Potential for La Crosse virus segment reassortment in nature

La Crosse virus neuroinvasive disease: the kids are not alright

La Crosse virus (LACV) is the most common cause of neuroinvasive mosquito-borne disease in children within the United States. Despite more than 50 years of recognized endemicity in the United States, the true burden of LACV disease is grossly underappreciated, and there remain severe knowledge gaps that inhibit public health interventions to reduce morbidity and mortality. Long-standing deficiencies in disease surveillance, clinical diagnostics and therapeutics, actionable entomologic and environmental risk indices, case response capacity, public awareness, and availability of community support groups clearly frame LACV disease as neglected. Here we synthesize salient prior research and contextualize our findings as an assessment of current gaps and opportunities to develop a framework to prevent, detect, and respond to LACV disease. The persistent burdens of LACV disease clearly require renewed public health attention, policy, and action.

Role of Anopheles Mosquitoes in Cache Valley Virus Lineage Displacement, New York, USA

Cache Valley virus (CVV) is a mosquitoborne virus that infects livestock and humans. We report results of surveillance for CVV in New York, USA, during 2000–2016; full-genome analysis of selected CVV isolates from sheep, horse, humans, and mosquitoes from New York and Canada; and phenotypic characterization of selected strains. We calculated infection rates by using the maximum-likelihood estimation method by year, region, month, and mosquito species. The highest maximum-likelihood estimations were for Anopheles spp. mosquitoes. Our phylogenetic analysis identified 2 lineages and found evidence of segment reassortment. Furthermore, our data suggest displacement of CVV lineage 1 by lineage 2 in New York and Canada. Finally, we showed increased vector competence of An. quadrimaculatus mosquitoes for lineage 2 strains of CVV compared with lineage 1 strains.

Phylogenetic Analysis of Massilia phlebovirus in Portugal

In the last two decades, molecular surveys of arboviruses have enabled the identification of several new viruses, contributing to the knowledge of viral diversity and providing important epidemiological data regarding possible new emerging viruses. A combination of diagnostic assays, Illumina sequencing and phylogenetic inference are here used to characterize two new Massilia phlebovirus strains isolated from sandflies collected in the Arrábida region, Portugal. Whole genome sequence analysis enabled their identification as reassortants and the recognition of genomic variants co-circulating in Portugal. Much is still unknown about the life cycle, geographic range, evolutionary forces and public health importance of these viruses in Portugal and elsewhere, and more studies are needed.

Genomic characterization of 99 viruses from the bunyavirus families Nairoviridae, Peribunyaviridae, and Phenuiviridae, including 35 previously unsequenced viruses

Bunyaviruses (Negarnaviricota: Bunyavirales) are a large and diverse group of viruses that include important human, veterinary, and plant pathogens. The rapid characterization of known and new emerging pathogens depends on the availability of comprehensive reference sequence databases that can be used to match unknowns, infer evolutionary relationships and pathogenic potential, and make response decisions in an evidence-based manner. In this study, we determined the coding-complete genome sequences of 99 bunyaviruses in the Centers for Disease Control and Prevention's Arbovirus Reference Collection, focusing on orthonairoviruses (family Nairoviridae), orthobunyaviruses (Peribunyaviridae), and phleboviruses (Phenuiviridae) that either completely or partially lacked genome sequences. These viruses had been collected over 66 years from 27 countries from vertebrates and arthropods representing 37 genera. Many of the viruses had been characterized serologically and through experimental infection of animals but were isolated in the pre-sequencing era. We took advantage of our unusually large sample size to systematically evaluate genomic characteristics of these viruses, including reassortment, and co-infection. We corroborated our findings using several independent molecular and virologic approaches, including Sanger sequencing of 197 genome segments, and plaque isolation of viruses from putative co-infected virus stocks. This study contributes to the described genetic diversity of bunyaviruses and will enhance the capacity to characterize emerging human pathogenic bunyaviruses.

