The phylogenetic and evolutionary history of Kokobera virus.

Abstract Objective To estimate the genetic diversity of Kokobera virus, the date of origin and the spread among different viruses in the endemic regions of Australia. Methods Two datasets were built. The first consisting of 29 sequences of the NS5/3′ UTR region of Kokobera group downloaded from GenBank, the second including only 24 sequences of Kokobera viruses, focus is on this group. Results Bayesian time analysis revealed two different entries in Australia of Kokobera virus in the 50s years with the dated ancestor in 1861 year. Clades A and B showed a clear separation of the Kokobera sequences according to the geographic region. Conclusions Data from the study showed as Kokobera virus, despite of its ancient origin and its circulation before the European colonization, remained limited to the Australian country and nowadays limited mostly to the regions were Australian marsupials are mostly found

Chikungunya virus, epidemiology, clinics and phylogenesis: A review.

Abstract Chikungunya virus is a mosquito-transmitted alphavirus that causes chikungunya fever, a febrile illness associated with severe arthralgia and rash. Chikungunya virus is transmitted by culicine mosquitoes; Chikungunya virus replicates in the skin, disseminates to liver, muscle, joints, lymphoid tissue and brain, presumably through the blood. Phylogenetic studies showed that the Indian Ocean and the Indian subcontinent epidemics were caused by two different introductions of distinct strains of East/Central/South African genotype of CHIKV. The paraphyletic grouping of African CHIK viruses supports the historical evidence that the virus was introduced into Asia from Africa. Phylogenetic analysis divided Chikungunya virus isolates into three distinct genotypes based on geographical origins: the first, the West Africa genotype, consisted of isolates from Senegal and Nigeria; the second contained strains from East/Central/South African genotype, while the third contained solely Asian. The most recent common ancestor for the recent epidemic, which ravaged Indian Ocean islands and Indian subcontinent in 2004 – 2007, was found to date in 2002. Asian lineage dated about 1952 and exhibits similar spread patterns of the recent Indian Ocean outbreak lineage, with successive epidemics detected along an eastward path. Asian group splitted into two clades: an Indian lineage and a south east lineage. Outbreaks of Chikungunya virus fever in Asia have not been associated necessarily with outbreaks in Africa. Phylogenetic tools can reconstruct geographic spread of Chikungunya virus during the epidemics wave. The good management of patients with acute Chikungunya virus infection is essential for public health in susceptible areas with current Aedes spp activity

HIV-2 infection in a migrant from Gambia: the history of the disease combined with phylogenetic analysis revealed the real source of infection

Human immunodeficiency virus type 2 (HIV-2) infection prevalence is increasing in some European countries. The increasing migratory flow from countries where HIV-2 is endemic has facilitated the spread of the virus into Europe and other regions. We describe a case of HIV-2 infection in a migrant individual in the Asylum Seeker Centre (ASC) in Italy. The patient's virus was sequenced, and found to be a typical HIV-2 genotype A virus. Bayesian evolutionary analysis revealed that the HIV-2 sequence from migrant dated back to 1986 in a subcluster including sequences from Guinea Bissau. This was coherent with the migrant history who lived in Guinea Bissau from his birth until 1998 when he was 13 years old. Monitoring for HIV-2 infection in migrants from western Africa is necessary using adequate molecular tools to improve the diagnosis and understand the real origin of infection

MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification

Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DNA analysis and has been addressed with several approaches, e.g., multiple alignments-, phylogenetic trees-, statistical- and character-based methods

The global spread of Middle East respiratory syndrome: an analysis fusing traditional epidemiological tracing and molecular phylodynamics

Table S1. List of sequences used for analysis. Column “Label” corresponds to labels for sequences. presented in Figures 3 and 4 with country (by 2-letter ISO country code) and year of collection; countries, sources, and dates (month-year) are based on information in GenBank or related publication (indicated in Reference column). (DOCX 128 kb

Genetic diversity in the env V1-V2 region of proviral quasispecies from long-term controller MHC-typed cynomolgus macaques infected with SHIVSF162P4cy

