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Fulltext A new member of the Pteropine Orthoreovirus species isolated from fruit bats imported to Italy

Lorusso A, Teodori L, Leone A, Marcacci M, Mangone I, Orsini M, et al.

Infect Genet Evol, 2015 Mar;30:55-58.
PMID: 25497353 DOI: 10.1016/j.meegid.2014.12.006

A novel member of the Pteropine Orthoreovirus species has been isolated and sequenced for the whole genome from flying foxes (Pteropus vampyrus) imported to Italy from Indonesia. The new isolate named Indonesia/2010 is genetically similar to Melaka virus which has been the first virus of this species to be shown to be responsible for human respiratory disease. Our findings highlight the importance of flying foxes as vectors of potentially zoonotic viruses and the biological hazard that lies in the import of animals from geographical areas that are ecologically diverse from Europe.
Analysis of codon usage patterns and influencing factors in rice tungro bacilliform virus

Nguyen TH, Wang D, Rahman SU, Bai H, Yao X, Chen D, et al.

Infect Genet Evol, 2021 06;90:104750.
PMID: 33548490 DOI: 10.1016/j.meegid.2021.104750

Rice tungro bacilliform virus (RTBV) belongs to genus Tungrovirus within the family Caulimoviridae harbors circular double-stranded DNA (dsDNA). Rice tungro disease (RTD) caused by RTBV, responsible for severe rice yield losses in South and Southeast Asia. Here, we performed a systematic evolutionary and codon usage bias (CUB) analysis of RTBV genome sequences. We analysed different bioinformatics techniques to calculate the nucleotide compositions, the relative synonymous codon usage (RSCU), and other indices. The results indicated slightly or low codon usage bias in RTBV isolates. Mutation and natural selection pressures have equally contributed to this low codon usage bias. Additionally, multiple factors such as host, geographical distribution also affect codon usage patterns in RTBV genomes. RSCU analysis revealed that RTBV shows mutation bias and prefers A and U ended codons to code amino acids. Codon usage patterns of RTBV were also found to be influenced by its host. This indicates that RTBV have evolved codon usage patterns that are specific to its host. The findings from this study are expected to increase our understanding of factors leading to viral evolution and fitness with respect to hosts and the environment.
Fulltext Association of Vitamin D receptor gene polymorphisms and clinical/severe outcomes of COVID-19 patients

Abdollahzadeh R, Shushizadeh MH, Barazandehrokh M, Choopani S, Azarnezhad A, Paknahad S, et al.

Infect Genet Evol, 2021 Dec;96:105098.
PMID: 34610433 DOI: 10.1016/j.meegid.2021.105098

INTRODUCTION: Growing evidence documented the critical impacts of vitamin D (VD) in the prognosis of COVID-19 patients. The functions of VD are dependent on the vitamin D receptor (VDR) in the VD/VDR signaling pathway. Therefore, we aimed to assess the association of VDR gene polymorphisms with COVID-19 outcomes.
METHODS: In the present study, eight VDR single nucleotide polymorphisms (SNPs) were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 500 COVID-19 patients in Iran, including 160 asymptomatic, 250 mild/moderate, and 90 severe/critical cases. The association of these polymorphisms with severity, clinical outcomes, and comorbidities were evaluated through the calculation of the Odds ratio (OR).
RESULTS: Interestingly, significant associations were disclosed for some of the SNP-related alleles and/or genotypes in one or more genetic models with different clinical data in COVID-19 patients. Significant association of VDR-SNPs with signs, symptoms, and comorbidities was as follows: ApaI with shortness of breath (P ˂ 0.001) and asthma (P = 0.034) in severe/critical patients (group III); BsmI with chronic renal disease (P = 0.010) in mild/moderate patients (group II); Tru9I with vomiting (P = 0.031), shortness of breath (P = 0.04), and hypertension (P = 0.030); FokI with fever and hypertension (P = 0.027) in severe/critical patients (group III); CDX2 with shortness of breath (P = 0.022), hypertension (P = 0.036), and diabetes (P = 0.042) in severe/critical patients (group III); EcoRV with diabetes (P ˂ 0.001 and P = 0.045 in mild/moderate patients (group II) and severe/critical patients (group III), respectively). However, the association of VDR TaqI and BglI polymorphisms with clinical symptoms and comorbidities in COVID-19 patients was not significant.
CONCLUSION: VDR gene polymorphisms might play critical roles in the vulnerability to infection and severity of COVID-19, probably by altering the risk of comorbidities. However, these results require further validation in larger studies with different ethnicities and geographical regions.
Fulltext Bioinformatics analysis reveals four major hexon variants of human adenovirus type-3 (HAdV-3) as the potential strains for development of vaccine and siRNA-based therapeutics against HAdV-3 respiratory infections