Combinatorial Minigenome Systems for Emerging Banyangviruses Reveal Viral Reassortment Potential and Importance of a Protruding Nucleotide in Genome "Panhandle" for Promoter Activity and Reassortment

Banyangvirus is a new genus (Phenuiviridae family, Bunyavirales order) that comprises a group of emerging tick-borne viruses with severe fever with thrombocytopenia syndrome virus (SFTSV) and Heartland virus (HRTV) as virulent representatives. As segmented RNA viruses, bunyaviruses may have genome reassortment potential, increasing the concern about new life-threatening bunyavirus emergence. Using a series of combinatory minigenome reporter assays based on transfection and superinfection, we showed that replication machinery proteins of designated banyangviruses can recognize genomic untranslated regions (UTRs) of other banyangviruses and assemble heterogenous minigenomes into functional ribonucleoproteins (RNPs). Moreover, both heterogenous and heterozygous RNPs were efficiently packaged by viral glycoproteins into infectious virus-like particles, manifesting remarkable reassortment potential of banyangviruses. Meanwhile, UTR promoter strength of the three banyangvirus segments appeared to be M > L > S. Secondary structure analysis revealed a conservative non-basepairing protruding nucleotide in the terminal UTR panhandles of M and L (but not S) segments of all banyangviruses and some related phleboviruses (Phlebovirus genus). Furthermore, not only a conserved panhandle region but also the protruding nucleotide proved important for UTR function. Removal of the protruding nucleotide abated M and L UTR activities and compatibilities with heterogenous viral proteins, and introduction of a protruding nucleotide into S panhandle, conversely, enhanced UTR promoter strength and compatibility, revealing the significance of the protruding nucleotide as a new signature of the genomic panhandle structure in both UTR activity and reassortment potential. The study demonstrates not only banyangvirus reassortment potential but also the notable role of the protruding nucleotide in UTR function and reassortment, providing clues to viral evolution and replication mechanisms and perhaps benefiting disease control and prevention in the future.

Host-dependence of in vitro reassortment dynamics among the Sathuperi and Shamonda Simbuviruses

Orthobunyaviruses are arboviruses (Arthropod Borne Virus) and possess multipartite genomes made up of three negative RNAs corresponding to the small (S), medium (M) and large (L) segments. Reassortment and recombination are evolutionary driving forces of such segmented viruses and lead to the emergence of new strains and species. Retrospective studies based on phylogenetical analysis are able to evaluate these mechanisms at the end of the selection process but fail to address the dynamics of emergence. This issue was addressed using two Orthobunyaviruses infecting ruminants and belonging to the Simbu serogroup: the Sathuperi virus (SATV) and the Shamonda virus (SHAV). Both viruses were associated with abortion, stillbirth and congenital malformations occurring after transplacental transmission and were suspected to spread together in different ruminant and insect populations. This study showed that different viruses related to SHAV and SATV are spreading simultaneously in ruminants and equids of the Sub-Saharan region. Their reassortment and recombination potential was evaluated in mammalian and in insect contexts. A method was set up to determine the genomic background of any clonal progeny viruses isolated after in vitro coinfections assays. All the reassortment combinations were generated in both contexts while no recombinant virus was isolated. Progeny virus populations revealed a high level of reassortment in mammalian cells and a much lower level in insect cells. In vitro selection pressure that mimicked the host switching (insect-mammal) revealed that the best adapted reassortant virus was connected with an advantageous replicative fitness and with the presence of a specific segment.

Arbovirus-Mosquito Vector-Host Interactions and the Impact on Transmission and Disease Pathogenesis of Arboviruses

Hundreds of viruses, designated as arboviruses, are transmitted by arthropod vectors in complex transmission cycles between the virus, vertebrate host, and the vector. With millions of human and animal infections per year, it is critical to improve our understanding of the interactions between the biological and environmental factors that play a critical role in pathogenesis, disease outcomes, and transmission of arboviruses. This review focuses on mosquito-borne arboviruses and discusses current knowledge of the factors and underlying mechanisms that influence infection and transmission of arboviruses and discusses critical factors and pathways that can potentially become targets for intervention and therapeutics.

