MyMedR

Fulltext Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani

Khayi S, Blin P, Pédron J, Chong TM, Chan KG, Moumni M, et al.

BMC Genomics, 2015;16:788.

PMID: 26467299 DOI: 10.1186/s12864-015-1997-z

Dickeya solani is an emerging pathogen that causes soft rot and blackleg diseases in several crops including Solanum tuberosum, but little is known about its genomic diversity and evolution.

Matched MeSH terms: Phylogeny

Fulltext Homogeneous Nature of Malaysian Marine Fish Epinephelus fuscoguttatus (Perciformes; Serranidae): Evidence Based on Molecular Markers, Morphology and Fourier Transform Infrared Analysis

Nurdalila AA, Bunawan H, Kumar SV, Rodrigues KF, Baharum SN

Int J Mol Sci, 2015 Jul 02;16(7):14884-900.

PMID: 26147421 DOI: 10.3390/ijms160714884

Taxonomic confusion exists within the genus Epinephelus due to the lack of morphological specializations and the overwhelming number of species reported in several studies. The homogenous nature of the morphology has created confusion in the Malaysian Marine fish species Epinephelus fuscoguttatus and Epinephelus hexagonatus. In this study, the partial DNA sequence of the 16S gene and mitochondrial nucleotide sequences of two gene regions, Cytochrome Oxidase Subunit I and III were used to investigate the phylogenetic relationship between them. In the phylogenetic trees, E. fuscoguttatus was monophyletic with E. hexagonatus species and morphology examination shows that no significant differences were found in the morphometric features between these two taxa. This suggests that E. fuscoguttatus is not distinguishable from E. hexagonatus species, and that E. fuscoguttatus have been identified to be E. hexagonatus species is likely attributed to differences in environment and ability to camouflage themselves under certain conditions. Interestingly, this finding was also supported by Principal Component Analysis on Attenuated Total Reflectance-Fourier-transform Infrared (ATR-FTIR) data analysis. Molecular, morphological and meristic characteristics were combined with ATR-FTIR analysis used in this study offer new perspectives in fish species identification. To our knowledge, this is the first report of an extensive genetic population study of E. fuscoguttatus in Malaysia and this understanding will play an important role in informing genetic stock-specific strategies for the management and conservation of this highly valued fish.

Matched MeSH terms: Phylogeny

SCAR markers and multiplex PCR-based identification of isomorphic species in the Anopheles dirus complex in Southeast Asia

Manguin S, Kengne P, Sonnier L, Harbach RE, Baimai V, Trung HD, et al.

Med Vet Entomol, 2002 Mar;16(1):46-54.

PMID: 11963981

The Anopheles dirus Peyton & Harrison complex of mosquitoes (Diptera: Culicidae) comprises seven known species, including important malaria vectors in Southeast Asia. Specific identification of each species of the complex, which cannot be distinguished using morphological characters, is crucial for understanding vector ecology and implementing effective control measures. Derived from individual random amplified polymorphic DNA (RAPD) markers, sequence characterized amplified regions (SCAR) were analysed for the design of specific paired-primers. Combination of six SCAR primers resulted in the development of a simple, robust, single multiplex PCR able to identify three important malaria vectors among the four most common species (A, B, C, D) of the complex: species A from several Southeast Asian countries, species B from Perlis, Malaysia, and species C and D from Thailand.

Matched MeSH terms: Phylogeny

A multi-locus approach resolves the phylogenetic relationships of the Simulium asakoae and Simulium ceylonicum species groups in Malaysia: evidence for distinct evolutionary lineages

Low VL, Takaoka H, Adler PH, Ya'cob Z, Norma-Rashid Y, Chen CD, et al.

Med Vet Entomol, 2015 Sep;29(3):330-7.

PMID: 25968459 DOI: 10.1111/mve.12120

A multi-locus approach was used to examine the DNA sequences of 10 nominal species of blackfly in the Simulium subgenus Gomphostilbia (Diptera: Simuliidae) in Malaysia. Molecular data were acquired from partial DNA sequences of the mitochondria-encoded cytochrome c oxidase subunit I (COI), 12S rRNA and 16S rRNA genes, and the nuclear-encoded 18S rRNA and 28S rRNA genes. No single gene, nor the concatenated gene set, resolved all species or all relationships. However, all morphologically established species were supported by at least one gene. The multi-locus sequence analysis revealed two distinct evolutionary lineages, conforming to the morphotaxonomically recognized Simulium asakoae and Simulium ceylonicum species groups.