Panda S, Banik U, Adhikary AK

Infect Genet Evol, 2020 11;85:104439.
PMID: 32585339 DOI: 10.1016/j.meegid.2020.104439

Human adenovirus type 3 (HAdV-3) encompasses 15-87% of all adenoviral respiratory infections. The significant morbidity and mortality, especially among the neonates and immunosuppressed patients, demand the need for a vaccine or a targeted antiviral against this type. However, due to the existence of multiple hexon variants (3Hv-1 to 3Hv-25), the selection of vaccine strains of HAdV-3 is challenging. This study was designed to evaluate HAdV-3 hexon variants for the selection of potential vaccine candidates and the use of hexon gene as a target for designing siRNA that can be used as a therapy. Based on the data of worldwide distribution, duration of circulation, co-circulation and their percentage among all the variants, 3Hv-1 to 3Hv-4 were categorized as the major hexon variants. Phylogenetic analysis and the percentage of homology in the hypervariable regions followed by multi-sequence alignment, zPicture analysis and restriction enzyme analysis were carried out. In the phylogram, the variants were arranged in different clusters. The HVR encoding regions of hexon of 3Hv-1 to 3Hv-4 showed 16 point mutations resulting in 12 amino acids substitutions. The homology in HVRs was 81.81-100%. Therefore, the major hexon variants are substantially different from each other which justifies their inclusion as the potential vaccine candidates. Interestingly, despite the significant differences in the DNA sequence, there were many conserved areas in the HVRs, and we have designed functional siRNAs form those locations. We have also designed immunogenic vaccine peptide epitopes from the hexon protein using bioinformatics prediction tool. We hope that our developed siRNAs and immunogenic vaccine peptide epitopes could be used in the future development of siRNA-based therapy and designing a vaccine against HAdV-3.
Fulltext Characterizing the genetic diversity of the monkey malaria parasite Plasmodium cynomolgi

Sutton PL, Luo Z, Divis PCS, Friedrich VK, Conway DJ, Singh B, et al.

Infect Genet Evol, 2016 06;40:243-252.
PMID: 26980604 DOI: 10.1016/j.meegid.2016.03.009

Plasmodium cynomolgi is a malaria parasite that typically infects Asian macaque monkeys, and humans on rare occasions. P. cynomolgi serves as a model system for the human malaria parasite Plasmodium vivax, with which it shares such important biological characteristics as formation of a dormant liver stage and a preference to invade reticulocytes. While genomes of three P. cynomolgi strains have been sequenced, genetic diversity of P. cynomolgi has not been widely investigated. To address this we developed the first panel of P. cynomolgi microsatellite markers to genotype eleven P. cynomolgi laboratory strains and 18 field isolates from Sarawak, Malaysian Borneo. We found diverse genotypes among most of the laboratory strains, though two nominally different strains were found to be genetically identical. We also investigated sequence polymorphism in two erythrocyte invasion gene families, the reticulocyte binding protein and Duffy binding protein genes, in these strains. We also observed copy number variation in rbp genes.
Comparative genome analysis of multiple vancomycin-resistant Enterococcus faecium isolated from two fatal cases

Lim SY, Yap KP, Teh CS, Jabar KA, Thong KL

Infect Genet Evol, 2017 04;49:55-65.
PMID: 28039075 DOI: 10.1016/j.meegid.2016.12.029

