Detection and molecular characterization of West Nile virus in Culex pipiens mosquitoes in Central Macedonia, Greece, 2019-2021

Since 2010 when West Nile virus (WNV) emerged in Greece, it causes seasonal outbreaks of human infections almost every year. During May-October of 2019-2021 a total number of 51,504 Culex pipiens mosquitoes were trapped in all seven regional units of Central Macedonia in northern Greece. They were grouped into 1099 pools and tested for WNV. The virus was detected in 5% of the mosquito pools (1.5%, 3.6% and 9.6% pools in 2019, 2020, and 2021, respectively), with significant rate differences among the regional units and years. The highest maximum likelihood estimation for WNV infection rates calculated per 1000 mosquitoes for 2019 and 2020 were 1.89 and 3.84 in Serres, and 7.08 for 2021 in Pella regional unit. Sixteen whole genome sequences were taken by applying a recently described PCR-based next generation sequencing protocol. Phylogenetic analysis showed that the sequences belonged to the Central European clade of WNV lineage 2, and that a virus strain introduced in Greece in 2019 continued to circulate and spread further during 2020-2021. The data are useful for public health and mosquito control programs' operational scheduling, while the whole genome sequences are an added value for molecular epidemiology and evolutionary studies.

Revised nomenclature and SNP barcode for Mycobacterium tuberculosis lineage 2

Mycobacterium tuberculosis (Mtb) lineage 2 (L2) strains are present globally, contributing to a widespread tuberculosis (TB) burden, particularly in Asia where both prevalence of TB and numbers of drug resistant TB are highest. The increasing availability of whole-genome sequencing (WGS) data worldwide provides an opportunity to improve our understanding of the global genetic diversity of Mtb L2 and its association with the disease epidemiology and pathogenesis. However, existing L2 sublineage classification schemes leave >20 % of the Modern Beijing isolates unclassified. Here, we present a revised SNP-based classification scheme of L2 in a genomic framework based on phylogenetic analysis of >4000 L2 isolates from 34 countries in Asia, Eastern Europe, Oceania and Africa. Our scheme consists of over 30 genotypes, many of which have not been described before. In particular, we propose six main genotypes of Modern Beijing strains, denoted L2.2.M1–L2.2.M6. We also provide SNP markers for genotyping L2 strains from WGS data. This fine-scale genotyping scheme, which can classify >98 % of the studied isolates, serves as a basis for more effective monitoring and reporting of transmission and outbreaks, as well as improving genotype-phenotype associations such as disease severity and drug resistance. This article contains data hosted by Microreact.

West Nile virus lineage 2 in Culex mosquitoes in Thessaly, Greece, 2019

West Nile virus is a flavivirus transmitted to humans mainly by mosquito bites. Outbreaks are observed in several European countries, and Greece is one of the most affected countries during the recent years. Thessaly was one of the most affected regions in Greece in 2019. A total of 3,025 Culex spp. mosquitoes collected in Thessaly were grouped into 47 pools and tested for West Nile virus (WNV). Eight (17%) pools were found positive. Whole genome sequences were obtained from two positive pools. Phylogenetic analysis showed that the causative strain was an evolutionary variant of the strains circulating in 2018 belonging to the Balkan subgroup of the Central European subclade of WNV lineage 2.

The role of IS6110 in micro- and macroevolution of Mycobacterium tuberculosis lineage 2

The insertion sequence 6110 (IS6110) is the most studied transposable element in the Mycobacterium tuberculosis complex species. The element plays a significant role in genome plasticity of this important human pathogen, but still many causes and consequences of its transposition have not been fully studied. Here, we analyzed insertion sites for 902 Mycobacterium tuberculosis lineage 2 strains using whole-genome sequencing data. In total, 17,972 insertions were found, corresponding to 827 independent positions in the genome of the reference strain H37Rv. To trace the history of IS6110 expansion since proto-Beijing strains up to modern sublineages, we looked at the distribution of IS6110 across the genome-wide SNP-based phylogenetic tree. This analysis demonstrated a stepwise transposition of IS6110 that occurs by «copy-and-paste» mechanism. Additionally, we detected evolutionary-scale and sublineage-specific integration sites, which can be used for typing and for understanding the reasons for the success of the lineage. A significant part of such insertions affected the genes that are essential for the pathogen. Finally, we identified and confirmed deletions that occurred between differently oriented elements, which is uncommon for this family of insertion elements and appears to be another mechanism of genome variability.

A PCR-based NGS protocol for whole genome sequencing of West Nile virus lineage 2 directly from biological specimens

Lineage 2 West Nile virus (WNV) strains have been implicated in severe encephalitis outbreaks in humans and equines residing in Europe. WNV molecular characterization is important for the development of diagnostic assays, as well as for obtaining molecular information, which is necessary for epidemiological investigations of virus transmission in areas at risk. For whole genome sequencing of lineage 2 WNV strains, directly from biological specimens, a PCR-based NGS protocol was developed. The method was applied in WNV-positive specimens obtained from animal, human and mosquito hosts in Greece. The results of its application indicate that, even in cases of low virus titers, the developed PCR-based NGS approach is able to provide whole genome sequences of lineage 2 WNV strains.

Emergence of West Nile virus lineage 2 belonging to the Eastern European subclade, Greece

West Nile virus (WNV) emerged in Greece in 2010 and since then human outbreaks occurred every year except 2015 and 2016. An early start and prolonged WNV transmission season was observed in 2018 with a record number of 316 reported cases and 47 fatalities. The Greek WNV strains detected during 2010-2018 clustered within the central European subclade of lineage 2. A novel WNV genetic variant was detected in August 2018 in one human case in the north-eastern region of Greece, at the land cross-border with Turkey and Bulgaria. The strain belongs to the Eastern European subclade of lineage 2 suggesting a new virus introduction in the country and the continuously changing epidemiology of the disease.

