Beta coronavirus

Beta coronavirus
MERS-CoV ( electron microscopic image)
Systematics
Classification : Viruses Area : Riboviria Empire : Orthornavirae Phylum : Pisuviricota Class : Pisoniviricetes Order : Nidovirals Subordination : Cornidovirineae Family : Coronaviridae Subfamily : Orthocoronavirinae Genre : Beta coronavirus
Taxonomic characteristics
Genome : (+) ssRNA linear Baltimore : Group 4 Symmetry : helical Cover : available
Scientific name
Beta coronavirus
Short name
Beta-CoV, BetaCoV
Left
NCBI  Taxonomy: 694002

Betacoronaviruses are one of four genera of coronaviruses of the subfamily Orthocoronavirinae in the family Coronaviridae of the order Nidovirales . In the older literature, this genus is also referred to as group 2 coronaviruses . They are enveloped single-stranded RNA viruses with positive polarity and zoonotic origin.

The coronavirus genera are each composed of various viral "lines" ( English lineage , lineage ' ) together with the genus Beta coronavirus contains four such lines (as of 2001), which now than four subgenera are classified plus another subgenus. In addition to the alphacoronavirus , they are the only genus that has been found in bat species (as of 2019).

The type species of the genus is murine coronavirus (German mouse coronavirus), to which the subspecies rat coronavirus belongs. The beta coronaviruses with the greatest clinical significance for humans are the human coronavirus OC43 and the human coronavirus HKU1 of the A line (subgenus Embecovirus ), SARS-CoV -1 and SARS-CoV-2 (alias 2019-nCoV) of the B line (Subgenus Sarbecovirus ) and MERS-CoV of the C line (subgenus Merbecovirus ).

Occurrence

With regard to the evolution of the coronaviruses, it can be shown that the genera Alphacoronavirus and Betacoronavirus come from the gene pool of bats . Representatives of both genera are able to infect humans .

Bat species from the smooth-nosed family (Vespertilionidae) are host animals of beta coronaviruses, for example the following species:

• Zwergfledermaus ( Pipistrellus pipistrellus ) and Pipistrellus abramus from the genus dwarf bats ( Pipistrellus )
• Alpine bat ( Hypsugo savii , synonym : Pipistrellus savii ) from the genus Hypsugo ,
• Eptesicus isabellinus from the genus broad-winged bats ( Eptesicus ) and
• Tylonycteris pachypus from the genus bamboo bats ( Tylonycteris ).

Also:

• Stoliczka trident leaf-nosed ( Aselliscus stoliczkanus ) from the family of hipposideridae ( Hipposideridae ).

Species from the horseshoe bat family (Rhinolophidae) are also host animals for beta coronaviruses, for example the following species

• Rhinolophus ferrumequinum ( greater horseshoe bat ),
• Rhinolophus macrotis ( large-eared horseshoe bat ),
• Rhinolophus pearsonii ( Pearson's horseshoe bat ),
• Rhinolophus sinicus ( Chinese horseshoe bat ) - virus species SARS-associated coronavirus  - and
• Rhinolophus affinis ( Java horseshoe bat , English intermediate horseshoe bat ) - virus species SARS-associated coronavirus.

Other host animals of betacoronaviruses are among the mammals u. a .:

• Virus species Betacoronavirus 1 :

• Cattle ( bovine coronavirus [BCoV]),
• Dogs ( canine respiratory coronavirus [CRCoV]),
• Horses ( equines coronavirus [ECoV]),
• Pigs ( Porcine Hemagglutinating Encephalitis Virus [PHEV]),

• Virus species Severe acute respiratory syndrome-related coronavirus :

• Roller larvae (larvae Roller-SARS coronavirus PC4-13 [civet-SARS-CoV-PC4-13] and larvae Roller-SARS coronavirus SZ3 [civet-SARS-CoV-SZ3]),
• Pangolins (scaly animal coronavirus [ Manis- CoV])

• Virus species Murine coronavirus :

• Old World Mice ( Murine Hepatitis Virus [MHV]),
• Rats ( rat coronavirus [RtCoV]).

Host animals of other vertebrate classes are demonstrably:

• Virus species Murine coronavirus :

• Birds ( Puffinosis coronavirus [PV], in black-billed shearwaters of the species Atlantic shearwaters , scientifically Puffinus puffinus )

Molecular genetics

Schematic structure of the virion (virus particle) of a coronavirus, the English terms used can be found in the text.