Enterococcus faecium is both a commensal of the human intestinal tract and an opportunistic pathogen. The increasing incidence of enterococcal infections is mainly due to the ability of this organism to develop resistance to multiple antibiotics, including vancomycin. The aim of this study was to perform comparative genome analyses on four vancomycin-resistant Enterococcus faecium (VREfm) strains isolated from two fatal cases in a tertiary hospital in Malaysia. Two sequence types, ST80 and ST203, were identified which belong to the clinically important clonal complex (CC) 17. This is the first report on the emergence of ST80 strains in Malaysia. Three of the studied strains (VREr5, VREr6, VREr7) were each isolated from different body sites of a single patient (patient Y) and had different PFGE patterns. While VREr6 and VREr7 were phenotypically and genotypically similar, the initial isolate, VREr5, was found to be more similar to VRE2 isolated from another patient (patient X), in terms of the genome contents, sequence types and phylogenomic relationship. Both the clinical records and genome sequence data suggested that patient Y was infected by multiple strains from different clones and the strain that infected patient Y could have derived from the same clone from patient X. These multidrug resistant strains harbored a number of virulence genes such as the epa locus and pilus-associated genes which could enhance their persistence. Apart from that, a homolog of E. faecalis bee locus was identified in VREr5 which might be involved in biofilm formation. Overall, our comparative genomic analyses had provided insight into the genetic relatedness, as well as the virulence potential, of the four clinical strains.
Comparative genomic and phylogenetic analysis of a toxigenic clinical isolate of Corynebacterium diphtheriae strain B-D-16-78 from Malaysia

Hong KW, Asmah Hani AW, Nurul Aina Murni CA, Pusparani RR, Chong CK, Verasahib K, et al.

Infect Genet Evol, 2017 Oct;54:263-270.
PMID: 28711373 DOI: 10.1016/j.meegid.2017.07.015

In this study, we report the comparative genomics and phylogenetic analysis of Corynebacterium diphtheriae strain B-D-16-78 that was isolated from a clinical specimen in 2016. The complete genome of C. diphtheriae strain B-D-16-78 was sequenced using PacBio Single Molecule, Real-Time sequencing technology and consists of a 2,474,151-bp circular chromosome with an average GC content of 53.56%. The core genome of C. diphtheriae was also deduced from a total of 74 strains with complete or draft genome sequences and the core genome-based phylogenetic analysis revealed close genetic relationship among strains that shared the same MLST allelic profile. In the context of CRISPR-Cas system, which confers adaptive immunity against re-invading DNA, 73 out of 86 spacer sequences were found to be unique to Malaysian strains which harboured only type-II-C and/or type-I-E-a systems. A total of 48 tox genes which code for the diphtheria toxin were retrieved from the 74 genomes and with the exception of one truncated gene, only nucleotide substitutions were detected when compared to the tox gene sequence of PW8. More than half were synonymous substitution and only two were nonsynonymous substitutions whereby H24Y was predicted to have a damaging effect on the protein function whilst T262V was predicted to be tolerated. Both toxigenic and non-toxigenic toxin-gene bearing strains have been isolated in Malaysia but the repeated isolation of toxigenic strains with the same MLST profile suggests the possibility of some of these strains may be circulating in the population. Hence, efforts to increase herd immunity should be continued and supported by an effective monitoring and surveillance system to track, manage and control outbreak of cases.
Comparative genomic provides insight into the virulence and genetic diversity of Vibrio parahaemolyticus associated with shrimp acute hepatopancreatic necrosis disease

Yu LH, Teh CSJ, Yap KP, Ung EH, Thong KL

Infect Genet Evol, 2020 09;83:104347.
PMID: 32360538 DOI: 10.1016/j.meegid.2020.104347

Acute hepatopancreatic necrosis disease (AHPND) is an important shrimp disease of economic importance which causes mass mortality of cultivated penaeid shrimps in Southeast Asian countries, Mexico and South America. This disease was originally caused by Vibrio parahaemolyticus (VPAHPND) which is reported to harbour a transferable plasmid carrying the virulent PirAB-like toxin genes (pirABvp). However, little is known about the pathogenicity of VPAHPND. To extend our understanding, comparative genomic analyses was performed in this study to identify the genetic differences and to understand the phylogenetic relationship of VPAHPND strains. Seven Vibrio parahaemolyticus strains (five VPAHPND strains and two non-VPAHPND strains) were sequenced and 31 draft genomes of V. parahaemolyticus were retrieved from NCBI database and incorporated into the genomic comparison to elucidate their genomic diversity. The study showed that the genome sizes of the VPAHPND strains were approximately 5 Mbp. Ten sequence types (STs) were identified among the VPAHPND strains using in silico-Multilocus Sequence Typing analysis (MLST) and ST 970 was the predominant ST. Phylogenetic analysis based on MLST and single nucleotide polymorphisms (SNP) showed that the VPAHPND strains were genetically diverse. Based on the comparative genomic analysis, several functional proteins were identified from diiferent categories associated with virulence-related proteins, secretory proteins, conserved domain proteins, transporter proteins, and phage proteins. The CRISPR analysis showed that VPAHPND strains contained less number of CRISPRs elements than non-VPAHPND strains while six prophages regions were identified in the genomes, suggested the lack of CRISPR might promote prophage insertion. The genomic information in this study provide improved understanding of the virulence of these VPAHPND strains.
Designing and evaluation of an antibody-targeted chimeric recombinant vaccine encoding Shigella flexneri outer membrane antigens