Intra-host evolution of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) has been shown by viral RNA analysis in subjects who naturally suppress plasma viremia to low levels, known as controllers. However, little is known about the variability of proviral DNA and the inter-relationships among contained systemic viremia, rate of reservoir reseeding and specific major histocompatibility complex (MHC) genotypes, in controllers. Here, we analysed the proviral DNA quasispecies of the env V1-V2 region, in PBMCs and in anatomical compartments of 13 long-term controller monkeys after 3.2 years of infection with simian/human immunodeficiency virus (SHIV)SF162P4cy. A considerable variation in the genetic diversity of proviral quasispecies was present among animals. Seven monkeys exhibited env V1-V2 proviral populations composed of both clusters of identical ancestral sequences and new variants, whereas the other six monkeys displayed relatively high env V1-V2 genetic diversity with a large proportion of diverse novel sequences. Our results demonstrate that in SHIVSF162P4cy-infected monkeys there exists a disparate pattern of intra-host viral diversity and that reseeding of the proviral reservoir occurs in some animals. Moreover, even though no particular association has been observed between MHC haplotypes and the long-term control of infection, a remarkably similar pattern of intra-host viral diversity and divergence was found within animals carrying the M3 haplotype. This suggests that in animals bearing the same MHC haplotype and infected with the same virus, viral diversity follows a similar pattern with similar outcomes and control of infection

Cytomegalovirus Glycoprotein B Genotype Distribution in Italian Transplant Patients.

Background: The cytomegalovirus (CMV) UL55 gene encodes for a glycoprotein implicated in virus pathogenesis. Based on UL55 polymorphism, CMV has been divided into 4 genotypes. Previous studies investigated the possible role of genotypes in the clinical outcome of infection in different categories of patients; however, few data are available, particularly in the transplant setting and Italian case records. Methods: Phylogenetic analysis through a maximum likelihood tree was used to evaluate the prevalence and distribution of CMV genotypes in whole blood specimens from 47 transplant patients and investigate the relation with demographic and clinical features. Results: Overall, 40.4% of patients were classified as single genotype (12.8% gB1, 23.4% gB2, 4.2% gB3); mixed genotypes were detected in 59.6%. Genotype 4 was detected only in mixed cases. In comparison to single genotypes, mixed genotypes were more frequently associated with a higher duration of DNA viremia and higher peak viral load. Conclusions: Mixed infections seem to be prevalent in Italian transplant patients; it is likely that mixed infections are more difficult to control by immunological response in comparison to single genotype infections. In this context, the genetic profile of infecting viruses and relation to clinical outcome should be investigated, also taking into account the CMV-specific cellular immune response

Phylogeny of Murray Valley encephalitis virus in Australia and Papua New Guinea

Abstract Objective To study the genetic diversity of Murray Valley encephalitis virus (MVEV) in Australia and Papua New Guinea. Methods MVEV envelope gene sequences were aligned using Clustal X and manual editing was performed with Bioedit. ModelTest v. 3.7 was used to select the simplest evolutionary model that adequately fitted the sequence data. Maximum likelihood analysis was performed using PhyML. The phylogenetic signal of the dataset was investigated by the likelihood mapping analysis. The Bayesian phylogenetic tree was built using BEAST. Results The phylogenetic trees showed two main clades. The clade Ⅰ including eight strains isolated from West Australia. The clade Ⅱ was characterized by at least four epidemic entries, three of which localized in Northern West Australia and one in Papua New Guinea. The estimated mean evolutionary rate value of the MVEV envelope gene was 0.407 × 10−3 substitution/site/year (95% HPD: 0.623 × 10−4–0.780 × 10−3). Population dynamics defines a relative constant population until the year 2000, when a reduction occurred, probably due to a bottleneck. Conclusions This study has been useful in supporting the probable connection between climate changes and viral evolution also by the vector point of view; multidisciplinary monitoring studies are important to prevent new viral epidemics inside and outside new endemic areas

Genetic and structural analyses reveal the low potential of the SARS‐CoV‐2 EG.5 variant

The severe acute respiratory syndrome coronavirus 2 EG.5 lineage is the latest variant under monitoring, and it is generating significant concern due to its recent upward trend in prevalence. Our aim was to gain insights into this emerging lineage and offer insights into its actual level of threat. Both genetic and structural data indicate that this novel variant presently lacks substantial evidence of having a high capacity for widespread transmission. Their viral population sizes expanded following a very mild curve and peaked several months after the earliest detected sample. Currently, neither the viral population size of EG.5 nor that of its first descendant is increasing. The genetic variability appear to be flattened, as evidenced by its relatively modest evolutionary rate (9.05 × 10−4 subs/site/year). As has been observed with numerous prior variants, attributes that might theoretically provide advantages seem to stem from genetic drift, enabling the virus to continually adjust to its host, albeit without a clear association with enhanced dangerousness. These findings further underscore the necessity for ongoing genome-based monitoring, ensuring preparedness and a well-documented understanding of the unfolding situation