, Moon JY1, Lee YK2, Cho A2, Lee HS3, Park HC4, Lee SH5.

Author information: 1 Division of Nephrology, Kyung Hee University College of Medicine, Seoul, Korea. 2 Hallym University College of Medicine, Internal Medicine, Seoul, Korea. 3 Hallym University College of Medicine, Psychiatry, Seoul, Korea. 4 Department of Internal Medicine, Armed Forces Capital Hospital, Seongnam, Korea. 5 Division of Nephrology, Kyung Hee University College of Medicine, Seoul, Korea. lshkidney@khu.ac.kr.

 

Abstract

During the outbreak of Middle East respiratory syndrome coronavirus(MERS-CoV) in 2015, one hemodialysis patient was infected with MERS-CoV, and the remaining hemodialysis(HD) patients (n = 83) and medical staff (n = 12) had to undergo dialysis treatment in an isolated environment. This study was performed to investigate the effects of stress caused by dialysis treatment under isolation. Plasma samples from the HD patients and medical staff were collected at the time of isolation(M0), the following month(M1), and three months after isolation(M3). Parameters for stress included circulating cell-free genomic DNA(ccf-gDNA), circulating cell-free mitochondria DNA(ccf-mtDNA), and pentraxin-3(PTX-3). Decreased values of Hct, kt/v and ca x p were recovered after the end of two weeks of isolation. The levels of ccf-gDNA and ccf-mtDNA were the highest at M0 and decreased gradually in both HD patients and the medical staff. The normalization of ccf-gDNA and ccf-mtDNA was significantly delayed in HD patients compared with the response in the medical staff. PTX-3 increased only in HD patients and was highest at M0, and it then gradually decreased. Medical isolation and subnormal quality of care during the MERS outbreak caused extreme stress in HD patients. Plasma cell-free DNA and PTX-3 seems to be good indicators of stress and quality of care in HD patients.

PMID: 30952879 DOI: 10.1038/s41598-019-41964-x

Keywords: MERS-CoV; Nosocomial Outbreaks; S. Korea.

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Identification of #Influenza C Virus in Young South #Korean #Children, from October 2013 to September 2016 (J Clin Virol., abstract)

[Source: Journal of Clinical Virology, full page: (LINK). Abstract, edited.]

Journal of Clinical Virology / Available online 27 March 2019 / In Press, Accepted Manuscript / Short communication

Identification of Influenza C Virus in Young South Korean Children, from October 2013 to September 2016

Han Sol Lee a,1, Sooyeon Lim a,b,1, Ji Yun Noh a, Joon Young Song a, Hee Jin Cheong a,c, Jung Hwa Lee d, Sung Il Woo e, Woo Joo Kim a,c

{a} Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, South Korea; {b} Division of Brain Korea 21 Program for Biomedicine Science, College of Medicine, Korea University, Seoul, South Korea; {c} Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, South Korea; {d} Department of Pediatrics, Korea University College of Medicine, Seoul, South Korea; {e} Department of Pediatrics, Chungbuk National University Hospital and College of Medicine, Cheongju, South Korea

Received 7 January 2019, Revised 8 March 2019, Accepted 26 March 2019, Available online 27 March 2019.

DOI: https://doi.org/10.1016/j.jcv.2019.03.016

 

Highlights

  • Five (1.22%) influenza C viruses were detected in 409 RV16 test negative samples during the influenza season.
  • Young children are infected with influenza C virus and are at risk for acute respiratory illness.
  • C/Sao Paulo/387/82-like lineage viruses circulated in South Korea.
  • Re-assortment event was observed in the C/Seoul/APD462/2015 strain.

 

Abstract

Background

Influenza C virus has been largely neglected, compared to influenza A orB viruses, and is not routinely tested in clinical practices. However, several studies have indicated that influenza C virus causes severe acute respiratory illness and pneumonia in all ages.

Objective

We conducted a study to identify influenza C virus among young children in South Korea.Study design. From October 2013 to September 2016, 973 young children with influenzalike illness (ILI) were enrolled at three university hospitals. We tested nasopharyngeal samples for 16 types of respiratory viruses. Among the tested samples, 564 were positive for one or more respiratory viruses. Except for the samples where 16 types of respiratory viruses were found, 409 negative samples were examined for the presence of influenza C virus, using a matrix gene specific primer set.

