Southeast Asian Strains Research Articles

An in-silico analysis decoding the differences between the viral proteins of the American and the South-East Asian strains of DENV-4

An <i>in-silico</i> analysis decoding the differences between the viral proteins of the American and the South-East Asian strains of DENV-4

Phylogenetically evolutionary analysis provides insights into the genetic diversity and adaptive evolution of porcine deltacoronavirus

BackgroundPorcine deltacoronavirus (PDCoV) is one of the emerging swine enteric coronaviruses (SECoVs), which has been widely prevalent in the North America and Asia. In addition to causing severe diarrhea in piglets, PDCoV also shows the potential to infect diverse host species, including calves, chickens, turkey poults, and humans. However, the clinical pathogenicity and genetic evolution of PDCoV is still not fully understood.ResultsHere, we recorded an outbreak of a novel recombinant PDCoV strain (CHN-HeN06-2022) in a large nursery fattening pig farm. Genomic analysis showed that the CHN-HeN06-2022 strain shared 98.3-98.7% sequence identities with the Chinese and American reference strains. To clarify the evolutionary relationships, phylogenetic analysis was performed using the PDCoV genome sequences available in the GenBank database. Based on genetic distance and geographical distribution, the phylogenetic tree clearly showed that all the PDCoV sequences could be divided into lineage 1 and lineage 2, which were further classified into sublineage 1.1 (Chinese strains), 1.2 (the North American strains), 2.1 (the Southeast Asian strains), and 2.2 (Chinese strains). Corresponding to the evolutionary tree, we found that, compared to lineage 1, lineage 2 strains usually contain a continuous 6-nt deletion in Nsp2 and a 9-nt deletion in Nsp3, respectively. Furthermore, recombination analysis suggested that the CHN-HeN06-2022 occurred segments exchange crossed Nsp2 and Nsp3 region between sublineage 1.1 and sublineage 2.1. Combined with previously reported recombinant strains, the highest recombination frequency occurred in Nsp2, Nsp3, and S gene. Additionally, we identified a total of 14 amino acid sites under positive selection in spike protein, most of which are located in the regions related with the viral attachment, receptor binding, and membrane fusion.ConclusionsTaken together, our studies provide novel insights into the genetic diversity and adaptive evolution of PDCoV. It would be helpful to the development of vaccine and potential antiviral agent.

Enterocytozoon hepatopenaei real-time and Shrimp MultiPathTM PCR assay validation for South-East Asian and Latin American strains of Penaeid shrimp.

Enterocytozoon hepatopenaei (EHP) infections are a global challenge for the Penaeid shrimp industry with a sharp rise in prevalence over the last 10 yr. EHP is known to cause sub-optimal growth, large size variation and reduced survival of shrimp. Molecular methods development has mainly focussed on 18S rRNA or spore wall protein 1 (SWP1). Due to the specificity and sensitivity issues with previously designed assays for both targets, new molecular assays are needed by the global shrimp industry and regulators to help manage the risks posed by EHP. This paper describes new real-time PCR (qPCR) methods developed for the novel EHP gene targets polar tube protein 2 (PTP2) and spore wall protein 26 (SWP26), whilst also presenting performance metrics of the new Shrimp MultiPathTM technology EHP assay. qPCR assays PTP2G and SWP26G show high amplification efficiency, a limit of detection (LOD) of between 1 and 4 copies, low assay variation and high diagnostic sensitivity (DSe) and specificity (DSp) compared to imperfect reference assays. Similar performance is seen with Shrimp MultiPathTM EHP showing an LOD of 8 copies, low assay variation and high DSe and DSp. These novel molecular targets for EHP and Shrimp MultiPathTM EHP strengthen global efforts to monitor and mitigate risks of EHP infections and outbreaks. Moreover, this study presents novel data on distribution of EHP in shrimp populations from South-East Asia and Latin America, and how sequence variations need to be considered when monitoring EHP in different geographies.

Plasmodium falciparum K13 mutations in Africa and Asia impact artemisinin resistance and parasite fitness.

