West Nile Virus Lineage 1 in Italy: Newly Introduced or a Re-Occurrence of a Previously Circulating Strain?

In Italy, West Nile virus (WNV) appeared for the first time in the Tuscany region in 1998. After 10 years of absence, it re-appeared in the areas surrounding the Po River delta, affecting eight provinces in three regions. Thereafter, WNV epidemics caused by genetically divergent isolates have been documented every year in the country. Since 2018, only WNV Lineage 2 has been reported in the Italian territory. In October 2020, WNV Lineage 1 (WNV-L1) re-emerged in Italy, in the Campania region. This is the first occurrence of WNV-L1 detection in the Italian territory since 2017. WNV was detected in the internal organs of a goshawk (Accipiter gentilis) and a kestrel (Falco tinnunculus). The RNA extracted in the goshawk tissue samples was sequenced, and a Bayesian phylogenetic analysis was performed by a maximum-likelihood tree. Genome analysis, conducted on the goshawk WNV complete genome sequence, indicates that the strain belongs to the WNV-L1 Western-Mediterranean (WMed) cluster. Moreover, a close phylogenetic similarity is observed between the goshawk strain, the 2008–2011 group of Italian sequences, and European strains belonging to the Wmed cluster. Our results evidence the possibility of both a new re-introduction or unnoticed silent circulation in Italy, and the strong importance of keeping the WNV surveillance system in the Italian territory active.

Genomic signatures of pre-resistance in Mycobacterium tuberculosis

Recent advances in bacterial whole-genome sequencing have resulted in a comprehensive catalog of antibiotic resistance genomic signatures in Mycobacterium tuberculosis. With a view to pre-empt the emergence of resistance, we hypothesized that pre-existing polymorphisms in susceptible genotypes (pre-resistance mutations) could increase the risk of becoming resistant in the future. We sequenced whole genomes from 3135 isolates sampled over a 17-year period. After reconstructing ancestral genomes on time-calibrated phylogenetic trees, we developed and applied a genome-wide survival analysis to determine the hazard of resistance acquisition. We demonstrate that M. tuberculosis lineage 2 has a higher risk of acquiring resistance than lineage 4, and estimate a higher hazard of rifampicin resistance evolution following isoniazid mono-resistance. Furthermore, we describe loci and genomic polymorphisms associated with a higher risk of resistance acquisition. Identifying markers of future antibiotic resistance could enable targeted therapy to prevent resistance emergence in M. tuberculosis and other pathogens.

Incrimination of shrews as a reservoir for Powassan virus

Powassan virus lineage 2 (deer tick virus) is an emergent threat to American public health, causing severe neurologic disease. Its life cycle in nature remains poorly understood. We use a host-specific retrotransposon-targeted real time PCR assay to test the hypothesis that white-footed mice, considered the main eastern U.S. reservoir of the coinfecting agent of Lyme disease, is the reservoir for deer tick virus. Of 20 virus-infected host-seeking nymphal black-legged ticks 65% fed on shrews and none on mice. The proportion of ticks feeding on shrews at a site is positively associated with prevalence of viral infection, but not the Lyme disease agent. Viral RNA is detected in the brain of one shrew. We conclude that shrews are a likely reservoir host for deer tick virus and that host bloodmeal analysis can provide direct evidence to incriminate reservoir hosts, thereby promoting our understanding of the ecology of tick-borne infections.

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.

373. Household transmission of SARS-CoV-2 B.1.1.7 lineage –2 U.S. States, 2021

Background In December 2020, B.1.1.7 lineage of SARS-CoV-2 was first detected in the United States and has since become the dominant lineage. Previous investigations involving B.1.1.7 suggested higher rates of transmission relative to non-B.1.1.7 lineages. We conducted a household transmission investigation to determine the secondary infection rates (SIR) of B.1.1.7 and non-B.1.1.7 SARS-CoV-2 lineages. Methods From January–April 2021, we enrolled members of households in San Diego County, CA, and Denver, CO metropolitan area (Tri-County), with a confirmed SARS-CoV-2 infection in a household member with illness onset date in the previous 10 days. CDC investigators visited households at enrollment and 14 days later at closeout to obtain demographic and clinical data and nasopharyngeal (NP) samples on all consenting household members. Interim visits, with collection of NP swabs, occurred if a participant became symptomatic during follow-up. NP samples were tested for SARS-CoV-2 using TaqPath™ RT-PCR test, where failure to amplify the spike protein results in S-Gene target failure (SGTF) may indicate B.1.1.7 lineage. Demographic characteristics and SIR were compared among SGTF and non-SGTF households using two-sided p-values with chi-square tests; 95% confidence intervals (CI) were calculated with Wilson score intervals. Results 552 persons from 151 households were enrolled. 91 (60%) households were classified as SGTF, 57 (38%) non-SGTF, and 3 (2%) indeterminant. SGTF and non-SGTF households had similar sex distribution (49% female and 52% female, respectively; P=0.54) and age (median 30 years, interquartile range (IQR 14–47) and 31 years (IQR 15–45), respectively). Hispanic people accounted for 24% and 32% of enrolled members of SGTF and non-SGTF households, respectively (p=0.04). At least one secondary case occurred in 61% of SGTF and 58% of non-SGTF households (P=0.66). SIR was 52% (95%[CI] 46%-59%) for SGTF and 45% (95% CI 37%-53%) for non-SGTF households (P=0.18). Conclusion SIRs were high in both SGTF and non-SGTF households; our findings did not support an increase in SIR for SGTF relative to non-SGTF households in this setting. Sequence confirmed SARS-CoV-2 samples will provide further information on lineage specific SIRs. Disclosures All Authors: No reported disclosures

