Reliable timescale inference of HBV genotype A origin and phylodynamics

The worldwide distributed Hepatitis B virus (HBV) genotype A is classified into three subgenotypes, and one quasi-subgenotype. The majority of HBV-A subgenotypes are widespread in Africa and in ethnic groups that have relatively recently emigrated from African countries, whereas HBV-A2 is highly prevalent among subjects at high risk for sexual exposure to HBV in north-western Europe and the USA.The aim of this study was to reconstruct the origin and dispersion of HBV-A subgenotypes on a reliable timescale using short-term calibration based on heterochronous sampling for HBV-A2, and long-term calibration based on historical data for the other subgenotypes.To this aim, we analysed 113 newly characterised HBV-A isolates with 247 reference sequences retrieved from a public database. The phylodynamic reconstruction was performed by a Bayesian framework.The common ancestor of the currently circulating A subgenotypes was placed in west-central Africa a mean 1057 years ago. The genotype diverged into two main clades at the beginning of the 13th century: one including all of the west-central African quasi-subgenotypes and the other corresponding to subgenotype A1, originating in east Africa and further segregating into two main subclades: an “African” and a “cosmopolitan” clade.It is likely that the slave trade was the main source the spread of cosmopolitan HBV-A1, which was exported to Asia in the 17th century as a result of Arab or Portuguese trade, and to Latin America in the 18th centuries through the trans-Atlantic slave trade.The origin of the currently circulating A2 strains dates back to the first decades of the 20th century, and the evolutionary demography analysis suggests an exponential growth of infections, between 1970s and the mid-1990s.In conclusion, the very different epidemiological and evolutionary histories of HBV-A subgenotypes justify the use of different calibration approaches to reconstruct their reciprocal phylodynamics.     

Phylogeography and evolutionary history of rodent-borne hantaviruses

Hantavirus (Family Bunyaviridae) are mostly associated to rodents and transmitted to man by inhalation of aerosolized infected excreta of these animals. The human infection by hantaviruses can lead to severe diseases such as hemorrhagic fever with renal syndrome (HFRS) in Asia and Europe, and pulmonary syndrome (HPS) in the Americas. To determine the origin, spreading and evolutionary dynamics of rodent-borne hantaviruses, 190 sequences of nucleoprotein (N) of hantaviruses identified in 30 countries, from 1985 to 2010, were retrieved from the GenBank and analyzed using the BEAST program. Our evolutionary analysis indicates that current genetic diversity of N gene of rodent-borne hantaviruses probably was originated around 2000 years ago. Hantavirus harbored by Murinae and Arvicolinae subfamilies, probably, were originated in Asia 500–700 years ago and later spread toward Siberia, Europe, Africa and North America. Hantavirus carried by Neotominae subfamily, probably, emerged 500–600 years ago in Central America and spread toward North America. Finally, hantaviruses associated to Sigmodontinae occurred in Brazil 400 years ago and were, probably, originated from Neotominae-associated virus from northern South America. These data offer subsidies to understand the time-scale and worldwide dissemination dynamics of rodent-borne hantaviruses.     

Epidemiological history and phylogeography of West Nile virus lineage 2

West Nile virus (WNV) was first isolated in Uganda. In Europe WNV was sporadically detected until 1996, since then the virus has been regularly isolated from birds and mosquitoes and caused several outbreaks in horses and humans. Phylogenetic analysis showed two main different WNV lineages. The lineage 1 is widespread and segregates into different subclades (1a–c). WNV-1a includes numerous strains from Africa, America, and Eurasia. The spatio-temporal history of WNV-1a in Europe was recently described, identifying two main routes of dispersion, one in Eastern and the second in Western Europe. The West Nile lineage 2 (WNV-2) is mainly present in sub-Saharan Africa but has been recently emerged in Eastern and Western European countries. In this study we reconstruct the phylogeny of WNV-2 on a spatio-temporal scale in order to estimate the time of origin and patterns of geographical dispersal of the different isolates, particularly in Europe. Phylogeography findings obtained from E and NS5 gene analyses suggest that there were at least two separate introductions of WNV-2 from the African continent dated back approximately to the year 1999 (Central Europe) and 2000 (Russia), respectively. The epidemiological implications and clinical consequences of lineage 1 and 2 cocirculation deserve further investigations.     