Full genomic characterization of California serogroup viruses, genus Orthobunyavirus, family Peribunyaviridae including phylogenetic relationships

Thorough molecular characterization of reference viruses supports the detection of emerging human pathogens as well as studies of evolutionary relationships. However, full characterization of the tripartite RNA genomes of many viruses of the clinically important family Peribunyaviridae remains incomplete, making it difficult to identify emerging strains. Here, we report the full genome sequences of nine viruses belonging to the California serogroup and describe multi-segment analyses of these and previously published California serogroup strain data to determine the role of segment reassortment in the evolution of this serogroup. Phylogenetic trees from the small, medium, and large segments suggest long term, independent evolution of the majority of strains. However, trees from each segment were not entirely congruent and evidence of reassortment among some strains is presented. Of unique interest, the L segment phylogeny reveals divergent branching patterns for encephalitic versus non-encephalitic viruses in both major clades of the California serogroup.

Mosquito-borne Inkoo virus in northern Sweden - isolation and whole genome sequencing

BACKGROUND

Inkoo virus (INKV) is a less known mosquito-borne virus belonging to Bunyaviridae, genus Orthobunyavirus, California serogroup. Studies indicate that INKV infection is mainly asymptomatic, but can cause mild encephalitis in humans. In northern Europe, the sero-prevalence against INKV is high, 41% in Sweden and 51% in Finland. Previously, INKV RNA has been detected in adult Aedes (Ae.) communis, Ae. hexodontus and Ae. punctor mosquitoes and Ae. communis larvae, but there are still gaps of knowledge regarding mosquito vectors and genetic diversity. Therefore, we aimed to determine the occurrence of INKV in its mosquito vector and characterize the isolates.

METHODS

About 125,000 mosquitoes were collected during a mosquito-borne virus surveillance in northern Sweden during the summer period of 2015. Of these, 10,000 mosquitoes were processed for virus isolation and detection using cell culture and RT-PCR. Virus isolates were further characterized by whole genome sequencing. Genetic typing of mosquito species was conducted by cytochrome oxidase subunit I (COI) gene amplification and sequencing (genetic barcoding).

RESULTS

Several Ae. communis mosquitoes were found positive for INKV RNA and two isolates were obtained. The first complete sequences of the small (S), medium (M), and large (L) segments of INKV in Sweden were obtained. Phylogenetic analysis showed that the INKV genome was most closely related to other INKV isolates from Sweden and Finland. Of the three INKV genome segments, the INKV M segment had the highest frequency of non-synonymous mutations. The overall G/C-content of INKV genes was low for the N/NSs genes (43.8-45.5%), polyprotein (Gn/Gc/NSm) gene (35.6%) and the RNA polymerase gene (33.8%) This may be due to the fact that INKV in most instances utilized A or T in the third codon position.

CONCLUSIONS

INKV is frequently circulating in northern Sweden and Ae. communis is the key vector. The high mutation rate of the INKV M segment may have consequences on virulence.

Bunyavirus-vector interactions

The Bunyaviridae family is comprised of more than 350 viruses, of which many within the Hantavirus, Orthobunyavirus, Nairovirus, Tospovirus, and Phlebovirus genera are significant human or agricultural pathogens. The viruses within the Orthobunyavirus, Nairovirus, and Phlebovirus genera are transmitted by hematophagous arthropods, such as mosquitoes, midges, flies, and ticks, and their associated arthropods not only serve as vectors but also as virus reservoirs in many cases. This review presents an overview of several important emerging or re-emerging bunyaviruses and describes what is known about bunyavirus-vector interactions based on epidemiological, ultrastructural, and genetic studies of members of this virus family.

Arboviruses: variations on an ancient theme

ABSTRACT 

Arboviruses utilize different strategies to complete their transmission cycle between vertebrate and invertebrate hosts. Most possess an RNA genome coupled with an RNA polymerase lacking proofreading activity and generate large populations of genetically distinct variants, permitting rapid adaptation to environmental changes. With mutation rates of between 10- 6 and 10-4 substitutions per nucleotide, arboviral genomes rapidly acquire mutations that can lead to viral emergence. Arboviruses can be described in seven families, four of which have medical importance: Togaviridae, Flaviviridae, Bunyaviridae and Reoviridae. The Togaviridae and Flaviviridae both have ssRNA genomes, while the Bunyaviridae and Reoviridae possess segmented RNA genomes. Recent epidemics caused by these arboviruses have been associated with specific mutations leading to enhanced host ranges, vector shifts and virulence.