High molecular weight glutenin gene diversity in Aegilops tauschii demonstrates unique origin of superior wheat quality

Central to the diversity of wheat products was the origin of hexaploid bread wheat, which added the D-genome of Aegilops tauschii to tetraploid wheat giving rise to superior dough properties in leavened breads. The polyploidization, however, imposed a genetic bottleneck, with only limited diversity introduced in the wheat D-subgenome. To understand genetic variants for quality, we sequenced 273 accessions spanning the known diversity of Ae. tauschii. We discovered 45 haplotypes in Glu-D1, a major determinant of quality, relative to the two predominant haplotypes in wheat. The wheat allele 2 + 12 was found in Ae. tauschii Lineage 2, the donor of the wheat D-subgenome. Conversely, the superior quality wheat allele 5 + 10 allele originated in Lineage 3, a recently characterized lineage of Ae. tauschii, showing a unique origin of this important allele. These two wheat alleles were also quite similar relative to the total observed molecular diversity in Ae. tauschii at Glu-D1. Ae. tauschii is thus a reservoir for unique Glu-D1 alleles and provides the genomic resource to begin utilizing new alleles for end-use quality improvement in wheat breeding programs.

Distribution and Identification of Mycobacterium tuberculosis Lineage in Kashgar Prefecture

Objectives In order to understand the composition of Mycobacterium tuberculosis(M.tb) lineage and find specific tags to distinguish lineage of the M.tb in Kashgar prefecture, so as to provide a basis for the prevention of tuberculosis in this area. Methods Whole genome sequencing (WGS) of M.tb clinical strains (161 cases) was conducted. The phylogenetic tree was constructed by Maximum Likelihood (ML) on the basis of single nucleotide polymorphisms (SNPs) and verified via principal component analysis (PCA). The composition structure of M.tb in different regions was analyzed by combining geographic information. Results The M.tb clinical strains were composed of lineage 2 (73/161, 45.34%), lineage 3 (52/161, 32.30%) and lineage 4 (36/161, 22.36%) in Kashgar prefecture. And the 3 lineages were subdivided into 11 sublineages, among which lineage 2 includes lineage 2.2.2/Asia Ancestral 1(9/73, 12.33%),lineage 2.2.1-Asia Ancestral 2(9/73, 12.33%)༌lineage 2.2.1-Asia Ancestral 3(18/73, 24.66%) and lineage 2.2.1-Modern Beijing(39/73, 53.42%).Lineage 3 includes lineage 3.2(14/52, 26.92%)and lineage 3.3(38/52, 73.08%)༌lineage 4 includes lineage 4.1(3/36, 8.33%)༌lineage 4.2(2/36, 5.66%)༌lineage 4.4.2(1/36, 2.78%)༌lineage 4.5(28/36, 77.78%) and lineage 4.8(2/36, 5.66%)༌all of which were consistent with the PCA results. Among the identified 21438 SNPs ,there are 136 markers proposed to discriminate known circulating strains. Reconstruction of a phylogenetic tree using the 136 SNPs for all 161 samples resulted in a tree with the same number of delineated clades. Based on geographical location analysis, the composition of Lineage 2 in Kashgar prefecture (45.34%) is lower than other regions level in China(54.35%-90.27%), and the composition of Lineage 3 (32.30%)is much higher than other regions level in China (0.92%-2.01%), but it is lower than the bordering Pakistan (70.40%). Conclusion In summary, M.tb clinical strains from Kashgar prefecture were identifed 3 lineages and 11 sublineages, with 136 Branch-Specific SNP. Kashgar borders countries with a high incidence of tuberculosis such as Pakistan and India, resulting in a large difference between the M.tb lineage and sublineage distribution in this region and other provinces in China. This research provides a theoretical basis for the prevention and control of tuberculosis in Xinjiang.

Global Geographical Distribution of Mycobacterium Tuberculosis Complex and the Association Between GHSI and Drug-Resistance

BackgroundMycobacterium tuberculosis complex (MTBC) is the causative agent of tuberculosis (TB). This study aims to map the global distribution of MTBC lineage and to explore the correlation between Global Health Security Index (GHSI) and drug resistance.MethodsWe mapped the global geographic distribution of MTBC lineages using the whole-genome sequencing (WGS) and verified data from the TBProfiler. The hierarchical structure was visualized in different continents and sublineages. We also performed two-dimensional twisted surface and interaction plots to explore the interactions. ResultsLineage 4 was widely distributed globally, while lineage 2 had the highest risk of developing DR-TB. We observed an interaction between GHSI and GDP on the prevalence of multidrug-resistant TB. In countries with ln(GDP per capita) ≥2.35, there was a negative association between GHSI and drug resistance. ConclusionsThere was a significantly different geographic distribution pattern of MTBC lineages in the world. The GHSI was related to the drug resistance of TB and was affected by the social-economic level.

