MEGA2: molecular evolutionary genetics analysis software

Kumar, Sudhir; Tamura, Koichiro; Jakobsen, Ingrid B.; Nei, Masatoshi

doi:10.1093/bioinformatics/17.12.1244

Cited by 5,418 publications

(3,660 citation statements)

References 3 publications

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“…Sequences were compared by using BioEdit ( 30 ) and ClustalW ( 31 ). Phylogenetic analyses were performed by using MEGA version 4.0.2 ( 32 ). The sequences of the 9 influenza viruses we studied were submitted to GenBank under accession nos.…”

Section: Methodsmentioning

confidence: 99%

Multiple Reassortment between Pandemic (H1N1) 2009 and Endemic Influenza Viruses in Pigs, United States

Ducatez¹,

Hause²,

Stigger-Rosser³

et al. 2011

Emerg. Infect. Dis.

161

100

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Section: Methodsmentioning

confidence: 99%

Multiple Reassortment between Pandemic (H1N1) 2009 and Endemic Influenza Viruses in Pigs, United States

Ducatez¹,

Hause²,

Stigger-Rosser³

et al. 2011

Emerg. Infect. Dis.

161

100

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show abstract

“…AIV representative sequences used for the alignments were obtained from the GenBank and EMBL database. The phylogenetic trees were constructed by using the neighbour-joining method with Kimura two-parameter distances by using MEGA version 3.1 [23]. The reliability of internal branches was assessed by 1000 bootstrap replications and p-distance substitution model.…”

Section: Methodsmentioning

confidence: 99%

Isolation and characterization of highly pathogenic avian influenza virus subtype H5N1 from donkeys

Abdel‐Moneim

Abdel-Ghany

Shany

2010

Journal of Biomedical Science

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BackgroundThe highly pathogenic H5N1 is a major avian pathogen that crosses species barriers and seriously affects humans as well as some mammals. It mutates in an intensified manner and is considered a potential candidate for the possible next pandemic with all the catastrophic consequences.MethodsNasal swabs were collected from donkeys suffered from respiratory distress. The virus was isolated from the pooled nasal swabs in specific pathogen free embryonated chicken eggs (SPF-ECE). Reverse transcriptase polymerase chain reaction (RT-PCR) and sequencing of both haemagglutingin and neuraminidase were performed. H5 seroconversion was screened using haemagglutination inhibition (HI) assay on 105 donkey serum samples.ResultsWe demonstrated that H5N1 jumped from poultry to another mammalian host; donkeys. Phylogenetic analysis showed that the virus clustered within the lineage of H5N1 from Egypt, closely related to 2009 isolates. It harboured few genetic changes compared to the closely related viruses from avian and humans. The neuraminidase lacks oseltamivir resistant mutations. Interestingly, HI screening for antibodies to H5 haemagglutinins in donkeys revealed high exposure rate.ConclusionsThese findings extend the host range of the H5N1 influenza virus, possess implications for influenza virus epidemiology and highlight the need for the systematic surveillance of H5N1 in animals in the vicinity of backyard poultry units especially in endemic areas.

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“…Bootstrap consensus analysis (500 replicates) was carried out to verify the robustness of the topologies obtained by PHYLIP (Felsestein, 1995). The cox2 sequences were aligned using Clustal W (Thompson et al, 1994), and a square matrix based on p-distance and K2P was performed using MEGA 3.1 (Kumar et al, 2001). Phylogenetic analyses at the interspecific level were performed using "maximum parsimony" (MP) by PAUP* version 4.0 (Swofford, 2003).…”

Section: Genetic Data Analysismentioning

confidence: 99%

“…Phylogenetic analyses at the interspecific level were performed using "maximum parsimony" (MP) by PAUP* version 4.0 (Swofford, 2003). UPGMA and Neighbour-Joining (NJ) analyses, based on K2P values, were performed using the MEGA 3.1 program (Kumar et al, 2001). The reliabilities of the phylogenetic relationships were evaluated using nonparametric bootstrap analysis (Felsenstein, 1985) for the MP and NJ trees.…”

Section: Genetic Data Analysismentioning

confidence: 99%

Genetic relationships among species ofContracaecumRailliet & Henry, 1912 andPhocascarisHöst, 1932 (Nematoda: Anisakidae) from pinnipeds inferred from mitochondrialcox2sequences, and congruence with allozyme data

et al. 2008

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Summary :The genetic relationships among 11 taxa, belonging to the genus Contracaecum (C. osculatum A, C. osculatum B, C. osculatum (s.s.), C. osculatum D, C. osculatum E, C. osculatum baicalensis, C. mirounga, C. radiatum, C. ogmorhini (s.s.), C. margolisi) and Phocascaris (Phocascaris cystophorae), parasites as adults of seals, were inferred from sequence analysis (519 bp) of the mitochondrial cytochrome c oxidase subunit II (mtDNA cox2) gene. Phylogenetic analyses obtained from Parsimony (MP) and Neighbour-Joining (NJ) K2P distance values generated similar topologies, each well supported at major nodes. All analyses delineated two main clades: the first encompassing the parasites of the phocid seals, i.e. the C. osculatum species complex, C. osculatum baicalensis, C. mirounga and C. radiatum, with the latter two species forming a separate subclade; the second including the parasites of otarids, i.e. C. ogmorhini (s.s.) and C. margolisi. An overall high congruence between mtDNA inferred tree topologies and those produced from nuclear data sets (20 allozyme loci) was observed. Comparison of the phylogenetic hypothesis here produced for Contracaecum spp. plus Phocascaris with those currently available for their definitive hosts (pinnipeds) suggests parallelism between hosts and parasite phylogenetic tree topologies.

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MEGA2: molecular evolutionary genetics analysis software

Abstract: s.kumar@asu.edu

Cited by 5,418 publications

References 3 publications

Multiple Reassortment between Pandemic (H1N1) 2009 and Endemic Influenza Viruses in Pigs, United States

Multiple Reassortment between Pandemic (H1N1) 2009 and Endemic Influenza Viruses in Pigs, United States

Isolation and characterization of highly pathogenic avian influenza virus subtype H5N1 from donkeys

Genetic relationships among species ofContracaecumRailliet & Henry, 1912 andPhocascarisHöst, 1932 (Nematoda: Anisakidae) from pinnipeds inferred from mitochondrialcox2sequences, and congruence with allozyme data

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