Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus

Abstract

A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East. We report the deep genome sequencing of the virus directly from a patient’s sputum sample. Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. Detailed phylogenetic analysis of the virus genome (England/Qatar/2012) revealed its close relationship to European bat coronaviruses circulating among the bat species of the Vespertilionidae family. Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events.

Respiratory Syncytial Virus: Infection, Detection, and New Options for Prevention and Treatment

“…Another NGS diagnostic approach is to use preferential amplification of pathogenic sequences (PATHseq) to identify nonhuman sequences (304). There are now multiple examples of NGS being used to diagnose viral infections in human patients in a nonbiased manner (305)(306)(307). A more routine role of NGS is thought to be possible with computing technology and decreases in cost (308).…”

Public health investigations required for protecting the population against novel coronaviruses

“…Bats are considered to be the hosts for animal coronaviruses and these novel viruses affecting humans are similar to a number of bat coronaviruses isolated in both the old and the new world [10]. While they bear some relationship to the SARS-CoV virus which caused severe acute respiratory syndrome (SARS), they are also sufficiently different to preclude the assumption that they will behave in the same way as SARS-CoV [9]. Indeed the signature characteristic of SARS outbreaks in humans-super spreading events-have not been described so far [3,5,7].…”

“…Indeed the signature characteristic of SARS outbreaks in humans-super spreading events-have not been described so far [3,5,7]. Analytic virological studies of nCoV have appeared with impressive speed in peer reviewed journals and some of the conclusions reached are concerning [9,[11][12][13]. The virus may have the potential to spread in a range of mammalian cells; binds to a receptor that is preserved across a number of species, including humans [11,13]; it can also infect and replicate with cytopathic effect in a wide range of cell-lines across various human tissue types and from other species [12].…”

“…The new viruses have been genetically sequenced [8,9]. Bats are considered to be the hosts for animal coronaviruses and these novel viruses affecting humans are similar to a number of bat coronaviruses isolated in both the old and the new world [10].…”

Middle East respiratory syndrome coronavirus: current knowledge and future considerations

“…Genetic material from specimens taken from MERS-CoV patients shows that MERS-CoV also has a close genetic relation with coronaviruses found in bats in southern China (12), South Africa (13), Europe (14,15), Thailand (16), Mexico (17), Ghana (15) and Saudi Arabia (18) as well as in other species, such as hedgehogs (19). Bats are thought to be the origin of a zoonotic infection transmitted to dromedary camels, and ultimately from camels to humans through close contact (20,21).…”