Host and infectivity prediction of Wuhan 2019 novel coronavirus using deep learning algorithm

Abstract

The recent outbreak of pneumonia in Wuhan, China caused by the 2019 Novel Coronavirus (2019-nCoV) emphasizes the importance of detecting novel viruses and predicting their risks of infecting people. In this report, we introduced the VHP (Virus Host Prediction) to predict the potential hosts of viruses using deep learning algorithm. Our prediction suggests that 2019-nCoV has close infectivity with other human coronaviruses, especially the severe acute respiratory syndrome coronavirus (SARS-CoV), Bat SARS-like Coronaviruses and the Middle East respiratory syndrome coronavirus (MERS-CoV). Based on our prediction, compared to the Coronaviruses infecting other vertebrates, bat coronaviruses are assigned with more similar infectivity patterns with 2019-nCoVs. Furthermore, by comparing the infectivity patterns of all viruses hosted on vertebrates, we found mink viruses show a closer infectivity pattern to 2019-nCov. These consequences of infectivity pattern analysis illustrate that bat and mink may be two candidate reservoirs of 2019-nCov.These results warn us to beware of 2019-nCoV and guide us to further explore the properties and reservoir of it. One Sentence Summary: It is of great value to identify whether a newly discovered virus has the risk of infecting human. Guo et al. proposed a virus host prediction method based on deep learning to detect what kind of host a virus can infect with DNA sequence as input.

2019 Novel coronavirus: where we are and what we know

“…Zhu and colleagues used deep learning algorithms to analyze the gene sequences of novel coronaviruses and other coronaviruses to predict potential viral hosts. Their results indicated that bats and minks may be the two potential hosts of the novel coronavirus, while minks may be the intermediate hosts of the virus [5]. The novel coronavirus showed a similar pattern of infection to other coronaviruses in humans, particularly severe acute respiratory syndrome coronavirus (SARS-nCoV), Bat SARS-like CoV, and Middle East respiratory syndrome coronavirus (MERS-nCoV).…”

Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species

“…: MN996532), with 96.2% nucleotide homology in the whole genome Zhou et al, 2020). Other groups suggest that pangolin, mink, snake, turtle may be potential intermediate hosts for the virus (Association, 2020;Guo et al, 2020;Ji et al, 2020;Lam et al, 2020;Li et al, 2020;Liu et al, 2020a;Liu et al, 2020b;Xiao et al, 2020;Zhang et al, 2020a;Zhang et al, 2020b), which still need more evidence to be confirmed.…”

Recent progress in understanding 2019 novel coronavirus (SARS-CoV-2) associated with human respiratory disease: detection, mechanisms and treatment

“…They considered that snake was a most probable wildlife animal reservoir, but the conclusion was controversial. Guo et al introduced VHP (Virus Host Prediction) to predict the potential hosts of viruses by deep learning algorithm and predicted that bat coronaviruses were assigned with more similar infectivity patterns with SARS-CoV-2 [14] . The results illustrated that bat and mink might be two candidate reservoirs of SARS-CoV-2.…”