Kazi A, Hisyam Ismail CMK, Anthony AA, Chuah C, Leow CH, Lim BH, et al.

Infect Genet Evol, 2020 06;80:104176.
PMID: 31923724 DOI: 10.1016/j.meegid.2020.104176

Shigellosis is one of the most common diseases found in the developing countries, especially those countries that are prone flood. The causative agent for this disease is the Shigella species. This organism is one of the third most common enteropathogens responsible for childhood diarrhea. Since Shigella can survive gastric acidity and is an intracellular pathogen, it becomes difficult to treat. Also, uncontrolled use of antibiotics has led to development of resistant strains which poses a threat to public health. Therefore, there is a need for long term control of Shigella infection which can be achieved by designing a proper and effective vaccine. In this study, emphasis was made on designing a candidate that could elicit both B-cell and T-cell immune response. Hence B- and T-cell epitopes of outer membrane channel protein (OM) and putative lipoprotein (PL) from S. flexneri 2a were computationally predicted using immunoinformatics approach and a chimeric construct (chimeric-OP) containing the immunogenic epitopes selected from OM and PL was designed, cloned and expressed in E. coli system. The immunogenicity of the recombinant chimeric-OP was assessed using Shigella antigen infected rabbit antibody. The result showed that the chimeric-OP was a synthetic peptide candidate suitable for the development of vaccine and immunodiagnostics against Shigella infection.
Differential expression of cytokine genes in THP-1-derived macrophages infected with mild and virulence strains of Shigella flexneri 2a

Shabani NRM, Mokhtar M, Leow CH, Lean QY, Chuah C, Singh KKB, et al.

Infect Genet Evol, 2020 11;85:104532.
PMID: 32911076 DOI: 10.1016/j.meegid.2020.104532

Shigella is an intracellular bacterial pathogen that causes bacterial dysentery called shigellosis. The assessment of pro- and anti-inflammatory mediators produced by immune cells against this bacteria are vital in identifying the effectiveness of the immune reaction in protecting the host. In Malaysia, Shigella is ranked as the third most common bacteria causing diarrheal disease among children below 5 years old. In the present study, we aim to examine the differential cytokine gene expressions of macrophages in response to two types of clinical strains of Shigella flexneri 2a (S. flexneri 2a) isolated from patients admitted in Hospital Universiti Sains Malaysia, Kelantan, Malaysia. THP-1-derived macrophages, as the model of human macrophages, were infected separately with S. flexneri 2a mild (SH062) and virulence (SH057) strains for 6, 12, and 24 h, respectively. The gene expression level of inflammatory mediators was identified using real-time quantitative polymerase chain reaction (RT-qPCR). The production of nitric oxide (NO) by the macrophages was measured by using a commercialized NO assay kit. The ability of macrophages to kill the intracellular bacteria was assessed by intracellular killing assay. Induction of tumor necrosis factor-alpha (TNFα), interleukin (IL)-1β, IL-6, IL-12, inducible NO synthase (iNOS), and NO, confirmed the pro-inflammatory reaction of the THP-1-derived macrophages in response to S. flexneri 2a, especially against the SH507 strain. The SH057 also induced a marked increase in the expression levels of the anti-inflammatory cytokine mRNAs at 12 h and 24 h post-infection. In the intracellular killing assay, both strains showed less viable, indicating the generation of pro-inflammatory cytokines in the presence of iNOS and NO was crucial in the stimulation of macrophages for the host defense against shigellosis. Transcription analysis of THP-1-derived macrophages in this study identifies differentially expressed cytokine genes that correlated with the virulence factor of S. flexneri 2a.
Fulltext Dispersal direction of Malaysian Fasciola gigantica from neighboring southeast Asian countries inferred using mitochondrial DNA analysis

