Complete #Genome Sequence of a Novel Swine Acute Diarrhea Syndrome #Coronavirus, CH/FJWT/2018, Isolated in #Fujian, #China, in 2018 (Microbiol Resour Announc., abstract)

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

Microbiol Resour Announc. 2018 Dec 6;7(22). pii: e01259-18. doi: 10.1128/MRA.01259-18. eCollection 2018 Dec.

Complete Genome Sequence of a Novel Swine Acute Diarrhea Syndrome Coronavirus, CH/FJWT/2018, Isolated in Fujian, China, in 2018.

Li K#1,2, Li H#1,2, Bi Z1,2, Gu J1,2, Gong W1,2, Luo S1,2, Zhang F1,2, Song D1,2, Ye Y1,2, Tang Y1,2.

Author information: 1 Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, China. 2 Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China. # Contributed equally

 

Abstract

The full-length genome sequence of a novel swine acute diarrhea syndrome coronavirus (SADS-CoV), CH/FJWT/2018, was determined, which was genetically most closely related to CN/GDWT/2017, recently discovered in Fujian, China. The indel sites of the spike (S) gene of CH/FJWT/2018 were most similar to those of bat-origin SADS-related coronaviruses.

PMID: 30533848 PMCID: PMC6284080 DOI: 10.1128/MRA.01259-18 Free full text

Keywords: Coronavirus; Pigs; SADS-CoV; Fujian; China.

—–

Advertisements

#Replication of #MERS and #SARS #coronaviruses in #bat cells offers insights to their ancestral origins (Emerg Microbes Infect., abstract)

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

Emerg Microbes Infect. 2018 Dec 10;7(1):209. doi: 10.1038/s41426-018-0208-9.

Replication of MERS and SARS coronaviruses in bat cells offers insights to their ancestral origins.

Lau SKP1,2,3,4, Fan RYY5, Luk HKH5, Zhu L5, Fung J5, Li KSM5, Wong EYM5, Ahmed SS5, Chan JFW6,5,7,8, Kok RKH6,5,7,8, Chan KH6,5,7,8, Wernery U9, Yuen KY6,5,7,8, Woo PCY10,11,12,13.

Author information: 1 State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. skplau@hku.hk. 2 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. skplau@hku.hk. 3 Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. skplau@hku.hk. 4 Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. skplau@hku.hk. 5 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. 6 State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. 7 Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. 8 Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. 9 Central Veterinary Research Laboratory, Dubai, United Arab Emirates. 10 State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. pcywoo@hku.hk. 11 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. pcywoo@hku.hk. 12 Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. pcywoo@hku.hk. 13 Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. pcywoo@hku.hk.

 

Abstract

Previous findings of Middle East Respiratory Syndrome coronavirus (MERS-CoV)-related viruses in bats, and the ability of Tylonycteris-BatCoV HKU4 spike protein to utilize MERS-CoV receptor, human dipeptidyl peptidase 4 hDPP4, suggest a bat ancestral origin of MERS-CoV. We developed 12 primary bat cell lines from seven bat species, including Tylonycteris pachypus, Pipistrellus abramus and Rhinolophus sinicus (hosts of Tylonycteris-BatCoV HKU4, Pipistrellus-BatCoV HKU5, and SARS-related-CoV respectively), and tested their susceptibilities to MERS-CoVs, SARS-CoV, and human coronavirus 229E (HCoV-229E). Five cell lines, including P. abramus and R. sinicus but not T. pachypus cells, were susceptible to human MERS-CoV EMC/2012. However, three tested camel MERS-CoV strains showed different infectivities, with only two strains capable of infecting three and one cell lines respectively. SARS-CoV can only replicate in R. sinicus cells, while HCoV-229E cannot replicate in any bat cells. Bat dipeptidyl peptidase 4 (DPP4) sequences were closely related to those of human and non-human primates but distinct from dromedary DPP4 sequence. Critical residues for binding to MERS-CoV spike protein were mostly conserved in bat DPP4. DPP4 was expressed in the five bat cells susceptible to MERS-CoV, with significantly higher mRNA expression levels than those in non-susceptible cells (P = 0.0174), supporting that DPP4 expression is critical for MERS-CoV infection in bats. However, overexpression of T. pachypus DPP4 failed to confer MERS-CoV susceptibility in T. pachypus cells, suggesting other cellular factors in determining viral replication. The broad cellular tropism of MERS-CoV should prompt further exploration of host diversity of related viruses to identify its ancestral origin.