Early ancient sublineages of Mycobacterium tuberculosis Beijing genotype: unexpected clues from phylogenomics of the pathogen and human history

ObjectiveThe Mycobacterium tuberculosis Beijing family is an epidemiologically important lineage subdivided into large-scale phylogenetic sublineages: ancient, endemic in East Asia, and global modern. Here, we analysed ancient sublineages of the Beijing genotype in the Omsk region of southwestern Siberia, an intriguing area at the intersection of European Russia, Siberia, and Central Asia.MethodsThe study included 423 M. tuberculosis strains isolated in 2013–2017 and subjected to drug susceptibility testing, genotyping, and whole genome sequencing.ResultsThe Beijing genotype constituted 280 out of 423 strains. Forty Beijing strains belonged to the early ancient sublineage (wild type mutT4-48). Of these, 11 belonged to the 14717-15 MIRU-VNTR cluster and had intact RD181, 29 belonged to the 1071-32 cluster and had the RD181 deletion. Thirty-nine ancient strains were multidrug-resistant (MDR) and 20 pre-extensively drug resistant (XDR)/XDR. Comparison with global data demonstrated that these clones circulate mainly in Asian Russia with certain phylogenetic affinity to strains from Japan, Korea, and northeastern China. The genome-wide analysis revealed 29–37 single nucleotide polymorphism distances between isolates from different Russian regions within these two clusters.ConclusionsBased on phylogenetic, phylogeographic, genomic, and historical data, we hypothesize that these two clones or their direct ancestors were probably brought to Russia ～70 years ago after the Second World War with Japanese prisoners of war and, until recently, were mainly circulating in Siberia and the Far East. Their elevated prevalence in Omsk along with the extremely strong association with not only MDR but also pre-XDR/XDR also observed in other locations highlight their epidemic potential and the need for monitoring and attention from health authorities.     

Genetic geography of Mycobacterium tuberculosis Beijing genotype: A multifacet mirror of human history?

The Beijing genotype of Mycobacterium tuberculosis has been shown in many settings to be hypervirulent and associated with multi-drug resistance. Its presently global and rapid dissemination makes it an important issue of public health. Here, I present a significantly enlarged update of the MIRU-VNTR global database of the M. tuberculosis Beijing genotype (11 loci). I further attempted to link the observed mycobacterial diversity with relevant events of the known human history. Large water masses have been the most efficient and drastic generators of the genetic divergence between human populations. The same situation appears true also for M. tuberculosis, which general diversity pattern amazingly resembles that of its human host. At the same time, less expected affinities observed between distant populations of M. tuberculosis may reflect hidden patterns of human migrations or yet unknown epidemiological links between distant regions.     

Molecular differentiation of Angiostrongylus taxa (Nematoda: Angiostrongylidae) by cytochrome c oxidase subunit I (COI) gene sequences