Results

Among 409 nasopharyngeal samples, five influenza C viruses were detected. The manifestation of influenza C virus infection in young children was observed acute respiratory illness, such as fever, rhinorrhea, and cough, but no pneumonia or severe respiratory illness. Nucleotide sequencing was conducted and a phylogenetic tree was generated. We found that C/Sao Paulo/387/82-like lineage viruses circulated in South Korea, and the fully sequenced virus (C/Seoul/APD462/2015) was closely related to C/Victoria/2/2012 and C/Tokyo/4/2014 strains.

Conclusions

This study was the first report of influenza C virus detection in South Korea. Although severe illness was not observed in this study, we suggest the necessity for influenza C virus testing in pediatric patients with ILI, considering other reports of severe illnesses caused by influenza C virus infections.

Keywords: Influenza C virus – South Korea – Phylogenetic analysis

1 These authors contributed equally to this work.

© 2019 Published by Elsevier B.V.

Keywords: Seasonal Influenza; Influenza C; South Korea.

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Sequential #Emergence and Wide Spread of Neutralization #Escape #MERS #Coronavirus #Mutants, South #Korea, 2015 (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 6—June 2019 / Research

Sequential Emergence and Wide Spread of Neutralization Escape Middle East Respiratory Syndrome Coronavirus Mutants, South Korea, 2015

Yeon-Sook Kim1, Abdimadiyeva Aigerim1, Uni Park1, Yuri Kim, Ji-Young Rhee, Jae-Phil Choi, Wan Beom Park, Sang Won Park, Yeonjae Kim, Dong-Gyun Lim, Kyung-Soo Inn, Eung-Soo Hwang, Myung-Sik Choi, Hyoung-Shik Shin2  , and Nam-Hyuk Cho2

Author affiliations: Chungnam National University School of Medicine, Daejeon, South Korea (Y.-S. Kim); Seoul National University College of Medicine, Seoul, South Korea (A. Aigerim, U. Park, Y. Kim, W.B. Park, S.W. Park, E.-S. Hwang, M.-S. Choi, N.-H. Cho); Dankook University College of Medicine, Cheonan, South Korea (J.-Y. Rhee); Seoul Medical Center, Seoul (J.-P. Choi); National Medical Center, Seoul (Y. Kim, D.-G. Lim, H.S. Shin); Kyung Hee University, Seoul (K.-S. Inn); Seoul National University Medical Research Center and Bundang Hospital, Seoul (N.H. Cho)

 

Abstract

The unexpectedly large outbreak of Middle East respiratory syndrome in South Korea in 2015 was initiated by an infected traveler and amplified by several “superspreading” events. Previously, we reported the emergence and spread of mutant Middle East respiratory syndrome coronavirus bearing spike mutations (I529T or D510G) with reduced affinity to human receptor CD26 during the outbreak. To assess the potential association of spike mutations with superspreading events, we collected virus genetic information reported during the outbreak and systemically analyzed the relationship of spike sequences and epidemiology. We found sequential emergence of the spike mutations in 2 superspreaders. In vivo virulence of the mutant viruses seems to decline in human patients, as assessed by fever duration in affected persons. In addition, neutralizing activity against these 2 mutant viruses in serum samples from mice immunized with wild-type spike antigen were gradually reduced, suggesting emergence and wide spread of neutralization escapers during the outbreak.

Keywords: MERS-CoV; South Korea.

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#Airflow as a Possible #Transmission #Route of #MERS at an Initial #Outbreak #Hospital in #Korea (Int J Environ Res Public Health., abstract)

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

Int J Environ Res Public Health. 2018 Dec 6;15(12). pii: E2757. doi: 10.3390/ijerph15122757.

Airflow as a Possible Transmission Route of Middle East Respiratory Syndrome at an Initial Outbreak Hospital in Korea.

Sung M1, Jo S2, Lee SE3, Ki M4, Choi BY5, Hong J6.