Matched MeSH terms: Phylogeny

Cystofilobasidium josepaulonis sp. nov., a novel basidiomycetous yeast species

Zhu HY, Wei XY, Liu XZ, Bai FY

Int J Syst Evol Microbiol, 2023 May;73(5).

PMID: 37191980 DOI: 10.1099/ijsem.0.005865

A yeast strain belonging to the basidiomycetous yeast genus Cystofilobasidium was isolated from a marine sediment sample collected in an intertidal zone in Shandong province, PR China. The results of phylogenetic analyses based on sequences of the D1/D2 domain of the 26S ribosomal RNA gene and the internal transcribed spacer (ITS) region indicate that this strain, together with three other strains isolated from basal ice collected in Norway, the gut of an insect and an alga collected in Russia, represent a novel species of the genus, for which the name Cystofilobasidium josepaulonis sp. nov. (holotype strain CGMCC 2.6672T) is proposed. The novel species differs from the known species of the genus Cystofilobasidium by 1.7 %-4.1 and 11.3 %-17.1 % mismatches in the D1/D2 domain and the ITS region, respectively. This species forms teliospores on potato dextrose agar (PDA) and 10 % V8 juice agar, but teliospore germination with basidia was not observed.

Matched MeSH terms: Phylogeny

Fulltext Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak

Zhang T, Wu Q, Zhang Z

Curr Biol, 2020 Apr 06;30(7):1346-1351.e2.

PMID: 32197085 DOI: 10.1016/j.cub.2020.03.022

An outbreak of coronavirus disease 2019 (COVID-19) caused by the 2019 novel coronavirus (SARS-CoV-2) began in the city of Wuhan in China and has widely spread worldwide. Currently, it is vital to explore potential intermediate hosts of SARS-CoV-2 to control COVID-19 spread. Therefore, we reinvestigated published data from pangolin lung samples from which SARS-CoV-like CoVs were detected by Liu et al. [1]. We found genomic and evolutionary evidence of the occurrence of a SARS-CoV-2-like CoV (named Pangolin-CoV) in dead Malayan pangolins. Pangolin-CoV is 91.02% and 90.55% identical to SARS-CoV-2 and BatCoV RaTG13, respectively, at the whole-genome level. Aside from RaTG13, Pangolin-CoV is the most closely related CoV to SARS-CoV-2. The S1 protein of Pangolin-CoV is much more closely related to SARS-CoV-2 than to RaTG13. Five key amino acid residues involved in the interaction with human ACE2 are completely consistent between Pangolin-CoV and SARS-CoV-2, but four amino acid mutations are present in RaTG13. Both Pangolin-CoV and RaTG13 lost the putative furin recognition sequence motif at S1/S2 cleavage site that can be observed in the SARS-CoV-2. Conclusively, this study suggests that pangolin species are a natural reservoir of SARS-CoV-2-like CoVs.

Matched MeSH terms: Phylogeny

Fulltext Novel insight into the genetic diversity of strongylid nematodes infecting South-East and East Asian primates

Mason B, Cervena B, Frias L, Goossens B, Hasegawa H, Keuk K, et al.

Parasitology, 2024 Apr;151(5):514-522.

PMID: 38629119 DOI: 10.1017/S0031182024000386

With many non-human primates (NHPs) showing continued population decline, there is an ongoing need to better understand their ecology and conservation threats. One such threat is the risk of disease, with various bacterial, viral and parasitic infections previously reported to have damaging consequences for NHP hosts. Strongylid nematodes are one of the most commonly reported parasitic infections in NHPs. Current knowledge of NHP strongylid infections is restricted by their typical occurrence as mixed infections of multiple genera, which are indistinguishable through traditional microscopic approaches. Here, modern metagenomics approaches were applied for insight into the genetic diversity of strongylid infections in South-East and East Asian NHPs. We hypothesized that strongylid nematodes occur in mixed communities of multiple taxa, dominated by Oesophagostomum, matching previous findings using single-specimen genetics. Utilizing the Illumina MiSeq platform, ITS-2 strongylid metabarcoding was applied to 90 samples from various wild NHPs occurring in Malaysian Borneo and Japan. A clear dominance of Oesophagostomum aculeatum was found, with almost all sequences assigned to this species. This study suggests that strongylid communities of Asian NHPs may be less species-rich than those in African NHPs, where multi-genera communities are reported. Such knowledge contributes baseline data, assisting with ongoing monitoring of health threats to NHPs.