NILAI BUDAYA PALI DAYAK NGAJU (CULTURAL VALUE AS REPRESENTED IN THE PALI OF DAYAK NGAJU)

Cultural Values as Represented in the Pali of Dayak Ngaju Community. This research aims to (1) describe the cultural values as represented in the pemali belonging to the Dayak Ngaju community towards nature, (2) describe the cultural values as represented in the pemali belonging to the Dayak Ngaju community towards the human interaction, (3) describe the cultural values as represented in the pemali belonging to the Dayak Ngaju community towards the spiritual performance. This research uses (1) recording techniques, both audio and audiovisual, (2) recording, (3) in-depth interviews, (4) literature study and documentation analysis.The results of the study show that the representation of cultural values of the pemali of the Dayak Ngaju Community in relation to nature includes: (1) the prohibition of not asking for permission when going to farming; (2) prohibition to kill animals carelessly while hunting; (3) prohibition of burning forest carelessly; (4) mapas lewu 'cleaning the village'; (5) manyanggar (‘someone should excuse me from the forest rangers’ otherwise it can cause danger and take victims); (6) prohibition of making images (statues) of animals carelessly in a forest inhabited by supernatural beings. The representations of cultural values of the pemali of the Dayak Ngaju Community concerning the human interactions, including: (1) prohibitions against marrying in the wrong lineage or the same lineage; (2) prohibition to take or interfere with the rights of others; (3) prohibition of entering another's house without permission; (4) prohibition to pick up the fallen fruit without the owner's consent; and (5) prohibition to swear/curse children carelessly.The representations of cultural values of the pemali of the Dayak Ngaju Community to the spiritual performance, including (1) the obligation to provide food to village guards (Pakanan Patahu); (2) the duty to always remember the Almighty while earning a living; (3) prohibition to laugh at broomstick; (4) prohibition of picking sawang leaves in front of the sangar patahu. Key words: value, representation, multiplier, dayak ngajuAbstrak Nilai Budaya Pali Dayak Ngaju. Tujuan Penelitian ini adalah (1) mendeskripsikan representasi nilai budaya pemali masyarakat Dayak Ngaju terhadap alam. (2) Mendeskripsikan representasi nilai budaya pemali masyarakat Dayak Ngaju terhadap interaksi sesama manusia. (3) Mendeskripsikan representasi nilai budaya pemali masyarakat Dayak Ngaju terhadap kemampuan spritual.Metode atau teknik pengumpulan data dalam penelitian ini menggunakan: (1) teknik perekaman, baik audio maupun audiovisual, (2) pencatatan, (3) wawancara yang mendalam, (4) studi kepustakaan dan analisis dokumentasi.Hasil penelitian menunjukan representasi nilai budaya pemali masyarakat Dayak Ngaju yang berhubungan dengan alam meliputi: (1) larangan tidak permisi jika hendak berladang; (2) tidak boleh membunuh binatang sembarangan saat berburu; (3) tidak boleh membakar hutan sembarangan; (4) mapas lewu ‘membersihkan Jurnal Bahasa, Sastra dan Pembelajarannya Vol 11, No 2, Oktober 2021 ISSN 2089-0117 (Print) Page 286 - 300 ISSN 2580-5932 (Online) Sugara,/ Jurnal Bahasa, Sastra dan Pembelajarannya 11 (2) 2021, 286 - 300 Jurnal Bahasa, Sastra dan Pembelajarannya ǀ 287 kampung’; (5) manyanggar ‘harus permisi dengan penjaga-penjaga hutan’ kalau tidak dapat menimbulkan bahaya dan memakan korban; (6) jangan membuat gambar (patung) hewan sembarangan di dalam hutan yang ada penunggunya.Representasi nilai budaya pemali Dayak Ngaju yang berhubungan dengan interaksi sesama manusia meliputi: (1) Tidak boleh menikah salah silsilah atau dalam satu garis keturunan yang sama; (2) tidak boleh mengambil atau mengganggu hak orang lain; (3) tidak boleh masuk rumah orang lain tanpa permisi; (4) tidak boleh mangambil buah yang jatuh tanpa izin pemiliknya; dan (5) tidak boleh menyumpahi/mengutuk anak sembarangan.Representasi nilai budaya pemali Dayak Ngaju yang berhubungan dengan kemampuan spritual adalah (1) tidak boleh tidak memberi makanan untuk penjaga kampung (Pakanan Patahu); (2) tidak boleh lupa dengan Sang Maha Kuasa saat mencari nafkah; (3) tidak boleh menertawakan sapundu; (4) tidak boleh memetik daun sawang di depan sangar patahu. Kata-kata kunci: nilai, representasi, pali, dayak ngaju