Ichikawa-Seki M, Hayashi K, Tashiro M, Khadijah S

Infect Genet Evol, 2022 Nov;105:105373.
PMID: 36202207 DOI: 10.1016/j.meegid.2022.105373

Fasciola gigantica and hybrid Fasciola flukes, responsible for the disease fasciolosis, are found in Southeast Asian countries. In the present study, we performed molecular species identification of Fasciola flukes distributed in Terengganu, Malaysia using multiplex PCR for phosphoenolpyruvate carboxykinase (pepck) and PCR-restriction fragment length polymorphism (RFLP) for DNA polymerase delta (pold). Simultaneously, phylogenetic analysis based on mitochondrial NADH dehydrogenase subunit 1 (nad1) was performed for the first time on Malaysian Fasciola flukes to infer the dispersal direction among neighboring countries. A total of 40 flukes used in this study were identified as F. gigantica. Eight nad1 haplotypes were identified in the F. gigantica population of Terengganu. Median-joining network analysis revealed that the Malaysian population was related to those obtained from bordering countries such as Thailand and Indonesia. However, genetic differentiation was detected using population genetics analyses. Nevertheless, the nucleotide diversity (π) value suggested that F. gigantica with the predominant haplotypes was introduced into Malaysia from Thailand and Indonesia. The dispersal direction suggested by population genetics in the present study may not be fully reliable since Fasciola flukes were collected from a single location in one state of Malaysia. Further studies analyzing more samples from many locations are required to validate the dispersal direction proposed herein.
Displacement of predominant respiratory syncytial virus genotypes in Malaysia between 1989 and 2011

Khor CS, Sam IC, Hooi PS, Chan YF

Infect Genet Evol, 2013 Mar;14:357-60.
PMID: 23305888 DOI: 10.1016/j.meegid.2012.12.017

From 1989 to 2011 in Kuala Lumpur, Malaysia, multiple genotypes from both respiratory syncytial virus (RSV) subgroups were found co-circulating each year. RSV-A subgroup predominated in 12 out of 17years with the remaining years predominated by RSV-B subgroup. Local RSV strains exhibited temporal clustering with RSV strains reported in previous epidemiological studies. Every few years, the existing predominant genotype was replaced by a new genotype. The RSV-A genotypes GA2, GA5 and GA7 were replaced by NA1 and NA2, while BA became the predominant RSV-B genotype. A unique local cluster, BA12, was seen in 2009, and the recently-described ON1 genotype with 72-nt duplication emerged in 2011. Our findings will have important implications for future vaccine intervention.
Disruption of predicted dengue virus type 3 major outbreak cycle coincided with switching of the dominant circulating virus genotype

Tan KK, Zulkifle NI, Abd-Jamil J, Sulaiman S, Yaacob CN, Azizan NS, et al.

Infect Genet Evol, 2017 Oct;54:271-275.
PMID: 28698156 DOI: 10.1016/j.meegid.2017.07.008

Dengue is hyperendemic in most of Southeast Asia. In this region, all four dengue virus serotypes are persistently present. Major dengue outbreak cycle occurs in a cyclical pattern involving the different dengue virus serotypes. In Malaysia, since the 1980s, the major outbreak cycles have involved dengue virus type 3 (DENV3), dengue virus type 1 (DENV1) and dengue virus type 2 (DENV2), occurring in that order (DENV3/DENV1/DENV2). Only limited information on the DENV3 cycles, however, have been described. In the current study, we examined the major outbreak cycle involving DENV3 using data from 1985 to 2016. We examined the genetic diversity of DENV3 isolates obtained during the period when DENV3 was the dominant serotype and during the inter-dominant transmission period. Results obtained suggest that the typical DENV3/DENV1/DENV2 cyclical outbreak cycle in Malaysia has recently been disrupted. The last recorded major outbreak cycle involving DENV3 occurred in 2002, and the expected major outbreak cycle involving DENV3 in 2006-2012 did not materialize. DENV genome analyses revealed that DENV3 genotype II (DENV3/II) was the predominant DENV3 genotype (67%-100%) recovered between 1987 and 2002. DENV3 genotype I (DENV3/I) emerged in 2002 followed by the introduction of DENV3 genotype III (DENV3/III) in 2008. These newly emerged DENV3 genotypes replaced DENV3/II, but there was no major upsurge of DENV3 cases that accompanied the emergence of these viruses. DENV3 remained in the background of DENV1 and DENV2 until now. Virus genome sequence analysis suggested that intrinsic differences within the different dengue virus genotypes could have influenced the transmission efficiency of DENV3. Further studies and continuous monitoring of the virus are needed for better understanding of the DENV transmission dynamics in hyperendemic regions.
Divergence of the dengue virus type 2 Cosmopolitan genotype associated with two predominant serotype shifts between 1 and 2 in Surabaya, Indonesia, 2008-2014