The emergence of mutant K13-mediated artemisinin (ART) resistance in Plasmodium falciparum malaria parasites has led to widespread treatment failures across Southeast Asia. In Africa, K13-propeller genotyping confirms the emergence of the R561H mutation in Rwanda and highlights the continuing dominance of wild-type K13 elsewhere. Using gene editing, we show that R561H, along with C580Y and M579I, confer elevated in vitro ART resistance in some African strains, contrasting with minimal changes in ART susceptibility in others. C580Y and M579I cause substantial fitness costs, which may slow their dissemination in high-transmission settings, in contrast with R561H that in African 3D7 parasites is fitness neutral. In Cambodia, K13 genotyping highlights the increasing spatio-temporal dominance of C580Y. Editing multiple K13 mutations into a panel of Southeast Asian strains reveals that only the R561H variant yields ART resistance comparable to C580Y. In Asian Dd2 parasites C580Y shows no fitness cost, in contrast with most other K13 mutations tested, including R561H. Editing of point mutations in ferredoxin or mdr2, earlier associated with resistance, has no impact on ART susceptibility or parasite fitness. These data underline the complex interplay between K13 mutations, parasite survival, growth and genetic background in contributing to the spread of ART resistance.

The origins of G12P[6] rotavirus strains detected in Lebanon.

The G12 rotaviruses are an increasingly important cause of severe diarrhoea in infants and young children worldwide. Seven human G12P[6] rotavirus strains were detected in stool samples from children hospitalized with gastroenteritis in Lebanon during a 2011-2013 surveillance study. Complete genomes of these strains were sequenced using VirCapSeq-VERT, a capture-based high-throughput viral-sequencing method, and further characterized based on phylogenetic analyses with global RVA and vaccine strains. Based on the complete genomic analysis, all Lebanese G12 strains were found to have Wa-like genetic backbone G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Phylogenetically, these strains fell into two clusters where one of them might have emerged from Southeast Asian strains and the second one seems to have a mixed backbone between North American and Southeast Asian strains. Further analysis of these strains revealed high antigenic variability compared to available vaccine strains. To our knowledge, this is the first report on the complete genome-based characterization of G12P[6] emerging in Lebanon. Additional studies will provide important insights into the evolutionary dynamics of G12 rotaviruses spreading in Asia.

Dengue Fever and Severe Dengue in Barbados, 2008-2016.

Analysis of the temporal, seasonal and demographic distribution of dengue virus (DENV) infections in Barbados was conducted using national surveillance data from a total of 3994 confirmed dengue cases. Diagnosis was confirmed either by DENV–specific real time reverse transcriptase polymerase chain reaction (rRT–PCR), or non–structural protein 1 (NS1) antigen or enzyme linked immunosorbent assay (ELISA) tests; a case fatality rate of 0.4% (10/3994) was observed. The dengue fever (DF) prevalence varied from 27.5 to 453.9 cases per 100,000 population among febrile patients who sought medical attention annually. DF cases occurred throughout the year with low level of transmission observed during the dry season (December to June), then increased transmission during rainy season (July to November) peaking in October. Three major dengue epidemics occurred in Barbados during 2010, 2013 and possibly 2016 with an emerging three–year interval. DF prevalence among febrile patients who sought medical attention overall was highest among the 10–19 years old age group. The highest DF hospitalisation prevalence was observed in 2013. Multiple serotypes circulated during the study period and Dengue virus serotype 2 (DENV–2) was the most prevalent serotype during 2010, whilst DENV–1 was the most prevalent serotype in 2013. Two DENV–1 strains from the 2013 DENV epidemic were genetically more closely related to South East Asian strains, than Caribbean or South American strains, and represent the first ever sequencing of DENV strains in Barbados. However, the small sample size (n = 2) limits any meaningful conclusions. DF prevalence was not significantly different between females and males. Public health planning should consider DENV inter–epidemic periodicity, the current COVID–19 pandemic and similar clinical symptomology between DF and COVID–19. The implementation of routine sequencing of DENV strains to obtain critical data can aid in battling DENV epidemics in Barbados.

Structure of cytotoxic associated antigen A protein of Helicobacter pylori from Bali and Lombok isolates of Indonesia.

