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Genome Sequencing and Analysis of a Porcine Delta Coronavirus from Eastern China

Sawaguchi H1*, Gose K2, Hanada S3 and Muraki M4

1Department of Respiratory Medicine and Allergology, Kindai University Nara Hospital

*Corresponding Author:
Hirochiyo S
Nara Hospital Kinki University Faculty of Medicine, Japan
Tel: +81 743 77 0880
E-mail: [email protected]

Received date: August 26, 2017; Accepted date: September 8, 2017; Published date: September 11, 2017

Citation: Sawaguchi H, Gose K, Hanada S, et al. (2017) Genome sequencing and analysis of a porcine delta coronavirus from eastern China. Eur Exp. Biol. Vol. 7 No. 5:26. doi: 10.21767/2248-9215.100026

Copyright: © 2017 Sawaguchi H, 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.

 
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Abstract

Porcine delta coronavirus (PDCoV) has been reported in many countries, including the United States, Canada, South Korea, China, Thailand, Vietnam and Laos. In December 2016, clinical diarrhea similar to that caused by porcine epidemic diarrhea virus (PEDV), but with a lower mortality rate, was reported on a swine farm in Shanghai, China. 6 Intestine samples were collected from dead suckling piglets (<3 weeks old) with clinical diarrhea, and they were assayed for the presence of swine enteric coronaviruses. Polymerase chain reaction results were positive for PDCoV (6/6), but negative for PEDV (0/6), transmissible gastroenteritis virus (TGEV) (0/6) and porcine rotavirus group A (Rota A) (0/6). The full-length genome sequence of the PDCoV strain SHJS/SL/2016 was determined. Phylogenetic trees demonstrated that PDCoV strain SHJS/SL/2016 belongs to the Chinese clade, which might share a common evolutionary ancestor with United States and South Korean clades, but it clustered separately from Thai and Laotian PDCoV strains. This report describes the complete genome sequence of SHJS/SL/2016, and the data will promote a better understanding of the molecular epidemiology and genetic diversity of PDCoV isolates in China.

Mini Review

Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne severe febrile thrombocytopenic syndrome caused by a new virus classified as Bunyaviridae

Phlebovirus genus announced in 2011 by on New England Journal of Medicine. It is associated high mortality rate and has been reported in China, South Korea and Japan [1]. Even if it is not sucked directly by ticks, it is possible that humans may get infected by SFTS virus by being bitten by animals sucked by ticks. Further, person to person transmission by body fluids has also been reported.

The latency period after infection is 6 to 14 days. When SFTS develops, fever and thrombocytopenia are recognized and bleeding tendency, gastrointestinal symptoms, neurologic symptoms, hepatic dysfunction, and leukopenia is often found. According to the Japanese Ministry of Health, Labor, and Welfare Blood cell phagocytosis image has been confirmed in a previous example in which a bone marrow biopsy was performed in japan. In Japan all case reports are mandated. According to the report of the National Institute of Infectious Disease in Japan, since the first case diagnosed SFTS reported in 2013, the number of reported cases of SFTS is 280 until July 28, 2017, many from early summer to early autumn, and it is reported in 21 prefectures mainly in western Japan3). The ratio between men and women was 133:147, and the median age at the time of notification was 74.0 years old. About 50 to 60 cases were reported per year and the mortality rate is as high as 10% or more. SFTS has also been reported from South Korea. According to Choi SJ, et al. 172 cases were reported from January 2013 to December 2015 throughout the country except in urban areas. They say that most cases occurred from May to October with increasing yearly incidence and the overall case fatality ratio was 32.6%. Park SW and colleagues reported about 170 cases SFTS in South Korea during the same period, and main age group is over 60 years old, and the annual case fatality rate exhibited a downward trend. According to [2], SFTS virus undergoes rapid changes owing to evolution, gene mutations, and re-assortment between different strains of SFTF virus. Furthermore, from 2010 to October 2016, SFTS cases reported had increased numbers yearly and the national average mortality rate was 5.3%, with higher risk to elder people in China. Although these reports suggest several trends, there are still many unclear points such as incidence or severity factor and currently no effective drugs or vaccines for SFTS.

However, various attempts have already been done. Regarding the vaccine have published a paper attempting to identify optimal strains for vaccines from the eight main strains of SFTS virus strains in China [3]. According to that paper, it is concluded that HB 29 strain will be optimal as a standard strain for vaccines because of its strong cross-reactivity with heterologous antibodies and high homology in the S segments with other SFTS virus strains. Now, effective vaccine production and establishment of therapy by cooperation across countries will be awaited.

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