The single-stranded RNA genome of the betacoronaviruses is approximately 29,000 to 31,100  nucleotides (nt) long. The complete RNA sequence analysis by means of reverse transcriptase polymerase chain reaction (RT-PCR) of three beta coronaviruses (HKU4, HKU5 and HKU9) isolated from bats shows a genome size of 29,017 to 30,488 nucleotides, the GC content (the proportion of the nucleobases guanine and cytosine ) is between 38 and 41 mol percent. The sequence of the genes largely corresponds to that of other coronaviruses : At the 5 ′ end are the two open reading frames ORF 1a and ORF 1b, which make up the largest part of the genome (20,800 to 21,000 nt) and for the non-structural proteins (NSP) 1a and 1b encoding . Followed by the genes for the hemagglutinin - esterase which (HE) spikes (S), viral envelope (E for English envelope , envelope ' ), matrix proteins (M) and nucleocapsid (N) encoding. Both at the 5 'end and at the 3' end there are short, non-coding regions (UTR, untranslated region ). The HE gene is only found in the beta coronaviruses.

The open reading frames (ORF) code for several putative ( putative ) proteins , including

• NSP 3 (contains the putative papain- like protease PLPro),
• NSP 5 (contains the putative chymotrypsin- like protease 3CLPro),
• NSP 12 (contains the putative RNA-dependent RNA polymerase , English RNA-dependent RNA polymerase RdRP),
• NSP 13 (contains the putative helicase ),
• NSP 14 (which contains the putative 3 '→ 5' - exonuclease exon)
• NSP 15 (contains the putative poly ( U ) -specific endoribonuclease XendoU) and
• NSP 16 (contains the putative S- adenosylmethionine -dependent 2'-O-ribose methyltransferase 2'-O-MT).

The non-structural proteins are created by specific proteolytic cleavage by the PLPro and 3CLPro from an initially generated replicase polyprotein 1ab .

Since betacoronaviruses have different hosts and parts of their genome are recombined , they pose a potential threat to human health. For example, a genetic comparison of a betacoronavirus isolated from human sputum in 2012 with beta-CoV, which occurs in bats, showed a match between the Nucleotide sequences from 82.0% - 87.7%.

Systematics

→ Main article : Coronaviridae

Cladogram based on the phylogenetic analysis of the virus genomes of representative virus isolates of the genus Betacoronavirus (as of 2020)
Sarbecovirus    Clade 3  SARS-CoV -1 (several isolates; 2003-2005)     Coronavirus BtRs-BetaCoV / GX2013 (2016)     Coronavirus BtRl-BetaCoV (2018)     Bat coronavirus (isolate BtCoV / 279/2005; 2006)     Bat SARS coronavirus HKU3-12 (2010)     Bat SARS coronavirus HKU3-3 (2005)     Bat SARS coronavirus HKU3-7 (2010)     Bat SARS-like coronavirus (Isolat Longquan-140; 2013)   Clade 2  SARS-CoV-2 (outdated 2019-nCoV, several isolates; 2020)     Bat SARS-like coronavirus (isolate bat-SL-CoVZC45; 2018)     Bat SARS-like coronavirus (isolate bat-SL-CoVZXC21; 2018)   Clade 1  SARS-related coronavirus ( strain BtKY72; 2019)     Bat coronavirus BM48-31 / BGR / 2008 (2010)   Hibecovirus  Bat Hp-betacoronavirus / Zhejiang2013 (Hp = Hipposideros pratti ; 2016)   Nobecovirus  Rousettus bat coronavirus (isolate GCCDC1 356; 2016)     Bat coronavirus HKU9-1 (Rousettus bat coronavirus HKU9, Ro-BatCoV-HKU9; 2007)   Merbecovirus  Bat coronavirus HKU5-1 ( Pipistrellus bat coronavirus HKU5, Pi-BatCoV-HKU5; 2007)     Bat coronavirus HKU4-1 ( Tylonycteris bat coronavirus HKU4, Ty-BatCoV-HKU4; 2007)     Human coronavirus EMC (human beta coronavirus 2c EMC / 2012, MERS-CoV ; 2012)     Betacoronavirus Erinaceus / VMC / DEU / 2012 (2014)   Embecovirus      Human coronavirus OC43 (HCoV-OC43; 2003)     Betacoronavirus HKU24 (strain HKU24-R05010I; 2015)     Murine Coronavirus (Murine Hepatitis Virus, MHV-1; 2006)     Human coronavirus HKU1 (HCoV-HKU1; 2004)
The upper part of the clade 3 is simplified due to the template limitation. To Virustaxonomie: English bat , bat '; SARS-related coronavirus (English) = SARS-associated coronavirus (German) = SARS-like coronavirus (English) = SARS virus (English) = SARS coronavirus (English), these are heterotypical synonyms ; SARS = Severe acute respiratory syndrome (English) = Severe acute respiratory syndrome (Ger.); The indication of the year in brackets refers to the publication of the genome analyzes, they can be called up in the NCBI GenBank. according to R. Lu et al. (2020), additional information according to JF-W. Chan et al. (2020)

Within the genus Betacoronavirus (formerly known as group 2 coronaviruses ), phylogenetic studies identified four subgroups ( lineage , line of descent), which are identified by letters (A, B, C and D or a, b, c and d ), Greek letters (α, β, γ and δ) and sometimes with numbers. In 2018 these subgroups were classified as subgenus , and a fifth subgenus Hibecovirus was defined.