Background and Aim:Helicobacter pylori is a well-known zoonotic agent with worldwide distribution. In Indonesia, only one report regarding the variation within the cytotoxic associated antigen A (CagA) protein of H. pylori has been described in the literature, which was conducted in Manado, South Sulawesi. There remains no report concerning the structure of this protein, particularly for the Bali and Lombok isolates. The objective of this study was to investigate the diversity of H. pylori CagA amino acid sequences of Bali and Lombok isolates, to predict their molecular structures and conduct toxicity examination of CagA on gastric cells.Materials and Methods:A total of 36 samples were used in equal proportions for each pathologic condition. DNA extraction was performed to subculture H. pylori Bali isolates. The amplification of the CagA 3′ variable region was carried out using the primers P1 (5′-GATAACAGGCAAGCTTTTTGAGG-3′) and P2 (5′-CTGCAAAAGATTGTTTGGCAG-3′). The W2, W9, and W35 fragments were selected as a representation of H. pylori Bali isolates, which were modeled through the threading modeling approach using I-TASSER.Results:According to the 12 CagA sequences obtained and phylogenetic analyses, the H. pylori strain originating from Bali can be grouped within the East Asian genotypes and is identical to the Lombok strain. In addition, the Bali isolates are phylogenetically more closely related to Southeast Asian strains, particularly the Filipino strain. The relationship between degree of inflammation induced and CagA-positive infection was not statistically significant.Conclusion:The structure of the H. pylori Bali isolate is identical to that of Lombok isolate, which belongs to the same group of East Asian genotypes, and bacterial virulence is not related to structure.

Sequence and phylogenetic analyses of Nsp2-HVII, ORF5, and ORF7 coding regions of highly pathogenic porcine reproductive and respiratory syndrome virus from Myanmar.

In this study, PRRSVs that spread during the outbreaks of 2011 in Myanmar were investigated. Sequences and phylogenetic analyses of the Nsp2 middle hypervariable region (Nsp2-HVII) encoding gene, ORF5, and ORF7 showed that they belonged to the North American (NA) genotype and were clustered with HP-PRRSV strains from other Southeast Asian countries. The discontinuous 30-amino acid deletions at positions 481 and 533-561 were found in the Nsp2-HVII of all Myanmarese PRRSVs, implying their derivation from HP-PRRSV. The phylogenetic trees also showed that Myanmarese strains were in the same group as other Southeast Asian strains from Cambodia, Thailand, and Laos suggesting their close relationships. Conversely, Vietnamese 07QN was in the same group as Chinese JXA1. The unique amino acid mutations found only in Myanmarese PRRSVs were L292F, P431S, and V621M in Nsp2-HVII and E170G in GP5, which may be used as a marker for monitoring genetic diversity of newly emerging HP-PRRSV strains.

Molecular characterization of bovine ephemeral fever virus in Thailand between 2013 and 2017

Bovine ephemeral fever (BEF) is an arthropod-borne disease caused by bovine ephemeral fever virus (BEFV), a negative sense, single-stranded RNA virus. BEFV is endemic in tropical and sub-tropical regions including Thailand, a country in mainland Southeast Asia. However, there are few studies on BEFV and no available information regarding molecular characteristics of BEFV in Thailand. Therefore, the aims of this study were to genetically characterize Thai BEFVs and reveal their evolutions by phylogenetic analysis of G gene ectodomain sequences. From 2013 to 2017, blood samples were collected from bovine that matched with BEF case definition from three regions of Thailand. Thai BEFV G genes and a whole genome of an isolate, East Asia/TH/LRI0045/2016, were sequenced and characterized. Additionally, their phylogenies were constructed. This is the first report on genetics of BEFV in Southeast Asia. G ectodomain encoding region of Thai BEFV found during 2013–2017 are closely related to the second and third sub-clades of East Asia lineage. In addition, we observed mutation in the putative P’ ORF of all Thai BEFVs which generated a premature stop codon. Thai G gene sequences are closely related to those of mainland Chinese and Taiwanese isolates. The whole genomic sequences of Thai BEFV and East Asia/China/JT02 L/2002 possess common characteristics, suggesting shared evolutionary relationship between East and Southeast Asian strains. Further studies on relationship between animal translocation, circulation of BEFV in Greater Mekong subregion and acquisition of more G gene sequences may improve understanding of BEFV epidemiology in mainland Southeast Asia.

