Evidence for an Ancestral Association of Human Coronavirus 229E with Bats

ABSTRACTWe previously showed that close relatives of human coronavirus 229E (HCoV-229E) exist in African bats. The small sample and limited genomic characterizations have prevented further analyses so far. Here, we tested 2,087 fecal specimens from 11 bat species sampled in Ghana for HCoV-229E-related viruses by reverse transcription-PCR (RT-PCR). Only hipposiderid bats tested positive. To compare the genetic diversity of bat viruses and HCoV-229E, we tested historical isolates and diagnostic specimens sampled globally over 10 years. Bat viruses were 5- and 6-fold more diversified than HCoV-229E in theRNA-dependent RNA polymerase(RdRp) andspikegenes. In phylogenetic analyses, HCoV-229E strains were monophyletic and not intermixed with animal viruses. Bat viruses formed three large clades in close and more distant sister relationships. A recently described 229E-related alpaca virus occupied an intermediate phylogenetic position between bat and human viruses. According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV-229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. Analyses of four full genomes from 229E-related bat CoVs revealed an eighth open reading frame (ORF8) located at the genomic 3′ end. ORF8 also existed in the 229E-related alpaca virus. Reanalysis of HCoV-229E sequences showed a conserved transcription regulatory sequence preceding remnants of this ORF, suggesting its loss after acquisition of a 229E-related CoV by humans. These data suggested an evolutionary origin of 229E-related CoVs in hipposiderid bats, hypothetically with camelids as intermediate hosts preceding the establishment of HCoV-229E.IMPORTANCEThe ancestral origins of major human coronaviruses (HCoVs) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a large sample of African bats and characterizing several bat viruses on a full-genome level. Our evolutionary analyses show that animal and human viruses are genetically closely related, can exchange genetic material, and form a single viral species. We show that the putative host switches leading to the formation of HCoV-229E were accompanied by major genomic changes, including deletions in the viral spike glycoprotein gene and loss of an open reading frame. We reanalyze a previously described genetically related alpaca virus and discuss the role of camelids as potential intermediate hosts between bat and human viruses. The evolutionary history of HCoV-229E likely shares important characteristics with that of the recently emerged highly pathogenic Middle East respiratory syndrome (MERS) coronavirus.

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Complete Genome Sequence of Human Coronavirus NL63 CN0601/14, First Isolated in South Korea

Genome Announcements ◽

10.1128/genomea.00152-18 ◽

2018 ◽

Vol 6 (12) ◽

Cited By ~ 1

Author(s):

Jeong-Min Kim ◽

Seung-Tae Kim ◽

Jeong-Sun Yang ◽

Sung Soon Kim ◽

Hyang-Min Cheong

Keyword(s):

South Korea ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Open Reading Frame ◽

Genome Sequences ◽

Human Coronavirus ◽

Reading Frame

ABSTRACT We report here the complete genome sequence of the human coronavirus NL63 CN0601/14 strain, first isolated from South Korea. It contains 18-nucleotide discontinuous deletions of the open reading frame 1a (ORF1a) and spike regions. This study will aid in our understanding of the complete genome sequences of isolated coronaviruses in South Korea.

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Ilarviruses Encode a Cucumovirus-Like 2b Gene That Is Absent in Other Genera within the Bromoviridae

Journal of Virology ◽

10.1128/jvi.72.8.6956-6959.1998 ◽

1998 ◽

Vol 72 (8) ◽

pp. 6956-6959 ◽

Cited By ~ 33

Author(s):

Hong-Wu Xin ◽

Liang-Hui Ji ◽

Simon W. Scott ◽

Robert H. Symons ◽

Shou-Wei Ding

Keyword(s):

Open Reading Frame ◽

Latent Virus ◽

Evolutionary Origin ◽

Protein Species ◽

Subgenomic Rna ◽

Reading Frame ◽

2B Protein ◽

Sequence Similarities

ABSTRACT We found that RNA 2 of the four ilarviruses sequenced to date encodes an additional conserved open reading frame (ORF), 2b, that overlaps the 3′ end of the previously known ORF, 2a. A novel RNA species of 851 nucleotides was found to accumulate to high levels in plants infected with spinach latent virus (SpLV). Further analysis showed that RNA 4A is a subgenomic RNA of RNA 2 and encodes all of ORF 2b. Moreover, a protein species of the size expected for SpLV ORF 2b was translated in vitro from the RNA 4A-containing virion RNAs. The data support the suggestion that the SpLV 2b protein is translated in vivo. The 2b gene of ilarviruses, which is not encoded by alfamoviruses and bromoviruses, shares several features with the previously reported cucumovirus 2b gene; however, their encoded proteins share no detectable sequence similarities. The evolutionary origin of the 2b gene is discussed.

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Human Coronavirus NL63 Open Reading Frame 3 encodes a virion-incorporated N-glycosylated membrane protein

Virology Journal ◽

10.1186/1743-422x-7-6 ◽

2010 ◽

Vol 7 (1) ◽

pp. 6 ◽

Cited By ~ 22

Author(s):

Marcel A Müller ◽

Lia van der Hoek ◽

Daniel Voss ◽

Oliver Bader ◽

Dörte Lehmann ◽

...

Keyword(s):

Membrane Protein ◽

Open Reading Frame ◽

Human Coronavirus ◽

Reading Frame

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Discovery of a 382-nt deletion during the early evolution of SARS-CoV-2

10.1101/2020.03.11.987222 ◽

2020 ◽

Cited By ~ 27

Author(s):

Yvonne CF Su ◽

Danielle E Anderson ◽

Barnaby E Young ◽

Feng Zhu ◽

Martin Linster ◽

...

Keyword(s):

Genetic Variants ◽

Human Population ◽

Host Adaptation ◽

Open Reading Frame ◽

N Gene ◽

Regulatory Sequence ◽

Reading Frame ◽

Replicative Fitness ◽

Similar Variation ◽

Entire Open Reading Frame

To date, the SARS-CoV-2 genome has been considered genetically more stable than SARS-CoV or MERS-CoV. Here we report a 382-nt deletion covering almost the entire open reading frame 8 (ORF8) of SARS-CoV-2 obtained from eight hospitalized patients in Singapore. The deletion also removes the ORF8 transcription-regulatory sequence (TRS), which in turn enhances the downstream transcription of the N gene. We also found that viruses with the deletion have been circulating for at least four weeks. During the SARS-CoV outbreak in 2003, a number of genetic variants were observed in the human population [1], and similar variation has since been observed across SARS-related CoVs in humans and bats. Overwhelmingly these viruses had mutations or deletions in ORF8, that have been associated with reduced replicative fitness of the virus [2]. This is also consistent with the observation that towards the end of the outbreak sequences obtained from human SARS cases possessed an ORF8 deletion that may be associated with host adaptation [1]. We therefore hypothesise that the major deletion revealed in this study may lead to an attenuated phenotype of SARS-CoV-2.

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