Nematodes of the genus Angiostrongylus are parasites of rodents and carnivores. They reside in the pulmonary or mesenteric arteries of their hosts. Two species are pathogenic in humans - Angiostrongylus cantonensis causes eosinophilic meningitis or meningoencephalitis, and Angiostrongylus costaricensis produces abdominal angiostrongyliasis. In addition Angiostrongylus malaysiensis may have the potential of being pathogenic in humans. The mitochondrial gene cytochrome c oxidase subunit I (COI) of these Angiostrongylus species and three geographical isolates (China, Hawaii and Thailand) of A. cantonensis were studied by polymerase chain reaction amplification and DNA sequencing. COI sequences of A. cantonensis, A. costaricensis and Angiostrongylus vasorum in the GenBank were included for comparison. Phylogenetic analysis by maximum-likelihood (ML), maximum-parsimony (MP), neighbour-joining (NJ) and Bayesian inference (BI) produced similar tree topology except variation in the bootstrap support values. There were two major clades - (1) A. cantonensis and A. malaysiensis, and (2) A. costaricensis and A. vasorum. The three geographical isolates of A. cantonensis formed a clade with low to high bootstrap values, and consisted of two subclades: (a) China and Hawaii isolates, and (b) monophyletic Thailand isolate. The individuals of each isolate formed a distinct cluster. In the second major clade, the Europe isolates of A. vasorum were distinctly different from the Brazil isolates. For A. costaricensis, the Costa Rica isolate was distinct from the Brazil isolate with an uncorrected (p) distance of 11.39%, indicating the possible occurrence of cryptic species. The present results indicate that COI sequences might be a useful marker for differentiating geographical isolates of A. cantonensis and in uncovering cryptic species. Efforts are being made to carry out an extensive collaborative study to cover a wide range of Angiostrongylus species and geographical isolates.     

Genetic diversity and geographical distribution of the Siberian subtype of the tick-borne encephalitis virus

The tick-borne encephalitis virus (TBEV), a member of the Flaviviridae family, is currently subdivided into three main subtypes—the European (TBEV-Eu), the Far-Eastern (TBEV-FE), and the Siberian (TBEV-Sib). The TBEV-Sib is the most common subtype and found in all regions where TBEV was detected, except for Central and Western Europe. Currently, four genetic lineages have been described within TBEV-Sib.In this study, detailed analysis of TBEV-Sib genetic diversity, geographic distribution, phylogeography and divergence time of different TBEV-Sib genetic lineages based on E gene fragments, complete genome sequences, and all currently available data in the GenBank database was performed. As a result, a novel Bosnia lineage within the TBEV-Sib was identified. It was demonstrated that the Zausaev lineage is the most widely distributed among the TBEV-Sib lineages, and was detected in all studied regions except the Far East. The Vasilchenko lineage was found from Western Siberia to the Far East. The Baltic lineage is presented from Europe to Western Siberia. The Obskaya lineage was found only in Western Siberia. TBEV strains from a newly described Bosnia lineage were detected in Bosnia, the Crimean peninsula, Kyrgyzstan and Kazakhstan. The greatest divergence of the TBEV-Sib genetic variants was observed in Western Siberia. Within the TBEV-Sib, the Obskaya lineage diverged from the common ancestor the earliest, after that the Bosnia lineage was separated, then the Baltic lineage, and the Zausaev and Vasilchenko lineages diverged most recently.     

Molecular phylogeography of Culex quinquefasciatus mosquitoes in central Bangladesh

Mosquitoes in the Culex pipiens complex are a major vector of numerous parasitic and arboviral diseases. Here we report the phylogeography of a prevalent Culex mosquito, Cx. quinquefasciatus, from three locations in Bangladesh: Dhaka, Savar and Mymensingh. Sequence analysis of the genes encoding mitochondrial cytochrome oxidase subunit II, nuclear elongation factor-1 alpha, and acetylcholinesterase-2 revealed the lack of a population genetic structure among the three locations. Moreover, the highly divergent ribosomal internal transcribed spacer 2 suggests that this locus has not evolved in concert. The results further show evidence of historical introgression of internal transcribed spacer 2 from Cx. pipiens to Cx. quinquefasciatus of Bangladesh, and that the introgression occurred before Cx. quinquefasciatus had dispersed within this region. The study also reveals historical population expansion in this region, followed by a post-expansion Wolbachia sweep.     

A systematic review of East African-Indian family of Mycobacterium tuberculosis in Brazil

Introduction

The Mycobacterium tuberculosis East African-Indian (EAI) spoligotyping family (belonging to lineage 1, Indo-Oceanic, defined by the region of deletion RD239) is distributed worldwide, but is more prevalent in Southeast Asia, India, and East Africa. Studies in Latin America have rarely identified EAI. In this study, we describe the occurrence of the EAI family in Brazil.