Characteristics of distribution of Mycobacterium tuberculosis lineages in China

The genotyping methods of Mycobacterium tuberculosis would dramatically improve our understanding of the molecular epidemiology of tuberculosis. 3,929 isolates, from a National Survey of Drug-Resistant Tuberculosis in 2007 in China, were successfully genotyped by large sequence polymorphisms and 15 loci variable number tandem repeats. We found that 2,905 (2,905/3,929, 73.9%) cases belonged to Lineage 2, dominated in the east and central regions, 975 cases (975/3,929, 24.8%) were Lineage 4, highly prevailed in the west regions, and 36 and 13 cases were Lineage 3 and Lineage 1, respectively. We also explored the associations between lineages (Lineage 2 vs. Lineage 4) and clinical characteristics by logistic regression. For Lineage 2, the risk factors were Han-ethnicity population and fever. However, for Lineage 4, they were occupation (farmer), and degree of education (non-literate). Fully understanding of the distribution of Mycobacterium tuberculosis lineage and its risk factors would play a critical role in tuberculosis prevention, control, and treatment.

West Nile virus host-vector-pathogen interactions in a colonial raptor

Background

Avian host species have different roles in the amplification and maintenance of West Nile virus (WNV), therefore identifying key taxa is vital in understanding WNV epidemics. Here, we present a comprehensive case study conducted on red-footed falcons, where host-vector, vector-virus and host-virus interactions were simultaneously studied to evaluate host species contribution to WNV circulation qualitatively.

Results

Mosquitoes were trapped inside red-footed falcon nest-boxes by a method originally developed for the capture of blackflies and midges. We showed that this approach is also efficient for trapping mosquitoes and that the number of trapped vectors is a function of host attraction. Brood size and nestling age had a positive effect on the number of attracted Culex pipiens individuals while the blood-feeding success rate of both dominant Culex species (Culex pipiens and Culex modestus) markedly decreased after the nestlings reached 14 days of age. Using RT-PCR, we showed that WNV was present in these mosquitoes with 4.2% (CI: 0.9–7.5%) prevalence. We did not detect WNV in any of the nestling blood samples. However, a relatively high seroprevalence (25.4% CI: 18.8–33.2%) was detected with an enzyme-linked immunoabsorbent assay (ELISA). Using the ELISA OD ratios as a proxy to antibody titers, we showed that older seropositive nestlings have lower antibody levels than their younger conspecifics and that hatching order negatively influences antibody levels in broods with seropositive nestlings.

Conclusions

Red-footed falcons in the studied system are exposed to a local sylvatic WNV circulation, and the risk of infection is higher for younger nestlings. However, the lack of individuals with viremia and the high WNV seroprevalence, indicate that either host has a very short viremic period or that a large percentage of nestlings in the population receive maternal antibodies. This latter assumption is supported by the age and hatching order dependence of antibody levels found for seropositive nestlings. Considering the temporal pattern in mosquito feeding success, maternal immunity may be effective in protecting progeny against WNV infection despite the short antibody half-life measured in various other species. We conclude that red-footed falcons seem to have low WNV host competence and are unlikely to be effective virus reservoirs in the studied region.

Chronic West Nile virus infection in kea (Nestor notabilis)

Six kea (Nestor notabilis) in human care, naturally infected with West Nile virus (WNV) lineage 2 in Vienna, Austria, in 2008, developed mild to fatal neurological signs. WNV RNA persisted and the virus evolved in the birds' brains, as demonstrated by (phylo)genetic analyses of the complete viral genomes detected in kea euthanized between 2009 and 2014. WNV antibodies persisted in the birds, too. Chronic WNV infection in the brain might contribute to the circulation of the virus through oral transmission to predatory birds.

Inactivated West Nile Virus (WNV) vaccine, Duvaxyn WNV, protects against a highly neuroinvasive lineage 2 WNV strain in mice

BACKGROUND

Lineage 2 West Nile Virus (WNV) is endemic to southern Africa and Madagascar, and has recently been associated with encephalitis outbreaks in humans and horses in South Africa, central Europe, Italy and Greece. Commercial vaccines have mostly been evaluated against WNV lineage 1 strains and their efficacy against lineage 2 strains rarely reported.

METHODS

To evaluate protection of Duvaxyn WNV vaccine against lineage 2 strains associated with encephalitis in South Africa, mice were vaccinated twice intramuscularly three weeks apart, and challenged four weeks later with highly neuroinvasive lineage 1 strain NY385/99 or lineage 2 strain SPU93/01. Neutralising antibody titres were measured at the time of challenge and three weeks later. Immunohistochemistry and reverse transcription polymerase chain reaction (RT-PCR) were conducted on brains of mice that succumbed during the trial, on controls and on vaccinated mice that survived.

RESULTS

Serum neutralising antibodies in vaccinated mice were detected but low three weeks after primovaccination. Three weeks post-challenge, vaccinated mice had significantly higher serum neutralising antibody titres against both lineages than unvaccinated controls. After challenge, all vaccinated mice remained healthy but all unvaccinated mice demonstrated severe neurological signs with 75% mortality rate. WNV was not detected in brains of vaccinated mice whereas virus replicated in most unvaccinated mice challenged with either lineage. Gross and microscopic lesions were found only in unvaccinated mice challenged with both lineages.

CONCLUSION

Duvaxyn WNV vaccine provided complete protection against challenge with lineage 2 WNV and stimulated significant cross protective neutralising antibodies in mice against lineage 2.