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The pandemic spread of African swine fever virus (ASFV) genotype II (GTII) has led to a global crisis. Since the circulating strains are almost identical, time and money have been mis-invested in whole-genome sequencing the last years. New methods, harmonised protocols for sample selection, sequencing, and bioinformatics are therefore urgently needed., Competing Interests: The authors have declared that no competing interests exist.

In the last decades, illegal logging has posed a serious threat for the integrity of forest ecosystems and for biodiversity conservation in tropical Africa. Although international treaties and regulatory plans have been implemented to reduce illegal logging, much of the total timber volume is harvested and traded illegally from tropical African forest regions. As a result, the development and the application of analytical tools to enhance the traceability and the identification of wood and related products is critical to enforce international regulations. Among available techniques, DNA barcoding is a promising approach for the molecular identification of plant species. However, although it has been used successfully for the discrimination of animal species, no set of genetic markers is available for the universal identification of plant species. In this work, we firstly characterized the genetic diversity of 17 highly-valuable African timber species from five genera (Afzelia, Guibourtia, Leplea, Milicia, Tieghemella) across their distribution ranges in West and Central Africa using the genome skimming approach in order to reconstruct their chloroplast genomes and nuclear ribosomal DNA. Next, we identified single-nucleotide polymorphisms (SNPs) for the discrimination of closely-related species. In this way, we successfully developed and tested novel species-specific genetic barcodes for species identification. [ABSTRACT FROM AUTHOR]

Tick-borne encephalitis virus (TBEV) is a flavivirus which causes an acute or sometimes chronic infection that frequently has severe neurological consequences, and is a major public health threat in Eurasia. TBEV is genetically classified into three distinct subtypes; however, at least one group of isolates, the Baikal subtype, also referred to as "886-84-like", challenges this classification. Baikal TBEV is a persistent group which has been repeatedly isolated from ticks and small mammals in the Buryat Republic, Irkutsk and Trans-Baikal regions of Russia for several decades. One case of meningoencephalitis with a lethal outcome caused by this subtype has been described in Mongolia in 2010. While recombination is frequent in Flaviviridae, its role in the evolution of TBEV has not been established. Here, we isolate and sequence four novel Baikal TBEV samples obtained in Eastern Siberia. Using a set of methods for inference of recombination events, including a newly developed phylogenetic method allowing for formal statistical testing for such events in the past, we find robust support for a difference in phylogenetic histories between genomic regions, indicating recombination at origin of the Baikal TBEV. This finding extends our understanding of the role of recombination in the evolution of this human pathogen. Author summary: Tick-borne encephalitis is a serious and frequently deadly infectious disease. It is caused by a virus of the same name with genome composed of single-stranded RNA. The known genomes of this virus fall into three large regional groups: Europe, Siberia, or the Russian Far East. These groups have originated from a common ancestor several hundred or thousand years ago and were assumed to have evolved independently since then. This study shows that a previously described group of viruses obtained in the vicinity of Lake Baikal in Russia have a mosaic genome: some parts of it are more closely related to those of the Siberian group, while others, to the Far Eastern group. Such a pattern probably arose through recombination–a process during which a cell infected with two distinct viruses produces "hybrid" viral progeny carrying genetic material from both parents. While recombination is frequent in other RNA viruses, it has not been previously described for the tick-borne encephalitis virus. These findings show that mixture of genetic information from distinct sources can contribute to genetic diversity of this group of viruses, and potentially accelerate their adaptation. [ABSTRACT FROM AUTHOR]

In this report, we present new data on the diversity and geographical distribution of genetic variants in Crimean-Congo hemorrhagic fever virus (CCHFV) in Russia. Partial S, M, and L segment sequences of the CCHFV genome were obtained from 500 serum samples from CCHF patients and 103 pools of ticks collected in the south of the European region of Russia in 2007–2017. The investigated viral strains belonged to the lineages Europe 1 (596 samples), Africa 3 (1 sample) and a new genetic lineage, Europe 3 (6 samples). The Russian CCHFV strains of the Europe 1 lineage formed four subgroups (Va-Vd) correlated with the geographical site of virus isolation. Segment reassortment events between strains of different subgroups within lineage Europe 1 were revealed. The complete S, M and L genome segments of 18 CCHFV strains belonging to different subgroups of the Europe 1 lineage and the complete S segments of 3 strains of the Europe 3 lineage and 1 strain of the Africa 3 lineage were sequenced. The analysis of the geographical distribution of CCHFV genetic variants in southern Russia revealed local viral populations with partially overlapping boundaries. [ABSTRACT FROM AUTHOR]

Balantidiasis is considered a neglected zoonotic disease with pigs serving as reservoir hosts. However, Balantidium coli has been recorded in many other mammalian species, including primates. Here, we evaluated the genetic diversity of B. coli in non-human primates using two gene markers (SSrDNA and ITS1-5.8SDNA-ITS2). We analyzed 49 isolates of ciliates from fecal samples originating from 11 species of captive and wild primates, domestic pigs and wild boar. The phylogenetic trees were computed using Bayesian inference and Maximum likelihood. Balantidium entozoon from edible frog and Buxtonella sulcata from cattle were included in the analyses as the closest relatives of B. coli, as well as reference sequences of vestibuliferids. The SSrDNA tree showed the same phylogenetic diversification of B. coli at genus level as the tree constructed based on the ITS region. Based on the polymorphism of SSrDNA sequences, the type species of the genus, namely B. entozoon, appeared to be phylogenetically distinct from B. coli. Thus, we propose a new genus Neobalantidium for the homeothermic clade. Moreover, several isolates from both captive and wild primates (excluding great apes) clustered with B. sulcata with high support, suggesting the existence of a new species within this genus. The cysts of Buxtonella and Neobalantidium are morphologically indistinguishable and the presence of Buxtonella-like ciliates in primates opens the question about possible occurrence of these pathogens in humans. Author Summary: Balantidium coli is a pathogenic ciliate occurring in various hosts, including primates. Balantidiasis is considered a neglected disease with zoonotic potential and it is associated with pigs as reservoirs. Although it is considered to be rare, a high prevalence of B. coli persists in tropical and subtropical areas. The infection can cause symptoms ranging from mild diarrhea to fulminating dysentery. Recently, balantidiasis has appeared to be a serious problem in immunocompromised persons. Although a chapter about balantidiasis is included in almost every parasitology textbook, many aspects of the occurrence of these ciliates in mammals, including humans, remain unknown. As balantidiasis can pose a serious health problem, a better understanding of this organism has important practical implications. We performed an extensive evaluation of genetic diversity in B. coli based on samples from non-human primates, together with comparative material from pigs and reference sequences. We find that the diversity of the cyst-forming ciliates in non-human primates is broader than expected. This discovery poses novel questions about the real spectrum of intestinal ciliates occurring in humans, and might explain unknown factors in the epidemiology and pathogenicity of ciliate infections. [ABSTRACT FROM AUTHOR]