Genomic and phylogenetic characterization of viruses included in the Manzanilla and Oropouche species complexes of the genus Orthobunyavirus, family Bunyaviridae

A thorough characterization of the genetic diversity of viruses present in vector and vertebrate host populations is essential for the early detection of and response to emerging pathogenic viruses, yet genetic characterization of many important viral groups remains incomplete. The Simbu serogroup of the genus Orthobunyavirus, family Bunyaviridae, is an example. The Simbu serogroup currently consists of a highly diverse group of related arboviruses that infect both humans and economically important livestock species. Here, we report complete genome sequences for 11 viruses within this group, with a focus on the large and poorly characterized Manzanilla and Oropouche species complexes. Phylogenetic and pairwise divergence analyses indicated the presence of high levels of genetic diversity within these two species complexes, on a par with that seen among the five other species complexes in the Simbu serogroup. Based on previously reported divergence thresholds between species, the data suggested that these two complexes should actually be divided into at least five species. Together these five species formed a distinct phylogenetic clade apart from the rest of the Simbu serogroup. Pairwise sequence divergences among viruses of this clade and viruses in other Simbu serogroup species complexes were similar to levels of divergence among the other orthobunyavirus serogroups. The genetic data also suggested relatively high levels of natural reassortment, with three potential reassortment events present, including two well-supported events involving viruses known to infect humans.

Isolation and characterization of a California encephalitis serogroup orthobunyavirus from Finnish mosquitoes

The mosquito-borne California encephalitis serogroup viruses of the genus Orthobunyavirus (family Bunyaviridae) include several causative agents of encephalitis in humans. Until recently, Inkoo virus (INKV) was the only orthobunyavirus isolated in Finland, showing high seroprevalence in the population. In this study, we recovered five orthobunyavirus isolates from mosquitoes collected in eastern Finland in the early autumns of 2007 and 2008 by inoculation of Vero cells. The isolates were determined by S, M and L segment sequences to represent the California encephalitis virus species but distinct from INKV (68% polyprotein amino acid (aa) identity). In genetic analyses, isolates clustered together with a number of westernmost Chatanga virus isolates (98% polyprotein aa identity) reported from Russia, forming a distinct phylogroup. However, the sequence homology of this phylogroup to the majority of Chatanga isolates, comprising three different geographically clustered phylogroups, was considerably lower (89-92% polyprotein aa identity). The five new isolates were designated as Möhkö isolates of Chatanga virus, according to the village of origin. The isolates were closely related to Snowshoe hare virus (SSHV) and La Crosse virus (LACV) with an aa identity of 87% and 82% within the M segment polyprotein, respectively. The genetic relatedness of Möhkö isolates to a number of human pathogenic orthobunyaviruses warrants further investigation on their potential disease associations and further serological analysis is needed to compare them to other Chatanga virus isolates and SSHV to determine their true antigenic relation.

Viruses of the family Bunyaviridae: are all available isolates reassortants?

Viruses of the family Bunyaviridae (the bunyaviruses) possess three distinct linear, single-stranded, negative sense or ambisense RNA segments (large, medium, and small). Dual infections of arthropod and perhaps vertebrate and plant hosts provide substantial opportunity for segment reassortment and an increasingly recognized number of the nearly 300 viruses in this family have been shown to be reassortants. Reassortment of RNA segments (genetic shift) complements genetic drift (accumulation of point mutations) as a powerful mechanism underlying bunyavirus evolution. Here we consider the possibility, if not likelihood, that most if not all bunyaviruses currently recognized may represent reassortants, some of which may be reassortants of existing viruses, and some of which may be reassortants of extinct viruses. If this hypothesis is correct, then the roots of the family and genus trees of bunyaviruses as currently described (or ignored) are incomplete or incorrect.

Genetic characterization of the Wyeomyia group of orthobunyaviruses and their phylogenetic relationships

Phylogenetic analyses can give new insights into the evolutionary history of viruses, especially of viruses with segmented genomes. However, sequence information for many viral families or genera is still limited and phylogenies based on single or short genome fragments can be misleading. We report the first genetic analysis of all three genome segments of Wyeomyia group viruses Wyeomyia, Taiassui, Macaua, Sororoca, Anhembi and Cachoeira Porteira (BeAr328208) in the genus Orthobunyavirus of the family Bunyaviridae. In addition, Tucunduba and Iaco viruses were identified as members of the Wyeomyia group. Features of Wyeomyia group members that distinguish them from other viruses in the Bunyamwera serogroup and from other orthobunyaviruses, including truncated NSs sequences that may not counteract the host's interferon response, were characterized. Our findings also suggest genome reassortment within the Wyeomyia group, identifying Macaua and Tucunduba viruses as M-segment reassortants that, in the case of Tucunduba virus, may have altered pathogenicity, stressing the need for whole-genome sequence information to facilitate characterization of orthobunyaviruses and their phylogenetic relationships.