Matched MeSH terms: Phylogeny

Fulltext Identification of Chikungunya virus strains circulating in Kelantan, Malaysia in 2009

Apandi Y, Lau SK, Izmawati N, Amal NM, Faudzi Y, Mansor W, et al.

Southeast Asian J Trop Med Public Health, 2010 Nov;41(6):1374-80.

PMID: 21329313

Malaysia experienced its first outbreak of chikungunya virus (CHIKV) infection in late 1998 in Klang District in Selangor; six years later the virus re-emerged in the state of Perak. All the CHIKV isolates in 1988 and 2006 shared high sequence similarities and belonged to the Asian genotype. In 2007 and 2008 CHIKV infection again reemerged but the genotype was the Central/East African genotype. This strain was found to be similar to the strains causing outbreaks in the India Ocean. In 2009, the strains circulating in Malaysia, including the state of Kelantan, based on the partial E1 gene, also belong to the Central/East African genotype.

Matched MeSH terms: Phylogeny

The mannose-binding lectin (MBL) gene cloned from Exopalaemon carinicauda plays a key role in resisting infection by Vibrio parahaemolyticus

Shi T, Gao J, Xu W, Liu X, Yan B, Azra MN, et al.

Comp Biochem Physiol B Biochem Mol Biol, 2024;274:111001.

PMID: 38908544 DOI: 10.1016/j.cbpb.2024.111001

Mannose-binding lectin (MBL) is a vital member of the lectin family, crucial for mediating functions within the complement lectin pathway. In this study, following the cloning of the mannose-binding lectin (MBL) gene in the ridgetail white prawn, Exopalaemon carinicauda, we examined its expression patterns across various tissues and its role in combating challenges posed by Vibrio parahaemolyticus. The results revealed that the MBL gene spans 1342 bp, featuring an open reading frame of 972 bp. It encodes a protein comprising 323 amino acids, with a predicted relative molecular weight of 36 kDa and a theoretical isoelectric point of 6.18. The gene exhibited expression across various tissues including the eyestalk, heart, gill, hepatopancreas, stomach, intestine, ventral nerve cord, muscle, and hemolymph, with the highest expression detected in the hepatopancreas. Upon challenge with V. parahaemolyticus, RT-PCR analysis revealed a trend of MBL expression in hepatopancreatic tissues, characterized by an initial increase followed by a subsequent decrease, peaking at 24 h post-infection. Employing RNA interference to disrupt MBL gene expression resulted in a significant increase in mortality rates among individuals challenged with V. parahaemolyticus. Furthermore, we successfully generated the Pet32a-MBL recombinant protein through the construction of a prokaryotic expression vector for conducting in vitro bacterial inhibition assays, which demonstrated the inhibitory effect of the recombinant protein on V. parahaemolyticus, laying a foundation for further exploration into its immune mechanism in response to V. parahaemolyticus challenges.

Matched MeSH terms: Phylogeny

Fulltext Rare rotavirus strains in children with severe diarrhea, Malaysia

Ch'ng LS, Lee WS, Kirkwood CD

Emerg Infect Dis, 2011 May;17(5):948-50.

PMID: 21529427 DOI: 10.3201/eid1705.101652

Matched MeSH terms: Phylogeny

Recombinant human enterovirus 71 in hand, foot and mouth disease patients

Chan YF, AbuBaker S

Emerg Infect Dis, 2004 Aug;10(8):1468-70.

PMID: 15496251

Hand, foot and mouth disease (HFMD) is a common illness of infants and young children <10 years of age. It is characterized by fever, ulcers in the oral cavity, and rashes with blisters that appear on the palm and sole. The most common causal agents of HFMD are coxsackievirus A16 (CV-A16) and human enterovirus 71 (HEV71), but other enteroviruses, including CV-A5 and CV-A10, can also cause it. When caused by CV-A16 infection, it is usually a mild disease, and patients normally recover without requiring any special medical attention.