Author information: 1 Department of Architectural Engineering, Sejong University, 209, Seoul 05006, Korea. mksung@sejong.ac.kr. 2 Department of Architectural Engineering, Sejong University, 209, Seoul 05006, Korea. joseongmin01@naver.com. 3 Division of Vectors and Parasitic Diseases, Korea Centers for Disease Control and Prevention, Cheongju 28159, Korea. ondalgl@korea.kr. 4 Department of Cancer Control and Population Health, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea. moranki@ncc.re.kr. 5 Department of Preventive Medicine, Hanyang University Medical College, Seoul 04763, Korea. bychoi@hanyang.ac.kr. 6 Department of HVAC & Firefighting Engineering, Gachon University, Seongnam 13120, Korea. jkhong@gachon.ac.kr.

 

Abstract

In this study, the results of an airflow investigation conducted on 7 June 2015 as part of a series of epidemiologic investigations at Pyeongtaek St. Mary’s Hospital, South Korea, were investigated. The study involved 38 individuals who were infected directly and indirectly with Middle East Respiratory Syndrome (MERS), by a super-spreader patient. Tracer gas experiments conducted on the eighth floor, where the initial patient was hospitalized, confirmed that the tracer gas spread to adjacent patient rooms and rooms across corridors. In particular, the experiment with an external wind direction and speed similar to those during the hospitalization of the initial patient revealed that the air change rate was 17⁻20 air changes per hour (ACH), with air introduced through the window in the room of the infected patient (room 8104). The tracer gas concentration of room 8110, which was the farthest room, was 7.56% of room 8104, indicating that a high concentration of gas has spread from room 8104 to rooms across the corridor. In contrast, the tracer gas was barely detected in a maternity ward to the south of room 8104, where there was no secondary infected patient. Moreover, MERS is known to spread mainly by droplets through close contact, but long-distance dispersion is probable in certain environments, such as that of a super-spreader patient hospitalized in a room without ventilation, hospitals with a central corridor type, and indoor airflow dispersion due to external wind.

KEYWORDS: Middle East Respiratory Syndrome; airflow analysis; infection outbreak; tracer gas; transmission route; ventilation

PMID: 30563206 DOI: 10.3390/ijerph15122757 [Indexed for MEDLINE]  Free full text

Keywords: MERS-CoV; Nosocomial outbreaks; S. Korea.

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#Difficulties in using #PPE: #Training experiences with the 2015 #outbreak of #MERS in #Korea (Am J Infect Control., abstract)

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

Am J Infect Control. 2018 Feb;46(2):235-237. doi: 10.1016/j.ajic.2017.08.041. Epub 2017 Oct 16.

Difficulties in using personal protective equipment: Training experiences with the 2015 outbreak of Middle East respiratory syndrome in Korea.

Kang J1, Kim EJ2, Choi JH3, Hong HK4, Han SH5, Choi IS6, Ryu JG7, Kim J8, Kim JY9, Park ES10.

Author information: 1 College of Nursing, Seoul National University, Seoul, Republic of Korea; Research Institute of Nursing Science, Seoul National University, Seoul, Republic of Korea. Electronic address: jahyunkang@gmail.com. 2 Seoul National University Hospital, Seoul, Republic of Korea. 3 Konkuk University Medical Center, Seoul, Republic of Korea. 4 Soonchunhyang University Bucheon Hospital, Bucheon-si, Gyeonggi-do, Republic of Korea. 5 Dankook University Hospital, Cheonan-si, Chungcheongnam-do, Republic of Korea. 6 Chung-Ang University Hospital, Seoul, Republic of Korea. 7 College of Nursing, Seoul National University, Seoul, Republic of Korea. 8 Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea. 9 Konyang University Hospital, Daejeon-si, Chungcheongnam-do, Republic of Korea. 10 Yonsei University Severance Hospital, Seoul, Republic of Korea.

 

Abstract

This study aimed to evaluate practical barriers to personal protective equipment (PPE) use found through health care personnel (HCP) training sessions held during and after the 2015 Middle East respiratory syndrome outbreak in Korea. Difficulties observed were ill-fitting sizes, anxiety, confusion from unstandardized protocols, doubts about PPE quality and effectiveness, and complexity of using several PPE items together. Further research to generate robust evidence and repeated HCP trainings are necessary to ensure HCP and patient safety in future outbreaks.

Copyright © 2018 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

KEYWORDS: Focus group interview; Health care personnel; Personal protective equipment

PMID: 29050907 DOI: 10.1016/j.ajic.2017.08.041 [Indexed for MEDLINE]

Keywords: MERS-CoV; PPE; HCW; S. Korea.

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