PMID: 30531999 DOI: 10.1038/s41426-018-0208-9

Keywords: Coronavirus; MERS-CoV; SARS; Bats.

—–

Middle East respiratory syndrome #coronavirus (#MERS-CoV): #Impact on #Saudi Arabia, 2015 (Saudi J Biol Sci., abstract)

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

Saudi J Biol Sci. 2018 Nov;25(7):1402-1405. doi: 10.1016/j.sjbs.2016.09.020. Epub 2016 Oct 1.

Middle East respiratory syndrome coronavirus (MERS-CoV): Impact on Saudi Arabia, 2015.

Faridi U1.

Author information: 1 Department of Biochemistry, Tabuk University, Tabuk, Saudi Arabia.

 

Abstract

Middle East respiratory syndrome is the acute respiratory syndrome caused by betacoronavirus MERS-CoV. The first case of this disease was reported from Saudi Arabia in 2012. This virus is lethal and is a close relative of a severe acute respiratory syndrome (SARS), which is responsible for more than 3000 deaths in 2002-2003. According to Ministry of Health, Saudi Arabia. The number of new cases is 457 in 2015. Riyadh has the highest number of reports in comparison to the other cities. According to this report, males are more susceptible than female, especially after the age of 40. Because of the awareness and early diagnosis the incidence is falling gradually. The pre-existence of another disease like cancer or diabetic etc. boosts the infection. MERS is a zoonotic disease and human to human transmission is low. The MERS-CoV is a RNA virus with protein envelope. On the outer surface, virus has spike like glycoprotein which is responsible for the attachment and entrance inside host cells. There is no specific treatment for the MERS-CoV till now, but drugs are in pipeline which bind with the spike glycoprotein and inhibit its entrance host cells. MERS-CoV and SAR-CoV are from the same genus, so it was thought that the drugs which inhibit the growth of SARS-CoV can also inhibit the growth of MERS-CoV but those drugs are not completely inhibiting virus activity. Until we don’t have proper structure and the treatment of MERS-CoV, We should take precautions, especially the health care workers, Camel owners and Pilgrims during Hajj and Umrah, because they are at a higher risk of getting infected.

KEYWORDS: Betacoronavirus; MERS-CoV; SARS; Saudi Arabia

PMID: 30505188 PMCID: PMC6252006  DOI: 10.1016/j.sjbs.2016.09.020

Keywords: Coronavirus; Betacoronavirus; MERS-CoV; SARS; Saudi Arabia; Human; Camels.

—–

Full #genome characterization of two novel Alpha- #coronavirus species from #Italian #bats (Virus Res., abstract)

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

Virus Res. 2018 Nov 14. pii: S0168-1702(18)30585-9. doi: 10.1016/j.virusres.2018.11.007. [Epub ahead of print]

Full genome characterization of two novel Alpha-coronavirus species from Italian bats.

Luca S1, Lelli D2, Faccin F2, Canziani S2, Di Bartolo I3, Vaccari G4, Moreno A2.

Author information: 1 Dept. of Sciences, University Roma Tre, Viale Guglielmo Marconi 446, 00146 Rome, Italy; Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy. 2 Department of Virology, Istituto Zooprofilattico Sperimentale Lombardia ed Emilia Romagna, Via Antonio Bianchi 9, 25124, Brescia, Italy. 3 Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy. 4 Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy. Electronic address: gabriele.vaccari@iss.it.