Identification of a phylogenetically distinct orthobunyavirus from group C

Apeu virus (APEUV) (family Bunyaviridae, genus Orthobunyavirus) was plaque purified and characterised by serological and molecular analysis. Neutralising assays confirmed cross-reactivity between purified APEUV clones and the Caraparu virus complex of group C orthobunyaviruses. Partial sequencing of the L, M and S segments of one APEUV clone (APEUV-CL5) was carried out. A phylogenetic tree constructed with the L amino acid sequences clustered APEUV-CL5 within the genus Orthobunyavirus, confirming its serological classification. Analysis of M segment sequences clustered APEUV-CL5 in the Caraparu virus complex (Group C), in agreement with serological tests and previous molecular characterisation. However, the sequence of the nucleocapsid gene (N) gave low identity values when compared to those of the group C viruses. The phylogenetic tree based on N nucleotide sequences clustered APEUV-CL5 next to the California and Bwamba groups. This remarkable S nucleotide variability suggests that APEUV-CL5 could be a genetic reassortant and that this evolutionary mechanism is present in the history of the group C viruses.

The spatial epidemiology and clinical features of reported cases of La Crosse virus infection in West Virginia from 2003 to 2007

BACKGROUND

La Crosse virus (LACV) is a major cause of pediatric encephalitis in the United States. Since the mid-1980s, the number of reported cases of LACV infection in West Virginia has continued to rise and the state currently reports the most cases in the United States. The purpose of this study was to investigate and describe the spatial epidemiology and clinical presentation of LACV infection cases reported in West Virginia, as well as to provide a description of the environmental conditions present at the residences of the LACV infection cases.

METHODS

Descriptive and spatial analyses were performed on LACV infection cases reported to the West Virginia Department of Health from 2003 to 2007. Clinical and environmental variables were available for 96 cases and residence data were available for 68 of these cases. Spatial analyses using the global Moran's I and Kulldorff's spatial scan statistic were performed using the population 15 years and younger at both the county and census tract levels to identify those geographic areas at the highest risk of infection.

RESULTS

Two statistically significant (p < 0.05) high-risk clusters, involving six counties, were detected at the county level. At the census tract level, one statistically significant high-risk cluster involving 41 census tracts spanning over six counties was identified. The county level cumulative incidence for those counties in the primary high-risk cluster ranged from 100.0 to 189.0 cases per 100,000 persons (median 189.0) and the census tract level cumulative incidence for those counties in the high-risk cluster ranged from 61.7 to 505.9 cases per 100,000 persons (median 99.0). The counties and census tracts within high-risk clusters had a relative risk four to nine times higher when compared to those areas not contained within high-risk clusters. The majority of LACV infection cases were reported during the summer months in children 15 years and younger. Fever, vomiting, photophobia, and nausea were the most commonly reported signs and symptoms. A case fatality rate (CFR) of 3.1% was observed. Wooded areas and containers were present at the majority of case residences.

CONCLUSIONS

The cumulative incidences of LACV infection from 2003 to 2007 were considerably higher than previously reported for West Virginia, and statistically significant high-risk clusters for LACV infection were detected at both the county and census tract levels. The finding of a high CFR and the identification of those areas at highest risk for infection will be useful for guiding future research and intervention efforts.