Matched MeSH terms: Phylogeny

Fulltext Reemergence of endemic Chikungunya, Malaysia

AbuBakar S, Sam IC, Wong PF, MatRahim N, Hooi PS, Roslan N

Emerg Infect Dis, 2007 Jan;13(1):147-9.

PMID: 17370532

Chikungunya virus infection recently reemerged in Malaysia after 7 years of nondetection. Genomic sequences of recovered isolates were highly similar to those of Malaysian isolates from the 1998 outbreak. The reemergence of the infection is not part of the epidemics in other Indian Ocean countries but raises the possibility that chikungunya virus is endemic in Malaysia.

Matched MeSH terms: Phylogeny

Isolation and molecular identification of Nipah virus from pigs

AbuBakar S, Chang LY, Ali AR, Sharifah SH, Yusoff K, Zamrod Z

Emerg Infect Dis, 2004 Dec;10(12):2228-30.

PMID: 15663869

Nipah viruses from pigs from a Malaysian 1998 outbreak were isolated and sequenced. At least two different Nipah virus strains, including a previously unreported strain, were identified. The findings highlight the possibility that the Malaysia outbreaks had two origins of Nipah virus infections.

Matched MeSH terms: Phylogeny

Fulltext Rickettsial infections in monkeys, Malaysia

Tay ST, Koh FX, Kho KL, Sitam FT

Emerg Infect Dis, 2015 Mar;21(3):545-7.

PMID: 25695615 DOI: 10.3201/eid2103.141457

Matched MeSH terms: Phylogeny

Fulltext Detection of east/central/south African genotype of chikungunya virus in Myanmar, 2010

Tun MM, Thant KZ, Inoue S, Nabeshima T, Aoki K, Kyaw AK, et al.

Emerg Infect Dis, 2014 Aug;20(8):1378-81.

PMID: 25062511 DOI: 10.3201/eid2008.131431

In 2010, chikungunya virus of the East Central South African genotype was isolated from 4 children in Myanmyar who had dengue-like symptoms. Phylogenetic analysis of the E1 gene revealed that the isolates were closely related to isolates from China, Thailand, and Malaysia that harbor the A226V mutation in this gene.

Matched MeSH terms: Phylogeny

Fulltext Outbreak of human infection with Sarcocystis nesbitti, Malaysia, 2012

Abubakar S, Teoh BT, Sam SS, Chang LY, Johari J, Hooi PS, et al.

Emerg Infect Dis, 2013 Dec;19(12):1989-91.

PMID: 24274071 DOI: 10.3201/eid1912.120530

An outbreak of fever associated with myalgia and myositis occurred in 2012 among 89 of 92 college students and teachers who visited Pangkor Island, Malaysia. The Sarcocystis nesbitti 18S rRNA gene and sarcocysts were obtained from muscle tissues of 2 students. Our findings indicate emergence of S. nesbitti infections in humans in Malaysia.

Matched MeSH terms: Phylogeny

Fulltext Novel Orthobunyavirus Causing Severe Kidney Disease in Broiler Chickens, Malaysia, 2014-2017

Palya V, Kovács EW, Marton S, Tatár-Kis T, Felföldi B, Forró B, et al.

Emerg Infect Dis, 2019 06;25(6):1110-1117.

PMID: 31107212 DOI: 10.3201/eid2506.181661

During 2014-2017, we isolated a novel orthobunyavirus from broiler chickens with severe kidney lesions in the state of Kedah, Malaysia; we named the virus Kedah fatal kidney syndrome virus (KFKSV). Affected chickens became listless and diarrheic before dying suddenly. Necropsies detected pale and swollen kidneys with signs of gout, enlarged and fragile livers, and pale hearts. Experimental infection of broiler chickens with KFKSV reproduced the disease and pathologic conditions observed in the field, fulfilling the Koch's postulates. Gene sequencing indicated high nucleotide identities between KFKSV isolates (99%) and moderate nucleotide identities with the orthobunyavirus Umbre virus in the large (78%), medium (77%), and small (86%) genomic segments. KFKSV may be pathogenic for other host species, including humans.

Matched MeSH terms: Phylogeny

Fulltext High Pathogenicity of Nipah Virus from Pteropus lylei Fruit Bats, Cambodia

Gaudino M, Aurine N, Dumont C, Fouret J, Ferren M, Mathieu C, et al.

Emerg Infect Dis, 2020 01;26(1):104-113.