Kotaki T, Yamanaka A, Mulyatno KC, Churrotin S, Sucipto TH, Labiqah A, et al.

Infect Genet Evol, 2016 Jan;37:88-93.
PMID: 26553170 DOI: 10.1016/j.meegid.2015.11.002

Indonesia is one of the biggest dengue endemic countries, and, thus, is an important place to investigate the evolution of dengue virus (DENV). We have continuously isolated DENV in Surabaya, the second biggest city in Indonesia, since 2008. We previously reported sequential changes in the predominant serotype from DENV type 2 (DENV-2) to DENV type 1 (DENV-1) in November 2008 and from DENV-1 to DENV-2 in July 2013. The predominance of DENV-2 continued in 2014, but not in 2015. We herein phylogenetically investigated DENV-2 transitions in Surabaya between 2008 and 2014 to analyze the divergence and evolution of DENV-2 concomitant with serotype shifts. All DENV-2 isolated in Surabaya were classified into the Cosmopolitan genotype, and further divided into 6 clusters. Clusters 1-3, dominated by Surabaya strains, were defined as the "Surabaya lineage". Clusters 4-6, dominated by strains from Singapore, Malaysia, and many parts of Indonesia, were the "South East Asian lineage". The most recent common ancestor of these strains existed in 1988, coinciding with the time that an Indonesian dengue outbreak took place. Cluster 1 appeared to be unique because no other DENV-2 isolate was included in this cluster. The predominance of DENV-2 in 2008 and 2013-14 were caused by cluster 1, whereas clusters 2 and 3 sporadically emerged in 2011 and 2012. The characteristic amino acids of cluster 1, E-170V and E-282Y, may be responsible for its prevalence in Surabaya. No amino acid difference was observed in the envelope region between strains in 2008 and 2013-14, suggesting that the re-emergence of DENV-2 in Surabaya was due to the loss or decrease of herd immunity in the 5-year period when DENV-2 subsided. The South East Asian lineage primarily emerged in Surabaya in 2014, probably imported from other parts of Indonesia or foreign countries.
Fulltext Emergence and molecular mechanisms of SARS-CoV-2 and HIV to target host cells and potential therapeutics

Saleemi MA, Ahmad B, Benchoula K, Vohra MS, Mea HJ, Chong PP, et al.

Infect Genet Evol, 2020 11;85:104583.
PMID: 33035643 DOI: 10.1016/j.meegid.2020.104583

The emergence of a new coronavirus, in around late December 2019 which had first been reported in Wuhan, China has now developed into a massive threat to global public health. The World Health Organization (WHO) has named the disease caused by the virus as COVID-19 and the virus which is the culprit was renamed from the initial novel respiratory 2019 coronavirus to SARS-CoV-2. The person-to-person transmission of this virus is ongoing despite drastic public health mitigation measures such as social distancing and movement restrictions implemented in most countries. Understanding the source of such an infectious pathogen is crucial to develop a means of avoiding transmission and further to develop therapeutic drugs and vaccines. To identify the etiological source of a novel human pathogen is a dynamic process that needs comprehensive and extensive scientific validations, such as observed in the Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and human immunodeficiency virus (HIV) cases. In this context, this review is devoted to understanding the taxonomic characteristics of SARS-CoV-2 and HIV. Herein, we discuss the emergence and molecular mechanisms of both viral infections. Nevertheless, no vaccine or therapeutic drug is yet to be approved for the treatment of SARS-CoV-2, although it is highly likely that new effective medications that target the virus specifically will take years to establish. Therefore, this review reflects the latest repurpose of existing antiviral therapeutic drug choices available to combat SARS-CoV-2.
Evolutionary history of Dengue virus type 4: insights into genotype phylodynamics