• Lineage A → subgenus embecovirus
• Lineage B → Subgenus Sarbecovirus
• Lineage C → subgenus Merbecovirus
• Lineage D → subgenus Nobecovirus
• Subgenus Hibecovirus

Due to the increasing number of genome analyzes that are published in databases, it is possible to create a phylogenetic system . In connection with the occurrence of the "novel coronavirus of 2019" (2019-nCoV, newer name: SARS-CoV-2), several groups of scientists have published the results of their phylogenetic studies. The evolutionary relationships between the representatives of the beta coronaviruses are also illustrated as a phylogenetic tree , which is the basis for the presentation in this article. The genome sequences are available in the GenBank of the National Center for Biotechnology Information (NCBI).

Medical importance

Several representatives of the genus Betacoronavirus are able to infect humans. Beta-CoV that have been involved in epidemics often cause fever and respiratory infections . Well-known examples are:

• SARS-CoV -1 that causes severe acute respiratory syndrome ( severe acute respiratory syndrome, SARS), first in 2002 in China occurred ( SARS pandemic 2002/2003 )
• MERS-CoV ("Middle East respiratory syndrome coronavirus"), several epidemics from 2012
• SARS-CoV-2 (formerly "2019-nCoV", "novel coronavirus of 2019"), COVID-19 pandemic