Complete Genome Sequence Analysis of an Imported Dengue Virus Serotype 1 Strain from Myanmar.

It has been determined that recent dengue virus epidemics in Yunnan, China, originated from Southeast Asian strains. Here, we report the first complete genome sequence and molecular characterization of the imported dengue virus serotype 1 strain YNPE1. Phylogenetic analysis revealed that strain YNPE1 belonged to genotype I.

Phylogenetic analysis of envelope gene of dengue virus serotype 2 in Guangzhou, 2001-2015

Objective: To investigate the molecular characteristics of dengue virus serotype 2 (DENV2) in Guangzhou during 2001-2015, and analyze the E gene of the strains isolated, the phylogenetic tree and molecular clock were constructed to know about the evolution of the strains. Methods: The serum samples of the patients were detected by real time PCR, and positive samples were used to isolate dengue virus by using C6/36 cells. The E gene of the isolated strains were sequenced. The phylogenetic tree was constructed by using software Mega 4.0, and the molecular clock was drawn by using software BEASTv1.8.2. Results: Twenty-six dengue virus strains were isolated between 2001 and 2015. They were all clustered into 2 genotypes, i.e. cosmopolitan genotype and Asian genotype Ⅰ. The strains isolated in Guangzhou shared high homology with Southeast Asian strains. The cosmopolitan genotype was divided into 2 sub-genotype at about 46 and 35 years ago. The substitution rate of dengue virus serotype 2 in Guangzhou was 7.1 × 10(-4) per year per site. Conclusions: There were close relationship between the Guangzhou strains and Southeast Asian strains. Guangzhou was at high risk of imported dengue fever, outbreak of dengue hemorrhagic fever and dengue shock syndrome. There might be two ways of introduction of cosmopolitan genotype. The substitution rate of the strains in Guangzhou was similar to that in the neighbor countries.

The genetic characteristics and evolution of Tembusu virus

BackgroundSince the turn of the 21st century, there have been several epidemic outbreaks of poultry diseases caused by Tembusu virus (TMUV). Although multiple mosquito and poultry-derived strains of TMUV have been isolated, no data exist about their comparative study, origin, evolution, and dissemination. MethodologyParallel virology was used to investigate the phenotypes of duck and mosquito-derived isolates of TMUV. Molecular biology and bioinformatics methods were employed to investigate the genetic characteristics and evolution of TMUV. Principal findingsThe plaque diameter of duck-derived isolates of TMUV was larger than that of mosquito-derived isolates. The cytopathic effect (CPE) in mammalian cells occurred more rapidly induced by duck-derived isolates than by mosquito-derived isolates. Furthermore, duck-derived isolates required less time to reach maximum titer, and exhibited higher viral titer. These findings suggested that poultry-derived TMUV isolates were more invasive and had greater expansion capability than the mosquito-derived isolates in mammalian cells. Variations in amino acid loci in TMUV E gene sequence revealed two mutated amino acid loci in strains isolated from Malaysia, Thailand, and Chinese mainland compared with the prototypical strain of the virus (MM1775). Furthermore, TMUV isolates from the Chinese mainland had six common variations in the E gene loci that differed from the Southeast Asian strains. Phylogenetic analysis indicated that TMUV did not exhibit a species barrier in avian species and consisted of two lineages: the Southeast Asian and the Chinese mainland lineages. Molecular traceability studies revealed that the recent common evolutionary ancestor of TMUV might have appeared before 1934 and that Malaysia, Thailand and Shandong Province of China represent the three main sources related to TMUV spread. ConclusionsThe current broad distribution of TMUV strains in Southeast Asia and Chinese mainland exhibited longer-range diffusion and larger-scale propagation. Therefore, in addition to China, other Asian and European countries linked to Asia have used improved measures to detect and monitor TMUV related diseases to prevent epidemics in poultry.

South-East Asian strains of Plasmodium falciparum display higherratio of non-synonymous to synonymous polymorphisms compared to African strains.