Villabona-Arenas CJ, Zanotto PM

Infect Genet Evol, 2011 Jul;11(5):878-85.
PMID: 21335103 DOI: 10.1016/j.meegid.2011.02.007

Dengue virus type 4 (DENV-4) circulates in tropical and subtropical countries from Asia and the Americas. Despite the importance of dengue virus distribution, little is known about the worldwide viral spread. Following a Bayesian phylogenetic approach we inferred the evolutionary history of 310 isolates sampled from 37 countries during the time period 1956-2008 and the spreading dynamics for genotypes I and II. The region (tropical rainforest biome) comprised by Malaysia-Thailand was the most likely ancestral area from which the serotype has originated and spread. Interestingly, cross-correlation analysis on demographic time series with the Asian sequences showed a statistically significant negative correlation that could be suggestive of competition among genotypes within the same serotype.
First evidence of local circulation of Plasmodium ovale curtisi and reliability of a malaria rapid diagnostic test among symptomatic outpatients in Douala, Cameroon

Kojom Foko LP, Kouemo Motse FD, Kamgain Mawabo L, Pande V, Singh V

Infect Genet Evol, 2021 07;91:104797.
PMID: 33676011 DOI: 10.1016/j.meegid.2021.104797

The performances of a commonly used Plasmodium falciparum-detecting rapid diagnostic test (RDT) were determined in symptomatic individuals living in Cameroon. Discrepancies between RDT and light microscopy (LM) results were further investigated, with a focus on non-falciparum malaria (NFM) which are still largely understudied in sub-Saharan Africa (sSA) countries. In the present study, a total of 355 individuals aged 1-65 years were enrolled in the study. Their signs/symptoms and sociodemographic characteristics were documented. The RDT reliability was evaluated using LM as gold standard method. Polymerase chain reaction (PCR) of Plasmodium 18S gene was performed for samples with discordant results between LM and RDT (i.e., RDT-/LM+, and RDT+/LM-). The PCR amplicons of NFM species were sequenced and BLASTed. The prevalence of malaria infection by LM was 95.7% (95% CI: 93.1-97.4%). The sensitivity and specificity of RDT for P. falciparum detection was 94.0% and 66.7%, respectively. By PCR assay, P. ovale curtisi (PoC) was found in 5 of the 30 discordant samples, and on sequence analysis these isolates were found to be phylogenetically closer to sequences reported from China-Myanmar border and Malaysia. This is the first report on molecular characterization of P. ovale subspecies in Cameroon. The study also outlines the good diagnostic performances of the RDT for detection of P. falciparum. Though, the presence of PoC indicated the importance of having RDTs targeting the NFM species in malaria diagnosis and treatment, which is presently limited in the country.
First genetic classification of Cryptosporidium and Giardia from HIV/AIDS patients in Malaysia

Lim YA, Iqbal A, Surin J, Sim BL, Jex AR, Nolan MJ, et al.

Infect Genet Evol, 2011 Jul;11(5):968-74.
PMID: 21439404 DOI: 10.1016/j.meegid.2011.03.007

