HyPhy: Hypothesis Testing Using Phylogenies

Pond, Sergei L. Kosakovsky; Muse, Spencer V.

doi:10.1007/0-387-27733-1_6

Cited by 385 publications

(424 citation statements)

References 10 publications

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“…Identified breakpoints were then assessed by testing the congruence of neighbor-joining trees generated by GARD for each fragment, using the Shimodaira-Hasegawa test in PAUP* (34). Analysis of lineage-specific selection pressure in the S genes of SARS-CoVs was conducted using the Genetic Algorithm (GA) in the program package HYPHY (19). We analyzed an alignment of the complete S genes (3,783 nucleotides and 1,261 codons) of six BtCoVs and three civet and three human SARS-CoVs and specified a neighbor-joining input tree (GTRϩI model) generated in PAUP* as described above.…”

Section: Methodsmentioning

confidence: 99%

Evolutionary Insights into the Ecology of Coronaviruses

Vijaykrishna

Smith

Zhang

et al. 2007

J Virol

258

208

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Although many novel members of the Coronaviridae have recently been recognized in different species, the ecology of coronaviruses has not been established. Our study indicates that bats harbor a much wider diversity of coronaviruses than any other animal species. Dating of different coronavirus lineages suggests that bat coronaviruses are older than those recognized in other animals and that the human severe acute respiratory syndrome (SARS) coronavirus was directly derived from viruses from wild animals in wet markets of southern China. Furthermore, the most closely related bat and SARS coronaviruses diverged in 1986, an estimated divergence time of 17 years prior to the outbreak, suggesting that there may have been transmission via an unknown intermediate host. Analysis of lineage-specific selection pressure also indicated that only SARS coronaviruses in civets and humans were under significant positive selection, also demonstrating a recent interspecies transmission. Analysis of population dynamics revealed that coronavirus populations in bats have constant population growth, while viruses from all other hosts show epidemic-like increases in population. These results indicate that diverse coronaviruses are endemic in different bat species, with repeated introductions to other animals and occasional establishment in other species. Our findings suggest that bats are likely the natural hosts for all presently known coronavirus lineages and that all coronaviruses recognized in other species were derived from viruses residing in bats. Further surveillance of bat and other animal populations is needed to fully describe the ecology and evolution of this virus family.

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Section: Methodsmentioning

confidence: 99%

Evolutionary Insights into the Ecology of Coronaviruses

Vijaykrishna

Smith

Zhang

et al. 2007

J Virol

258

208

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“…Positively selected codon sites in the CHIKV genome were estimated by the internal fixed-effects likelihood method using HYPHY package 56 . This method only accounts for substitutions along internal branches, therefore is more suitable for selection pressure estimation at population level, where external transient mutations will not be fixed 57 .…”

Section: Methodsmentioning

confidence: 99%

Multi-peaked adaptive landscape for chikungunya virus evolution predicts continued fitness optimization in Aedes albopictus mosquitoes

et al. 2014

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Host species-specific fitness landscapes largely determine the outcome of host switching during pathogen emergence. Using chikungunya virus (CHIKV) to study adaptation to a mosquito vector, we evaluated mutations associated with recently evolved sub-lineages. Multiple Aedes albopictus-adaptive fitness peaks became available after CHIKV acquired an initial adaptive (E1-A226V) substitution, permitting rapid lineage diversification observed in nature. All second-step mutations involved replacements by glutamine or glutamic acid of E2 glycoprotein amino acids in the acid-sensitive region, providing a framework to anticipate additional A. albopictus-adaptive mutations. The combination of second-step adaptive mutations into a single, 'super-adaptive' fitness peak also predicted the future emergence of CHIKV strains with even greater transmission efficiency in some current regions of endemic circulation, followed by their likely global spread.

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“…Detection of recombination. The Genetic Algorithm for Recombination Detection in the program package HYPHY was used to determine if this novel CoV contains recombinant genes (8,9). It must be noted that recombination analysis was conducted only within gene segments.…”

Section: Methodsmentioning

confidence: 99%

Detection of a Novel and Highly Divergent Coronavirus from Asian Leopard Cats and Chinese Ferret Badgers in Southern China

Dong

Liu

Fan

et al. 2007

J Virol

134

124

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Since an outbreak of severe acute respiratory syndrome (SARS) was averted in 2004, many novel coronaviruses have been recognized from different species, including humans. Bats have provided the most diverse assemblages of coronaviruses, suggesting that they may be the natural reservoir. Continued virological surveillance has proven to be the best way to avert this infectious disease at the source. Here we provide the first description of a previously unidentified coronavirus lineage detected from wild Asian leopard cats (Prionailurus bengalensis) and Chinese ferret badgers (Melogale moschata) during virological surveillance in southern China. Partial genome analysis revealed a typical coronavirus genome but with a unique putative accessory gene organization. Phylogenetic analyses revealed that the envelope, membrane, and nucleoprotein structural proteins and the two conserved replicase domains, putative RNA-dependent RNA polymerase and RNA helicase, of these novel coronaviruses were most closely related to those of group 3 coronaviruses identified from birds, while the spike protein gene was most closely related to that of group 1 coronaviruses from mammals. However, these viruses always fell into an outgroup phylogenetic relationship with respect to other coronaviruses and had low amino acid similarity to all known coronavirus groups, indicating that they diverged early in the evolutionary history of coronaviruses. These results suggest that these viruses may represent a previously unrecognized evolutionary pathway, or possibly an unidentified coronavirus group. This study demonstrates the importance of systematic virological surveillance in market animals for understanding the evolution and emergence of viruses with infectious potential.Since the severe acute respiratory syndrome (SARS) outbreak in early 2003, many new viruses of the family Coronaviridae have been identified in diverse host species, including birds, humans, and other mammals (7, 12-14, 18, 25, 27, 28, 29). Of these hosts, bats have provided the highest genetic diversity of novel coronaviruses (CoVs) (23,29). Analyses of the genomic organization and phylogenetic relationships of CoVs from bats and other host species indicate that bats are the likely natural reservoirs for all known CoVs from other hosts (23,26). This research also suggests that CoVs resident in bats may be introduced into other animals and subsequently become established in these hosts.Interspecies transmission of CoV from its natural reservoir to another species might result in disease outbreaks in naive hosts. The emerging pathway of SARS CoV in humans and market civets is an example of this (4, 5). Accumulated information has demonstrated that many SARS-like CoVs are harbored in bat species (12,13,23). However, the cross homologies between civet and human SARS CoV and bat SARS-like CoVs are still relatively low (about 92%), even in the most conserved regions of the replicase gene (13). Phylogenetic analyses and divergence dates of these CoVs indicate that the likely interme...

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HyPhy: Hypothesis Testing Using Phylogenies

Cited by 385 publications

References 10 publications

Evolutionary Insights into the Ecology of Coronaviruses

Evolutionary Insights into the Ecology of Coronaviruses

Multi-peaked adaptive landscape for chikungunya virus evolution predicts continued fitness optimization in Aedes albopictus mosquitoes

Detection of a Novel and Highly Divergent Coronavirus from Asian Leopard Cats and Chinese Ferret Badgers in Southern China

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