Resistance to frontline anti-malarial drugs, including artemisinin, has repeatedly arisen in South-East Asia, but the reasons for this are not understood. Here we test whether evolutionary constraints on Plasmodium falciparum strains from South-East Asia differ from African strains. We find a significantly higher ratio of non-synonymous to synonymous polymorphisms in P. falciparum from South-East Asia compared to Africa, suggesting differences in the selective constraints on P. falciparum genome in these geographical regions. Furthermore, South-East Asian strains showed a higher proportion of non-synonymous polymorphism at conserved positions, suggesting reduced negative selection. There was a lower rate of mixed infection by multiple genotypes in samples from South-East Asia compared to Africa. We propose that a lower mixed infection rate in South-East Asia reduces intra-host competition between the parasite clones, reducing the efficiency of natural selection. This might increase the probability of fixation of fitness-reducing mutations including drug resistant ones.

South-East Asian strains of Plasmodium falciparum display higher ratio of non-synonymous to synonymous polymorphisms compared to African strains

Resistance to frontline anti-malarial drugs, including artemisinin, has repeatedly arisen in South-East Asia, but the reasons for this are not understood. Here we test whether evolutionary constraints on Plasmodium falciparum strains from South-East Asia differ from African strains. We find a significantly higher ratio of non-synonymous to synonymous polymorphisms in P. falciparum from South-East Asia compared to Africa, suggesting differences in the selective constraints on P. falciparum genome in these geographical regions. Furthermore, South-East Asian strains showed a higher proportion of non-synonymous polymorphism at conserved positions, suggesting reduced negative selection. There was a lower rate of mixed infection by multiple genotypes in samples from South-East Asia compared to Africa. We propose that a lower mixed infection rate in South-East Asia reduces intra-host competition between the parasite clones, reducing the efficiency of natural selection. This might increase the probability of fixation of fitness-reducing mutations including drug resistant ones.

South-East Asian strains of Plasmodium falciparum display higher ratio of non-synonymous to synonymous polymorphisms compared to African strains

Resistance to frontline anti-malarial drugs, including artemisinin, has repeatedly arisen in South-East Asia, but the reasons for this are not understood. Here we test whether evolutionary constraints on Plasmodium falciparum strains from South-East Asia differ from African strains. We find a significantly higher ratio of non-synonymous to synonymous polymorphisms in P. falciparum from South-East Asia compared to Africa, suggesting differences in the selective constraints on P. falciparum genome in these geographical regions. Furthermore, South-East Asian strains showed a higher proportion of non-synonymous polymorphism at conserved positions, suggesting reduced negative selection. There was a lower rate of mixed infection by multiple genotypes in samples from South-East Asia compared to Africa. We propose that a lower mixed infection rate in South-East Asia reduces intra-host competition between the parasite clones, reducing the efficiency of natural selection. This might increase the probability of fixation of fitness-reducing mutations including drug resistant ones.

Genome-wide re-sequencing of multidrug-resistant Mycobacterium leprae Airaku-3

Genotyping and molecular characterization of drug resistance mechanisms in Mycobacterium leprae enables disease transmission and drug resistance trends to be monitored. In the present study, we performed genome-wide analysis of Airaku-3, a multidrug-resistant strain with an unknown mechanism of resistance to rifampicin. We identified 12 unique non-synonymous single-nucleotide polymorphisms (SNPs) including two in the transporter-encoding ctpC and ctpI genes. In addition, two SNPs were found that improve the resolution of SNP-based genotyping, particularly for Venezuelan and South East Asian strains of M. leprae.

Morphology and molecular characterization of the epiphytic benthic dinoflagellate Ostreopsis cf. ovata in the temperate waters off Jeju Island, Korea