Given the HIV epidemic in Malaysia, genetic information on opportunistic pathogens, such as Cryptosporidium and Giardia, in HIV/AIDS patients is pivotal to enhance our understanding of epidemiology, patient care, management and disease surveillance. In the present study, 122 faecal samples from HIV/AIDS patients were examined for the presence of Cryptosporidium oocysts and Giardia cysts using a conventional coproscopic approach. Such oocysts and cysts were detected in 22.1% and 5.7% of the 122 faecal samples, respectively. Genomic DNAs from selected samples were tested in a nested-PCR, targeting regions of the small subunit (SSU) of nuclear ribosomal RNA and the 60kDa glycoprotein (gp60) genes (for Cryptosporidium), and the triose-phosphate isomerase (tpi) gene (for Giardia), followed by direct sequencing. The sequencing of amplicons derived from SSU revealed that Cryptosporidium parvum was the most frequently detected species (64% of 25 samples tested), followed by C. hominis (24%), C. meleagridis (8%) and C. felis (4%). Sequencing of a region of gp60 identified C. parvum subgenotype IIdA15G2R1 and C. hominis subgenotypes IaA14R1, IbA10G2R2, IdA15R2, IeA11G2T3R1 and IfA11G1R2. Sequencing of amplicons derived from tpi revealed G. duodenalis assemblage A, which is of zoonotic importance. This is the first report of C. hominis, C. meleagridis and C. felis from Malaysian HIV/AIDS patients. Future work should focus on an extensive analysis of Cryptosporidium and Giardia in such patients as well as in domestic and wild animals, in order to improve the understanding of transmission patterns and dynamics in Malaysia. It would also be particularly interesting to establish the relationship among clinical manifestation, CD4 cell counts and genotypes/subgenotypes of Cryptosporidium and Giardia in HIV/AIDS patients. Such insights would assist in a better management of clinical disease in immuno-deficient patients as well as improved preventive and control strategies.
From discovery to spread: The evolution and phylogeny of Getah virus

Li YY, Liu H, Fu SH, Li XL, Guo XF, Li MH, et al.

Infect Genet Evol, 2017 11;55:48-55.
PMID: 28827175 DOI: 10.1016/j.meegid.2017.08.016

Getah virus (GETV) was first isolated in Malaysia in 1955. Since then, epidemics in horses and pigs caused by GETV have resulted in huge economic losses. At present, GETV has spread across Eurasia and Southeast Asia, including mainland China, Korea, Japan, Mongolia, and Russia. Data show that the Most Recent Common Ancestor (MRCA) of GETV existed about 145years ago (95% HPD: 75-244) and gradually evolved into four distinct evolutionary populations: Groups I-IV. The MRCA of GETVs in Group III, which includes all GETVs isolated from mosquitoes, pigs, horses, and other animals since the 1960s (from latitude 19°N to 60°N), existed about 51years ago (95% HPD: 51-72). Group III is responsible for most viral epidemics among domestic animals. An analysis of the GETV E2 protein sequence and structure revealed seven common amino acid mutation sites. These sites are responsible for the structural and electrostatic differences detected between widespread Group III isolates and the prototype strain MM2021. These differences may account for the recent geographical radiation of the virus. Considering the economic significance of GETV infection in pigs and horses, we recommend the implementation of strict viral screening and monitoring programs.
Genetic characterization of Theileria species infecting bovines in India

Kundave VR, Ram H, Shahzad M, Garg R, Banerjee PS, Nehra AK, et al.

Infect Genet Evol, 2019 11;75:103962.
PMID: 31302242 DOI: 10.1016/j.meegid.2019.103962

Genetic characterization of Theileria species infecting bovines in India was attempted targeting the 18S ribosomal RNA region of the parasite. Blood samples of bovines (n = 452), suspected for haemoprotozoan infections, from 9 different states of the country were microscopically examined for Theileria species infection. Four Theileria spp. positive blood samples from each state were randomly utilized for PCR amplification of the 18S rRNA gene (approx. 1529 bp) followed by cloning and sequencing. The sequence data analysis of all the 36 isolates revealed that 33 isolates had high sequence similarity with published sequences of T. annulata, whereas 3 isolates (MF287917, MF287924 and MF287928) showed close similarity with published sequences of T. orientalis. Sequence homology within the isolates ranged between 95.8 and 100% and variation in the length of targeted region was also noticed in different isolates (1527-1538 nt). Phylogenetic tree created for T. annulata sequences revealed that a total of 24 Indian isolates formed a major clade and grouped together with isolates originating from countries like China, Spain, Turkey and USA. Remaining 09 isolates clustered in a separate group and were closely related to the TA5 isolate of T. annulata (a new genotype) originating from India and also with the isolates from East Asian countries like Japan and Malaysia. All the three T. orientalis isolates had minimal intraspecific variation (99-100% homology) amongst themselves. Further, in the phylogenetic analysis T. orientalis Indian isolates were found to cluster away from other 14 isolates of T. buffeli/sergenti/orientalis originating from different countries (Australia, China, Indonesia and Spain). However, these 3 isolates clustered together with the T. buffeli Indian isolate (EF126184). Present study confirmed the circulation of different genotypes of T. annulata in India, along with T. orientalis isolates.

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