 

Abstract

Coronaviruses (CoVs) have been detected worldwide in several bat species, which are considered the main reservoir. The attention to the high diversity of CoVs hosted by bats has increased during the last decade due to the high number of human infections caused by two zoonotic Beta-CoVs, SARS-CoV and MERS-CoV, that cause several respiratory diseases. Among coronaviruses, two Alpha-CoV strains (HuCoV-229E and HuCoV-NL63) cause mild respiratory disease that can change to severe disease in children, elderly and individuals affected by illnesses. Phylogenetic analysis conducted on bat Alpha-CoV strains revealed their evolutive correlation to human strains, suggesting their origin in bats. The genome of CoVs is characterized by a high frequency of mutations and recombination events, increasing their ability to switch hosts and their zoonotic potential. In this study, three strains of Alpha-CoV genera detected in Italian bats (Pipistrellus kuhlii) were fully sequenced by Next Generation Sequencing (NGS) and characterized. The complete genome analysis showed the correlation of the Italians strains with a Chinese strain detected in 2013 and, based on CoV molecular species demarcation, two new Alpha-CoV species were established. The analysis of a fragment of the RNA-dependent RNA polymerase (RdRp) showed the correlation of the Italian strains with CoVs was only detected in the bat Pipistrellus genera (Pipistrellus kuhlii and Pipistrellus Pipistrellus) in European countries.

KEYWORDS: Alpha-CoV viruses; Bats; Full genome sequencing; Italy

PMID: 30447246 DOI: 10.1016/j.virusres.2018.11.007

Keywords: Coronavirus; Alphacoronavirus; Italy; Bats.

——

Molecular #identification of #Betacoronavirus in #bats from #Sardinia (#Italy): first detection and phylogeny (Virus Genes., abstract)

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

Virus Genes. 2018 Nov 13. doi: 10.1007/s11262-018-1614-8. [Epub ahead of print]

Molecular identification of Betacoronavirus in bats from Sardinia (Italy): first detection and phylogeny.

Lecis R1,2, Mucedda M3, Pidinchedda E3, Pittau M4,5, Alberti A4,5.

Author information: 1 Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy. rlecis@uniss.it. 2 Mediterranean Centre for Disease Control, University of Sassari, Via Vienna 2, 07100, Sassari, Italy. rlecis@uniss.it. 3 Centro Pipistrelli Sardegna, Via G. Leopardi 1, 07100, Sassari, Italy. 4 Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy. 5 Mediterranean Centre for Disease Control, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.

 

Abstract

Bats may be natural reservoirs for a large variety of emerging viruses, including mammalian coronaviruses (CoV). The recent emergence of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) in humans, with evidence that these viruses may have their ancestry in bats, highlights the importance of virus surveillance in bat populations. Here, we report the identification and molecular characterization of a bat β-Coronavirus, detected during a viral survey carried out on different bat species in the island of Sardinia (Italy). Cutaneous, oral swabs, and faecal samples were collected from 46 bats, belonging to 15 different species, and tested for viral presence. Coronavirus RNA was detected in faecal samples from three different species: the greater horseshoe bat (Rhinolophus ferrumequinum), the brown long-eared bat (Plecotus auritus), and the European free-tailed bat (Tadarida teniotis). Phylogenetic analyses based on RNA-dependent RNA polymerase (RdRp) sequences assigned the detected CoV to clade 2b within betacoronaviruses, clustering with SARS-like bat CoVs previously reported. These findings point to the need for continued surveillance of bat CoV circulating in Sardinian bats, and extend the current knowledge on CoV ecology with novel sequences detected in bat species not previously described as β-Coronavirus hosts.

KEYWORDS: Bats; Coronavirus; RNA-dependent RNA polymerase; Rhinolophus ferrumequinum; Sardinia

PMID: 30426315 DOI: 10.1007/s11262-018-1614-8

Keywords: Coronavirus; Betacoronavirus; SARS; Bats; Italy.

——

#Human #Coronavirus in Hospitalized #Children with #Respiratory Tract #Infections: A Nine-year-long, Population-based Study from #Norway (J Infect Dis., abstract)

[Source: Journal of Infectious Diseases, full page: (LINK). Abstract, edited.]

