Back

Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019

Wong, M. C.; Javornik Cregeen, S. J.; Ajami, N. J.; Petrosino, J. F.

2020-02-13 microbiology
10.1101/2020.02.07.939207 bioRxiv
Show abstract

A novel coronavirus (nCoV-2019) was the cause of an outbreak of respiratory illness detected in Wuhan, Hubei Province, China in December of 2019. Genomic analyses of nCoV-2019 determined a 96% resemblance with a coronavirus isolated from a bat in 2013 (RaTG13); however, the receptor binding motif (RBM) of these two genomes share low sequence similarity. This divergence suggests a possible alternative source for the RBM coding sequence in nCoV-2019. We identified high sequence similarity in the RBM between nCoV-2019 and a coronavirus genome reconstructed from a viral metagenomic dataset from pangolins possibly indicating a more complex origin for nCoV-2019.

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
Viruses
○ 332 papers in training set
Top 0.1%
23.0%
Similar papers in this journal
2
Journal of Medical Virology
○ 140 papers in training set
Top 0.1%
12.2%
Similar papers in this journal
3
Virus Evolution
◐ 155 papers in training set
Top 0.3%
6.9%
Similar papers in this journal
4
Scientific Reports
○ 3612 papers in training set
Top 9%
6.9%
Similar papers in this journal
5
Archives of Virology
○ 15 papers in training set
Top 0.1%
5.6%
Similar papers in this journal
50% of probability mass above
6
Journal of General Virology
● 53 papers in training set
Top 0.2%
2.7%
7
Frontiers in Microbiology
○ 427 papers in training set
Top 4%
2.7%
8
Virology Journal
○ 32 papers in training set
Top 0.2%
2.2%
9
Frontiers in Cellular and Infection Microbiology
○ 109 papers in training set
Top 1%
2.2%
10
Microbiology Resource Announcements
● 25 papers in training set
Top 0.2%
2.0%
11
Microbiology Spectrum
● 469 papers in training set
Top 6%
2.0%
12
Pathogens
○ 56 papers in training set
Top 0.5%
1.8%
13
Frontiers in Virology
○ 15 papers in training set
Top 0.1%
1.7%
14
Virology
○ 61 papers in training set
Top 0.7%
1.7%
15
iScience
○ 1154 papers in training set
Top 20%
1.5%
16
PeerJ
◐ 308 papers in training set
Top 6%
1.5%
17
Infection, Genetics and Evolution
○ 42 papers in training set
Top 0.5%
1.4%
18
Access Microbiology
● 25 papers in training set
Top 0.4%
1.2%
19
PLOS Pathogens
● 820 papers in training set
Top 7%
1.2%
20
Microorganisms
○ 106 papers in training set
Top 3%
1.1%
21
Virus Research
○ 37 papers in training set
Top 0.6%
1.1%
22
Emerging Microbes & Infections
○ 74 papers in training set
Top 1%
1.0%
23
F1000Research
○ 88 papers in training set
Top 3%
0.9%
24
mSphere
● 302 papers in training set
Top 6%
0.9%
25
Journal of Infection
○ 78 papers in training set
Top 1%
0.9%
26
Vaccines
○ 198 papers in training set
Top 4%
0.6%
27
Heliyon
○ 152 papers in training set
Top 9%
0.6%
28
Journal of Virology
● 499 papers in training set
Top 3%
0.6%
29
Microbial Genomics
● 225 papers in training set
Top 3%
0.6%
30
PLOS ONE
● 5266 papers in training set
Top 61%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.