Ostreopsis is an epiphytic and potentially toxic dinoflagellate. Here, we have provided the first report about the occurrence of Ostreopsis cf. ovata in Korean waters. In general, the morphology of the Korean strain of O. cf. ovata isolated from the waters off Jeju Island, Korea, was similar to the original description of O. ovata isolated from Japanese water. However, the cell length of the Korean strain was 20–30% smaller than that of the Japanese strain. In addition, the cingulum of the Korean strain was displaced and undulated in the ventral view, but that of the Japanese strain was not displaced. We have reported, for the first time, the presence of a line of small knobs on the Po plate. The plates of the O. cf. ovata Korean strain were arranged in a Kofoidian series of Po, 3′, 7″, 6c, 6s, Vp, Rp, 5‴, 1p, and 2⁗. When properly aligned, the small subunit (SSU) rDNA sequence of the O. cf. ovata Korean strain was 5.8% different to the O. cf. ovata Malaysian strain, which is the closest strain. In addition, compared to the south-east Asian, Pacific, Atlantic, and Mediterranean strains of Ostreopsis sp., O. ovata, and O. cf. ovata, the sequences of the internal transcribed spacer region (ITS1 and ITS2) plus 5.8S, D1–D3, and D8–D10 large subunit (LSU) rDNA of the O. cf. ovata Korean strain showed a difference of 3.6–16%, 15.8–19.7%, and 0–3%. Furthermore, in the phylogenetic trees based on D1–D3 LSU rDNA regions, the O. cf. ovata Korean strain was located in the basal position of the other O. ovata and O. cf. ovata clades. Therefore, we suggest that the O. cf. ovata Korean strain is genetically distinct among the O. ovata and O. cf. ovata strains reported to date.

Evolutionary and transmission characteristics of rabies viruses in Asia

To understand the rabies virus (RABV) evolutionary relationship between the strains of China and Asia and to know the evolution and transmission characteristics of RABV in Asia. The G sequences of representative strains from China were selected and combined the sequences of other countries in Asia to analyze using BEAST and MigraPhyla software. The phylogenetic analysis showed that six groups (China I-VI) of China had different epidemic range: China I , II and V groups just cycled in our country; China VI group, from Guangxi and Yunnan provinces, crossed with Southeast Asian strains; China III group and IV group also have closer genetic relationship with Asian country strains. Geographic migration in Asia showed that Thailand and India may be two rabies transmission centers in Asia.

Twenty Years of DENV-2 Activity in Brazil: Molecular Characterization and Phylogeny of Strains Isolated from 1990 to 2010

In Brazil, dengue has been a major public health problem since its introduction in the 1980s. Phylogenetic studies constitute a valuable tool to monitor the introduction and spread of viruses as well as to predict the potential epidemiological consequences of such events. Aiming to perform the molecular characterization and phylogenetic analysis of DENV-2 during twenty years of viral activity in the country, viral strains isolated from patients presenting different disease manifestations (n = 34), representing six states of the country, from 1990 to 2010, were sequenced. Partial genome sequencing (genes C/prM/M/E) was performed in 25 DENV-2 strains and full-length genome sequencing (coding region) was performed in 9 strains. The percentage of similarity among the DENV-2 strains in this study and reference strains available in Genbank identified two groups epidemiologically distinct: one represented by strains isolated from 1990 to 2003 and one from strains isolated from 2007 to 2010. No consistent differences were observed on the E gene from strains isolated from cases with different clinical manifestations analyzed, suggesting that if the disease severity has a genetic origin, it is not only due to the differences observed on the E gene. The results obtained by the DENV-2 full-length genome sequencing did not point out consistent differences related to a more severe disease either. The analysis based on the partial and/or complete genome sequencing has characterized the Brazilian DENV-2 strains as belonging to the Southeast Asian genotype, however a distinction of two Lineages within this genotype has been identified. It was established that strains circulating prior DENV-2 emergence (1990–2003) belong to Southeast Asian genotype, Lineage I and strains isolated after DENV-2 emergence in 2007 belong to Southeast Asian genotype, Lineage II. Furthermore, all DENV-2 strains analyzed presented an asparagine (N) in E390, previously identified as a probable genetic marker of virulence observed in DHF strains from Asian origin. The percentage of identity of the latter with the Dominican Republic strain isolated in 2001 combined to the percentage of divergence with the strains first introduced in the country in the 1990s suggests that those viruses did not evolve locally but were due to a new viral Lineage introduction in the country from the Caribbean.

Complete Genome Sequence of Dengue Virus Serotype 3 from Guangzhou, China

In 2009, dengue virus serotype 3 (DENV-3) was first detected in Guangzhou, China. In this study, we identified another isolated strain belonging to genotype II. Phylogenetic analysis shows that the GZ/10476/2012 strain has a close relationship with the DENV-3 genotype II from Southeast Asian strains.