Human Coronavirus in Hospitalized Children with Respiratory Tract Infections: A Nine-year-long, Population-based Study from Norway

Inger Heimdal, Nina Moe, Sidsel Krokstad, Andreas Christensen, Lars Høsøien Skanke, Svein Arne Nordbø, Henrik Døllner

The Journal of Infectious Diseases, jiy646, https://doi.org/10.1093/infdis/jiy646

Published: 10 November 2018

 

Abstract

Background

The burden of Human Coronavirus- (HCoV) associated respiratory tract infections (RTIs) in hospitalized children is poorly defined. We studied the occurrence and hospitalization rates of HCoV over nine years.

Methods

Children from Sør-Trøndelag County, Norway, hospitalized with RTIs and asymptomatic controls, were prospectively enrolled from 2006 to 2015. Nasopharyngeal aspirates were analyzed with semi-quantitative polymerase chain reaction (PCR) tests for HCoV subtypes OC43, 229E, NL63 and HKU1, and 13 other respiratory pathogens.

Results

HCoV was present in 9.1% (313/3458) of all RTI episodes: 46.6% OC43, 32.3% NL63, 16.0% HKU1 and 5.8% 229E. Hospitalization rates for HCoV-positive children with lower RTIs were 1.5 and 2.8 per 1,000 <5 and <1 years of age, respectively. The detection rate among controls was 9.4% (60/639). Co-detections occurred in 68.1% of the patients and 73.3% of the controls. In a logistic regression analysis, high HCoV genomic loads (cycle threshold <28 in PCR-analysis) were associated with RTIs (OR = 2.16, P = .032) adjusted for relevant factors.

Conclusions

HCoVs occurred in one out of 11 hospitalized children with RTIs and asymptomatic controls. A high HCoV genomic load was associated with RTI. HCoVs are associated with a substantial burden of RTIs in need of hospitalization.

Human Coronaviruses, children, hospitalization rates, respiratory tract infections, asymptomatic controls

Issue Section: Major Article

© The Author(s) 2018. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Coronavirus; Human; Norway.

——

#Genomic characterization and infectivity of a novel #SARS-like #coronavirus in Chinese #bats (Emerg Microbes Infect., abstract)

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

Emerg Microbes Infect. 2018 Sep 12;7(1):154. doi: 10.1038/s41426-018-0155-5.

Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats.

Hu D1,2, Zhu C2, Ai L2, He T2, Wang Y3, Ye F2, Yang L2, Ding C2, Zhu X2, Lv R2, Zhu J2, Hassan B4, Feng Y5, Tan W6, Wang C7,8.

Author information: 1 Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China. 2 Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China. 3 Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu Province, 214064, P.R. China. 4 Stony Brook University, Stony Brook, 11794, USA. 5 Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China. fengyj@zju.edu.cn. 6 Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China. njcdc@163.com. 7 Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China. science2008@hotmail.com. 8 Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China. science2008@hotmail.com.

 

Abstract

SARS coronavirus (SARS-CoV), the causative agent of the large SARS outbreak in 2003, originated in bats. Many SARS-like coronaviruses (SL-CoVs) have been detected in bats, particularly those that reside in China, Europe, and Africa. To further understand the evolutionary relationship between SARS-CoV and its reservoirs, 334 bats were collected from Zhoushan city, Zhejiang province, China, between 2015 and 2017. PCR amplification of the conserved coronaviral protein RdRp detected coronaviruses in 26.65% of bats belonging to this region, and this number was influenced by seasonal changes. Full genomic analyses of the two new SL-CoVs from Zhoushan (ZXC21 and ZC45) showed that their genomes were 29,732 nucleotides (nt) and 29,802 nt in length, respectively, with 13 open reading frames (ORFs). These results revealed 81% shared nucleotide identity with human/civet SARS CoVs, which was more distant than that observed previously for bat SL-CoVs in China. Importantly, using pathogenic tests, we found that the virus can reproduce and cause disease in suckling rats, and further studies showed that the virus-like particles can be observed in the brains of suckling rats by electron microscopy. Thus, this study increased our understanding of the genetic diversity of the SL-CoVs carried by bats and also provided a new perspective to study the possibility of cross-species transmission of SL-CoVs using suckling rats as an animal model.

PMID: 30209269 DOI: 10.1038/s41426-018-0155-5

Keywords: Coronavirus; Bats; China.

——