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

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

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

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

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

Characterization of spotted fever group Rickettsiae in ticks from a city park of Rome, Italy

 Background: Ticks are vectors and important reservoirs for microbial agents that cause disease in humans and animals. Among these pathogens, the members of Rickettsia species play an important role in public health.Aim and Methods: One hundred twenty-nine ticks belonging to four tick species (Ixodes ricinus, Rhipicephalus turanicus, Dermacentor marginatus, and Haemaphysalis punctata) were collected at different sites of the Insugherata Natural Reserve, localized in the urban area of Rome, Italy. Questing ticks were tested by PCR for Rickettsia spp., amplifying partial gene of ompA.Results: Forty-six ticks were found to be infected with Rickettsia species. Five SFG rickettsiae were identified: three human pathogens Rickettsia conorii, Rickettsia massiliae and Rickettsia aeschlimannii, and two putative new strains Rickettsia sp. strain RM1 and Rickettsia sp. strain RM2. The phylogenetic analysis of partial gene sequences of ompA, gltA, and 17-kd antigen showed that they clustered with several rickettsiae with unidentified pathogenicity. However, Rickettsia sp. strain RM1 and Rickettsia sp. strain RM2 clustered in a statistically supported clade with R. massiliae, and R. monacensis, respectively.Conclusion: Our findings suggest that Rickettsia species other than R. conorii are implicated in human disease in Italy

Tidal notches in Mediterranean Sea: a comprehensive analysis

Recent works (Evelpidou et al., 2012) suggest that the modern tidal notch is disappearing worldwide due sea level rise over the last century. In order to assess this hypothesis, we measured modern tidal notches in several of sites along the Mediterranean coasts. We report observations on tidal notches cut along carbonate coasts from 73 sites from Italy, France, Croatia, Montenegro, Greece, Malta and Spain, plus additional observations carried outside the Mediterranean. At each site, we measured notch width and depth, and we described the characteristics of the biological rim at the base of the notch. We correlated these parameters with wave energy, tide gauge datasets and rock lithology. Our results suggest that, considering \u2018the development of tidal notches the consequence of midlittoral bioerosion\u2019 (as done in Evelpidou et al., 2012) is a simplification that can lead to misleading results, such as stating that notches are disappearing. Important roles in notch formation can be also played by wave action, rate of karst dissolution, salt weathering and wetting and drying cycles. Of course notch formation can be augmented and favoured also by bioerosion which can, in particular cases, be the main process of notch formation and development. Our dataset shows that notches are carved by an ensemble rather than by a single process, both today and in the past, and that it is difficult, if not impossible, to disentangle them and establish which one is prevailing. We therefore show that tidal notches are still forming, challenging the hypothesis that sea level rise has drowned them