PMID: 31855143 DOI: 10.3201/eid2601.191284

We conducted an in-depth characterization of the Nipah virus (NiV) isolate previously obtained from a Pteropus lylei bat in Cambodia in 2003 (CSUR381). We performed full-genome sequencing and phylogenetic analyses and confirmed CSUR381 is part of the NiV-Malaysia genotype. In vitro studies revealed similar cell permissiveness and replication of CSUR381 (compared with 2 other NiV isolates) in both bat and human cell lines. Sequence alignments indicated conservation of the ephrin-B2 and ephrin-B3 receptor binding sites, the glycosylation site on the G attachment protein, as well as the editing site in phosphoprotein, suggesting production of nonstructural proteins V and W, known to counteract the host innate immunity. In the hamster animal model, CSUR381 induced lethal infections. Altogether, these data suggest that the Cambodia bat-derived NiV isolate has high pathogenic potential and, thus, provide insight for further studies and better risk assessment for future NiV outbreaks in Southeast Asia.

Matched MeSH terms: Phylogeny

Fulltext The gut virome in two indigenous populations from Malaysia

Lee CZ, Zoqratt MZHM, Phipps ME, Barr JJ, Lal SK, Ayub Q, et al.

Sci Rep, 2022 Feb 03;12(1):1824.

PMID: 35115615 DOI: 10.1038/s41598-022-05656-3

The human gut contains a complex microbiota dominated by bacteriophages but also containing other viruses and bacteria and fungi. There are a growing number of techniques for the extraction, sequencing, and analysis of the virome but currently no standardized protocols. This study established an effective workflow for virome analysis to investigate the virome of stool samples from two understudied ethnic groups from Malaysia: the Jakun and Jehai Orang Asli. By using the virome extraction and analysis workflow with the Oxford Nanopore Technology, long-read sequencing successfully captured close to full-length viral genomes. The virome composition of the two indigenous Malaysian communities were remarkably different from those found in other parts of the world. Additionally, plant viruses found in the viromes of these individuals were attributed to traditional food-seeking methods. This study establishes a human gut virome workflow and extends insights into the healthy human gut virome, laying the groundwork for comparative studies.

Matched MeSH terms: Phylogeny

Fulltext Expert consensus statement on the science of HIV in the context of criminal law

Barré-Sinoussi F, Abdool Karim SS, Albert J, Bekker LG, Beyrer C, Cahn P, et al.

J Int AIDS Soc, 2018 Jul;21(7):e25161.

PMID: 30044059 DOI: 10.1002/jia2.25161

INTRODUCTION: Globally, prosecutions for non-disclosure, exposure or transmission of HIV frequently relate to sexual activity, biting, or spitting. This includes instances in which no harm was intended, HIV transmission did not occur, and HIV transmission was extremely unlikely or not possible. This suggests prosecutions are not always guided by the best available scientific and medical evidence.

DISCUSSION: Twenty scientists from regions across the world developed this Expert Consensus Statement to address the use of HIV science by the criminal justice system. A detailed analysis of the best available scientific and medical research data on HIV transmission, treatment effectiveness and forensic phylogenetic evidence was performed and described so it may be better understood in criminal law contexts. Description of the possibility of HIV transmission was limited to acts most often at issue in criminal cases. The possibility of HIV transmission during a single, specific act was positioned along a continuum of risk, noting that the possibility of HIV transmission varies according to a range of intersecting factors including viral load, condom use, and other risk reduction practices. Current evidence suggests the possibility of HIV transmission during a single episode of sex, biting or spitting ranges from no possibility to low possibility. Further research considered the positive health impact of modern antiretroviral therapies that have improved the life expectancy of most people living with HIV to a point similar to their HIV-negative counterparts, transforming HIV infection into a chronic, manageable health condition. Lastly, consideration of the use of scientific evidence in court found that phylogenetic analysis alone cannot prove beyond reasonable doubt that one person infected another although it can be used to exonerate a defendant.

CONCLUSIONS: The application of up-to-date scientific evidence in criminal cases has the potential to limit unjust prosecutions and convictions. The authors recommend that caution be exercised when considering prosecution, and encourage governments and those working in legal and judicial systems to pay close attention to the significant advances in HIV science that have occurred over the last three decades to ensure current scientific knowledge informs application of the law in cases related to HIV.

Matched MeSH terms: Phylogeny

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