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Ljungan virus (LV) (family Picornaviridae, genus Parechovirus) is a suspected zoonotic pathogen with associations to human disease in Sweden. LV is a single-stranded RNA virus with a positive sense genome. There are five published Ljungan virus strains, three isolated from Sweden and two from America, and are classified into four genotypes. A further two strains described here were isolated from wild bank voles (Myodes glareolus) caught in Västmanlands county, Sweden in 1994. These strains were sequenced using next generation pyrosequencing technology on the GS454flx platform. Genetic and phylogenetic analysis of the obtained genomes confirms isolates LV340 and LV342 as two new putative members of genotype 2 along with LV145SL, with 92% and 99% nucleotide identities respectively. Only two codon sites throughout the entire genome were identified as undergoing positive selection, both situated within the VP3 structural region, in or near to major antigenic sites. Whilst these two strains do not constitute new genotypes they provide evidence, though weakly supported, which suggests the evolution of Ljungan viruses to be relatively slow, a characteristic unlike other picornaviruses. Additional genomic sequences are urgently required for Ljungan virus strains, particularly from different locations or hosts, to fully understand the evolutionary and epidemiological properties of this potentially zoonotic virus., (Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.)

Rabies is endemic in Sudan and remains a continual threat to public health as transmission to humans is principally dog-mediated. Additionally, large-scale losses of livestock occur each year causing economic and social dilemmas. In this study, we analysed a cohort of 143 rabies viruses circulating in Sudan collected from 10 different animal species between 1992 and 2006. Partial nucleoprotein sequence data (400 bp) were obtained and compared to available sequence data of African classical rabies virus (RABV) isolates. The Sudanese sequences formed a discrete cluster within the Africa 1a group, including a small number of sequences that clustered with sequences from Ethiopian RABV. These latter sequences share an Aspartic Acid at position 106 (Asp(106)) with all other Africa 1a group members, in contrast to the remaining Sudanese strains, which encode Glutamic Acid at this position (Glu(106)). Furthermore, when representatives of other African and European lineages were aligned, Glu(106) is unique to Sudan, which supports the concept of a single distinct virus strain circulating in Sudan. The high sequence identity in all Sudanese isolates studied, demonstrates the presence of a single rabies virus biotype for which the principal reservoir is the domestic dog.

Molecular typing has consistently identified European bat lyssaviruses from Germany as EBLV type 1a (EBLV-1a). This report confirms the presence of the closely related EBLV-1b in southern Germany, a group previously reported from The Netherlands, France and Spain. Furthermore, two of three German EBLV-1b isolates contain a 6 base pair insertion within the 3' untranslated region (UTR) of the nucleoprotein gene. This feature was shared with a third EBLV-1b isolate from a region of France adjacent to the French-German border. Further investigation revealed a two base pair insertion in a single isolate of EBLV-2 at the same genomic location. Although the length of the nucleoprotein gene 3'UTRs do vary between lyssavirus genotypes, such insertions have not been recorded within genotypes and could be the result of duplications within the nucleoprotein mRNA transcript polyadenylation signal.

We report a molecular epidemiological study of rabies in Arctic countries by comparing a panel of novel Greenland isolates to a larger cohort of viral sequences from both Arctic and Baltic regions. Rabies virus isolates originating from wildlife (Arctic/red foxes, raccoon-dogs and reindeer), from domestic animals (dogs/cats) and from two human cases were investigated. The resulting 400 bp N-gene sequences were compared with isolates representing neighbouring Arctic or Baltic countries from North America, the former Soviet Union and Europe. Phylogenetic analysis demonstrated similarities between sequences from the Arctic and Arctic-like viruses, which were distinct from rabies isolates originating in the Baltic region of Europe, the Steppes in Russia and from North America. The Arctic-like group consist of isolates from India, Pakistan, southeast Siberia and Japan. The Arctic group was differentiated into two lineages, Arctic 1 and Arctic 2, with good bootstrap support. Arctic 1 is mainly comprised of Canadian isolates with a single fox isolate from Maine in the USA. Arctic 2 was further divided into sub-lineages: 2a/2b. Arctic 2a comprises isolates from the Arctic regions of Yakutia in northeast Siberia and Alaska. Arctic 2b isolates represent a biotype, which is dispersed throughout the Arctic region. The broad distribution of rabies in the Arctic regions including Greenland, Canada and Alaska provides evidence for the movement of rabies across borders.