Individual evidence

1. ↑ ICTV Taxonomy history: Betacoronavirus, ICTV Master Species List 2018b, MSL # 34. February 2019, accessed February 1, 2020 . 
2. ↑ ^{a b c d} ICTV: ICTV Taxonomy history: Severe acute respiratory syndrome-related coronavirus , EC 51, Berlin, Germany, July 2019; Email ratification March 2020 (MSL # 35)
3. ↑ ^{a b c d e f} Matthew Cotten, Tommy T. Lam, Simon J. Watson, Anne L. Palser, Velislava Petrova, Paul Grant, Oliver G. Pybus, Andrew Rambaut, Y. i. Guan, Deenan Pillay, Paul Kellam, Eleni Nastouli: Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus . In: Emerging Infectious Diseases . tape 19 , no. 5 , May 2013, p. 736-742 , doi : 10.3201 / eid1905.130057 , PMID 23693015 , PMC 3647518 (free full text).
4. ^ Antonio CP Wong, Xin Li, Susanna KP Lau and Patrick CY Woo: Global Epidemiology of Bat Coronaviruses . Abstract. In: Viruses . Volume, no. 11 . MDPI, February 20, 2019, p. 174 , doi : 10.3390 / v11020174 , PMID 30791586 , PMC 6409556 (free full text) - (English, full text [PDF; 2.2 MB ; accessed on May 31, 2020]).
5. ↑ ICTV: ICTV Master Species List 2019.v1. MSL # 35, March 2020
6. ↑ ^{a b c d} Kristian G. Andersen, Andrew Rambaut, W. Ian Lipkin, Edward C. Holmes, Robert F. Garry: The Proximal Origin of SARS-CoV-2. In: virologica.org , source: ARTIC Network, February 17, 2020
7. ↑ ^{a b} Patrick CY Woo, Susanna KP Lau: Viruses and Bats . In: Viruses . tape 11 , no. October 10 , 2019, p. 884 , doi : 10.3390 / v11100884 , PMID 31546572 , PMC 6832948 (free full text).
8. ↑ ^{a b c d} PCY Woo, M. Wang, SKP Lau, H. Xu, RWS Poon, R. Guo, BHL Wong, K. Gao, H.-w. Tsoi, Y. Huang, KSM Li, CSF Lam, K.-h. Chan, B.-j. Zheng, K.-y. Yuen: Comparative Analysis of Twelve Genomes of Three Novel Group 2c and Group 2d Coronaviruses Reveals Unique Group and Subgroup Features . In: Journal of Virology . tape 81 , no. 4 , February 2007, p. 1574–1585 , doi : 10.1128 / JVI.02182-06 , PMID 17121802 , PMC 1797546 (free full text).
9. ↑ ^{a b c} TRBA (Technical Rules for Biological Agents) 462: Classification of viruses in risk groups. In: Website of the Federal Institute for Occupational Safety and Health (BAuA). April 25, 2012, pp. 23-24 , accessed on February 1, 2020 (last change on July 3, 2018).  
10. ↑ ^{a b c d} International Committee on Taxonomy of Viruses (ICTV): Complete Coronavirus Genome Sequences. 2019, accessed February 1, 2020 .  
11. ↑ Ben Hu, Lei-Ping Zeng, Xing-Lou Yang, Xing-Yi Ge, Wei Zhang et al. : Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus , in: PLOS Pathogens, November 30, 2017, doi: 10.1371 / journal.ppat.1006698
12. ↑ Stefan Hintsche: System of living beings: Rhinolophidae (2013)
13. ↑ Horseshoe- nosed bats. Protection Association of German Forests , Oberursel from December 16, 2015
14. ↑ Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu, Lei Zhang, Wei Zhang, Hao-Rui Si, Yan Zhu, Bei Li, Chao-Lin Huang, Hui-Dong Chen, Jing Chen, Yun Luo, Hua Guo, Ren-Di Jiang, Mei-Qin Liu, Ying Chen, Xu-Rui Shen, Xi Wang, Xiao-Shuang Zheng, Kai Zhao, Quan-Jiao Chen, Fei Deng, Lin-Lin Liu, Bing Yan, Fa- Xian Zhan, Yan-Yi Wang, Geng-Fu Xiao, Zheng-Li Shi: A pneumonia outbreak associated with a new coronavirus of probable bat origin . In: Nature . February 3, 2020, doi : 10.1038 / s41586-020-2012-7 (English, this article was published on bioRxiv on January 23, 2020 in advance without peer review).
15. ↑ Chengxin Zhang et al. : Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1 , in: American Chemical Society: J. Proteome Res. From March 22, 2020, doi: 10.1021 / acs.jproteome.0c00129 ; PrePrint , PrePrint full text (PDF) from February 8, 2020
16. ↑ Taxonomy Browser Severe acute respiratory syndrome-related coronavirus. In: National Center for Biotechnology Information (NCBI) website . Retrieved February 7, 2020 .  
17. ↑ ^{a b} Roujian Lu, Xiang Zhao, Juan Li, Peihua Niu, Bo Yang, Honglong Wu, Wenling Wang, Hao Song, Baoying Huang, Na Zhu, Yuhai Bi, Xuejun Ma, Faxian Zhan, Liang Wang, Tao Hu, Hong Zhou , Zhenhong Hu, Weimin Zhou, Li Zhao, Jing Chen, Yao Meng, Ji Wang, Yang Lin, Jianying Yuan, Zhihao Xie, Jinmin Ma, William J Liu, Dayan Wang, Wenbo Xu, Edward C Holmes, George F Gao, Guizhen Wu, Weijun Chen, Weifeng Shi, Wenjie Tan: Genomic characterization and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding . In: The Lancet . January 29, 2020, doi : 10.1016 / S0140-6736 (20) 30251-8 .
18. ↑ ^{a b} Jasper Fuk-Woo Chan, Shuofeng Yuan, Kin-Hang Kok, Kelvin Kai-Wang To, Hin Chu, Jin Yang, Fanfan Xing, Jieling Liu, Cyril Chik-Yan Yip, Rosana Wing-Shan Poon, Hoi-Wah Tsoi, Simon Kam-Fai Lo, Kwok-Hung Chan, Vincent Kwok-Man Poon, Wan-Mui Chan, Jonathan Daniel Ip, Jian-Piao Cai, Vincent Chi-Chung Cheng, Honglin Chen, Christopher Kim-Ming Hui, Kwok- Yung Yuen: A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster . In: The Lancet . January 24, 2020, doi : 10.1016 / S0140-6736 (20) 30154-9 .
19. ^ Antonio CP Wong, Xin Li, Susanna KP Lau, Patrick CY Woo: Global Epidemiology of Bat Coronaviruses . In: Viruses . tape 11 , no. 2 , February 2019, p. 174 , doi : 10.3390 / v11020174 , PMID 30791586 , PMC 6409556 (free full text).
20. ↑ International Committee on Taxonomy of Viruses (ICTV): Virus Taxonomy: 2018b Release. February 2019, accessed February 1, 2020 .  
21. ↑ Taxonomy Browser Betacoronavirus. In: National Center for Biotechnology Information (NCBI) website . Retrieved on February 7, 2020 ( there are web links to the genome and nucleotide database in the Taxonomy Browser ).