Insights into arbovirus evolution and adaptation from experimental studies

Arthropod-borne viruses (arboviruses) are maintained in nature by cycling between vertebrate hosts and haematophagous invertebrate vectors. These viruses are responsible for causing a significant public health burden throughout the world, with over 100 species having the capacity to cause human disease. Arbovirus outbreaks in previously naïve environments demonstrate the potential of these pathogens for expansion and emergence, possibly exacerbated more recently by changing climates. These recent outbreaks, together with the continued devastation caused by endemic viruses, such as Dengue virus which persists in many areas, demonstrate the need to better understand the selective pressures that shape arbovirus evolution. Specifically, a comprehensive understanding of host-virus interactions and how they shape both host-specific and virus-specific evolutionary pressures is needed to fully evaluate the factors that govern the potential for host shifts and geographic expansions. One approach to advance our understanding of the factors influencing arbovirus evolution in nature is the use of experimental studies in the laboratory. Here, we review the contributions that laboratory passage and experimental infection studies have made to the field of arbovirus adaptation and evolution, and how these studies contribute to the overall field of arbovirus evolution. In particular, this review focuses on the areas of evolutionary constraints and mutant swarm dynamics; how experimental results compare to theoretical predictions; the importance of arbovirus ecology in shaping viral swarms; and how current knowledge should guide future questions relevant to understanding arbovirus evolution.

Genetic reassortment between high-virulent and low-virulent Dobrava-Belgrade virus strains

The tri-segmented RNA genome of hantaviruses facilitates genetic reassortment by segment swapping when cells are co-infected with different virus strains. We found efficient in vitro reassortment between members of two different genetic lineages of the Dobrava-Belgrade virus species, the weakly virulent DOBV-Aa and highly virulent DOBV-Af. In all reassortants, S and L segments originated from the same parental strain, and only the M segment was exchanged. To identify functional differences between the parental strains DOBV-Aa and DOBV-Af in cell culture and to compare them with the reassortants, we studied elements of the innate immunity in virus-infected cells. The contrasting phenotypes of the parental viruses were maintained by the reassortants carrying the respective S and L segments of the parental virus and were not influenced by the origin of the M segment.

Temporal and geographic evidence for evolution of Sin Nombre virus using molecular analyses of viral RNA from Colorado, New Mexico and Montana

Background

All viruses in the family Bunyaviridae possess a tripartite genome, consisting of a small, a medium, and a large RNA segment. Bunyaviruses therefore possess considerable evolutionary potential, attributable to both intramolecular changes and to genome segment reassortment. Hantaviruses (family Bunyaviridae, genus Hantavirus) are known to cause human hemorrhagic fever with renal syndrome or hantavirus pulmonary syndrome. The primary reservoir host of Sin Nombre virus is the deer mouse (Peromyscus maniculatus), which is widely distributed in North America. We investigated the prevalence of intramolecular changes and of genomic reassortment among Sin Nombre viruses detected in deer mice in three western states.

Methods

Portions of the Sin Nombre virus small (S) and medium (M) RNA segments were amplified by RT-PCR from kidney, lung, liver and spleen of seropositive peromyscine rodents, principally deer mice, collected in Colorado, New Mexico and Montana from 1995 to 2007. Both a 142 nucleotide (nt) amplicon of the M segment, encoding a portion of the G2 transmembrane glycoprotein, and a 751 nt amplicon of the S segment, encoding part of the nucleocapsid protein, were cloned and sequenced from 19 deer mice and from one brush mouse (P. boylii), S RNA but not M RNA from one deer mouse, and M RNA but not S RNA from another deer mouse.

Results

Two of 20 viruses were found to be reassortants. Within virus sequences from different rodents, the average rate of synonymous substitutions among all pair-wise comparisons (π_s) was 0.378 in the M segment and 0.312 in the S segment sequences. The replacement substitution rate (π_a) was 7.0 × 10^-4 in the M segment and 17.3 × 10^-4 in the S segment sequences. The low π_a relative to π_s suggests strong purifying selection and this was confirmed by a Fu and Li analysis. The absolute rate of molecular evolution of the M segment was 6.76 × 10^-3 substitutions/site/year. The absolute age of the M segment tree was estimated to be 37 years. In the S segment the rate of molecular evolution was 1.93 × 10^-3 substitutions/site/year and the absolute age of the tree was 106 years. Assuming that mice were infected with a single Sin Nombre virus genotype, phylogenetic analyses revealed that 10% (2/20) of viruses were reassortants, similar to the 14% (6/43) found in a previous report.

Conclusion

Age estimates from both segments suggest that Sin Nombre virus has evolved within the past 37–106 years. The rates of evolutionary changes reported here suggest that Sin Nombre virus M and S segment reassortment occurs frequently in nature.