esm

Data of the weight, egg to adult survival, development time, starvation, and response to stres

For_DRYAD

The file is a zip archive of four files: Wolbachia_phylogenomic_90genes_concatenate.faa (the catenated aminoacid alignemtn of 90 genes), Wolbachia_phylogenomic_90genes_concatenate.ffn (the catenated nucleic acid alignemtn of 90 genes), Wolbachia_phylogenomic_OrthoMCL_cluster_aminoacidic_multifastas.zip (a zip file of the amino acid/protein sequences of clusters generated from the Wolbachia genomes using orthoMCL) and Wolbachia_phylogenomic_OrthoMCL_cluster_nucleotidic_multifastas.zip (a zip file of the nucleic acid sequences of clusters generated from the Wolbachia genomes using orthoMCL

COVID-19 risk-mitigation in reopening mass cultural events: population-based observational study for the UK Events Research Programme in Liverpool City Region

Objectives: To understand SARS-CoV-2 transmission risks, perceived risks, and the feasibility of risk-mitigations from experimental mass cultural events before COVID-19 restrictions were lifted. Design: Prospective, population-wide observational study. Setting: Four events (two nightclubs; outdoor music festival; business conference) open to Liverpool City Region UK residents, requiring a negative lateral flow test (LFT) within the 36 hours before the event, but not requiring social distancing or face-coverings. Participants: 12,256 individuals attending one or more event between 28th April and 2nd May 2021. Main outcome measures: SARS-CoV-2 infections detected using audience self-swabbed (5-7 days post-event) PCR tests, with viral genomic analysis of cases, plus linked NHS COVID-19 testing data. Audience experiences were gathered via questionnaires, focus groups and social media. Indoor CO2 concentrations were monitored. Results: 12 PCR-positive cases (likely 4 index; 8 primary or secondary), 10 from the nightclubs. Two further cases had positive LFTs but no PCR. 11,896 (97.1%) participants with scanned tickets were matched to a negative pre-event LFT: 4972 (40.6%) returned a PCR within a week. CO2 concentrations showed areas for improving ventilation at the nightclubs. Population infection rates were low, yet with a concurrent outbreak of >50 linked cases around a local swimming pool without equivalent risk-mitigations. Audience anxiety was low and enjoyment high. Conclusions: We observed minor SARS-CoV-2 transmission and low perceived risks around events when prevalence was low and risk-mitigations prominent. Partnership between audiences, event organisers and public health services, supported by information systems with real-time linked data can improve health security for mass cultural events.</p

<i>Phlebotomus papatasi</i> circadian rhythm pathway annotation.

Phlebotomus papatasi circadian rhythm pathway annotation.</p

Chitinase family annotation.

Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.</div

Molecular phylogenetic analysis of <i>Lu</i>. <i>longipalpis</i>, <i>P</i>. <i>papatasi</i> and <i>D</i>. <i>melanogaster</i> TRP channel sequences.

The different TRP subfamilies are displayed on the right. The evolutionary history was inferred by using the Maximum Likelihood method based on the Whelan and Goldman +Freq. model with 1000 bootstrap replicates. (TIF)</p

Glycosidase Hydrolase family 13 annotation.

Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.</div

Conflicting phylogenetic signals.

Analysis of the gene phylogenies of individual orthologous groups identified three major topologies with sand fly-mosquito (41%), sand fly-fly (37%), or mosquito-fly (22%) sister clades. Comparisons of average branch lengths for each topology suggest that, although substitution rates in flies are always higher, orthologs that support the sand fly-mosquito topology show the lowest substitution rates in flies and the smallest differences in substitution rates among the fly, sand fly, and mosquito clades. In contrast, the sand fly-fly and mosquito-fly topologies show much higher substitution rates in flies and much greater differences in substitution rates among the three clades. (TIF)</p

Admixture cross validation error.

Violin plot of the cross-validation error for each of 30 replicates for each K value. (A) Phlebotomus papatasi populations. (B) Lutzomyia longipalpis populations. (TIF)</p

<i>Lutzomyia longipalpis</i> population structure.

Inferred population structure of Lu. longipalpis individuals collected from Marajó (MAR; pink), Lapinha (LAP; blue), from Jacobina (JAC; red), and Sobral, including Sobral 1S (S1S; orange) and 16 Sobral 2S (S2S; green). (A) Rooted neighbor joining (NJ) radial tree. We included both N. intermedia (INT; yellow) and M. migonei (MIG; purple) and used M. migonei to root the trees. Bootstrap values represent the percentage of 1,000 replicates. (B) Principal component analysis (PCA). Individuals were plotted according to their coordinates on the first two principal components (PC1 and PC2). (C) Admixture analysis. Ancestry proportions for Admixture models from K = 2 to K = 7 ancestral populations. Each individual is represented by a thin vertical line, partitioned into K coloured segments representing the individual’s estimated membership fractions to the K clusters. These data are the average of the major q-matrix clusters derived by CLUMPAK analysis.</p