A lung-specific mutational signature enables inference of viral and bacterial respiratory niche

Exposure to different mutagens leaves distinct mutational patterns that can allow inference of pathogen replication niches. We therefore investigated whether SARS-CoV-2 mutational spectra might show lineage-specific differences, dependent on the dominant site(s) of replication and onwards transmission, and could therefore rapidly infer virulence of emergent variants of concern (VOCs). Through mutational spectrum analysis, we found a significant reduction in G>T mutations in the Omicron variant, which replicates in the upper respiratory tract (URT), compared to other lineages, which replicate in both the URT and lower respiratory tract (LRT). Mutational analysis of other viruses and bacteria indicates a robust, generalizable association of high G>T mutations with replication within the LRT. Monitoring G>T mutation rates over time, we found early separation of Omicron from Beta, Gamma and Delta, while mutational patterns in Alpha varied consistent with changes in transmission source as social restrictions were lifted. Mutational spectra may be a powerful tool to infer niches of established and emergent pathogens.Fil: Ruis, Christopher. University of Cambridge; Estados UnidosFil: Peacock, Thomas P.. Imperial College London; Reino UnidoFil: Polo Ilacqua, Luis Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Masone, Diego Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Alvarez, Maria Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Hinrichs, Angie S.. University Of California At Santa Cruz.; Estados UnidosFil: Turakhia, Yatish. University of California at San Diego; Estados UnidosFil: Cheng, Ye. University of California at San Diego; Estados UnidosFil: McBroome, Jakob. University Of California At Santa Cruz.; Estados UnidosFil: Corbett Detig, Russell. University Of California At Santa Cruz.; Estados UnidosFil: Parkhill, Julian. University of Cambridge; Reino UnidoFil: Floto, R. Andres. University of Cambridge; Reino Unid

Factors associated with dental attendance among adolescents in Santiago, Chile

BACKGROUND: Dental treatment needs are commonly unmet among adolescents. It is therefore important to clarify the determinants of poor utilization of dental services among adolescents. METHODS: A total of 9,203 Chilean students aged 12–21 years provided information on dental visits, oral health related behavior, perceived oral health status, and socio-demographic determinants. School headmasters provided information on monthly tuition and annual fees. Based on the answers provided, three outcome variables were generated to reflect whether the respondent had visited the dentist during the past year or not; whether the last dental visit was due to symptoms; and whether the responded had ever been to a dentist. Aged adjusted multivariable logistic regression models were used to assess the influence of the covariates gender; oral health related behaviors (self-reported tooth brushing frequency & smoking habits); and measures of social position (annual education expenses; paternal income; and achieved parental education) on each outcome. RESULTS: Analyses showed that students who had not attended a dentist within the past year were more likely to be male (OR = 1.3); to report infrequent tooth brushing (OR = 1.3); to have a father without income (OR = 1.8); a mother with only primary school education (OR = 1.5); and were also more likely to report a poor oral health status (OR = 2.0), just as they were more likely to attend schools with lower tuition and fees (OR = 1.4). Students who consulted a dentist because of symptoms were more likely to have a father without income (OR = 1.4); to attend schools with low economic entry barriers (OR = 1.4); and they were more likely to report a poor oral health status (OR = 2.9). Students who had never visited a dentist were more likely to report infrequent tooth brushing (OR = 1.9) and to have lower socioeconomic positions independently of the indicator used. CONCLUSION: The results demonstrate that socioeconomic and behavioral factors are independently associated with the frequency of and reasons for dental visits in this adolescent population and that self-perceived poor oral health status is strongly associated with infrequent dental visits and symptoms

Percentage Africanized and European bees by county.

<p>Percentage Africanized and European bees by county.</p

Africanized bees extend their distribution in California

<div><p>Africanized honey bees (<i>Apis mellifera</i>) arrived in the western hemisphere in the 1950s and quickly spread north reaching California in the 1990s. These bees are highly defensive and somewhat more difficult to manage for commercial purposes than the European honey bees traditionally kept. The arrival of these bees and their potentially replacing European bees over much of the state is thus of great concern. After a 25 year period of little systematic sampling, a recent small scale study found Africanized honey bees in the Bay Area of California, far north of their last recorded distribution. The purpose of the present study was to expand this study by conducting more intensive sampling of bees from across northern California. We found Africanized honey bees as far north as Napa and Sacramento. We also found Africanized bees in all counties south of these counties. Africanized honey bees were particularly abundant in parts of the central valley and Monterey. This work suggests the northern spread of Africanized honey bees may not have stopped. They may still be moving north at a slow rate, although due to the long gaps in sampling it is currently impossible to tell for certain. Future work should routinely monitor the distribution of these bees to distinguish between these two possibilities.</p></div

Probability of sampling zero AHBs for all counties sampled without AHB presence using the binomial distribution.

<p>For Yolo, for example, there was over 80% chance of sampling zero AHBs assuming AHBs are present at 2.5%. Yolo, Sutter, Placer, and Butte were sampled with insufficient depth to rule out significant AHB presence.</p

Current distribution of AHBs in California.

<p>Percentage of AHBs in each county sampled by the present study only are shown. Counties highlighted in red have been found to be inhabited by AHBs. Counties in pink had no AHBs, but had poor sampling.</p

Fine-mapping complex inversion breakpoints and investigating somatic pairing in the anopheles gambiae species complex using proximity-ligation sequencing

Chromosomal inversions are fundamental drivers of genome evolution. In the main Afrotropical malaria vector species, belonging to the Anopheles gambiae species complex, inversions play an important role in local adaptation and have a rich history of cytological study. Despite the importance and ubiquity of some chromosomal inversions across the species complex, inversion breakpoints are often challenging to map molecularly due to the presence of large repetitive regions. Here, we develop an approach that uses Hi-C sequencing data to molecularly fine-map the breakpoints of inversions. We demonstrate that this approach is robust and likely to be widely applicable for both identification and fine-mapping inversion breakpoints in species whose inversions have heretofore been challenging to characterize. We apply our method to interrogate the previously unknown inversion breakpoints of 2Rbc and 2Rd in An. coluzzii. We found that inversion breakpoints occur in large repetitive regions, and, strikingly, among three inversions analyzed, two breakpoints appear to be reused in two separate inversions. These breakpoint-adjacent regions are strongly enriched for the presence of a 30 bp satellite repeat sequence. Because low frequency inversion breakpoints are not correlated with genomic regions containing this satellite, we suggest that interrupting this particular repeat may result in arrangements with higher relative fitness. Additionally, we use heterozygous individuals to quantitatively investigate the impacts of somatic pairing in the regions immediately surrounding inversion breakpoints. Finally, we discuss important considerations for possible applications of this approach for inversion breakpoint identification in a range of organisms

A lung-specific mutational signature enables inference of viral and bacterial respiratory niche.

Exposure to different mutagens leaves distinct mutational patterns that can allow inference of pathogen replication niches. We therefore investigated whether SARS-CoV-2 mutational spectra might show lineage-specific differences, dependent on the dominant site(s) of replication and onwards transmission, and could therefore rapidly infer virulence of emergent variants of concern (VOCs). Through mutational spectrum analysis, we found a significant reduction in G&gt;T mutations in the Omicron variant, which replicates in the upper respiratory tract (URT), compared to other lineages, which replicate in both the URT and lower respiratory tract (LRT). Mutational analysis of other viruses and bacteria indicates a robust, generalizable association of high G&gt;T mutations with replication within the LRT. Monitoring G&gt;T mutation rates over time, we found early separation of Omicron from Beta, Gamma and Delta, while mutational patterns in Alpha varied consistent with changes in transmission source as social restrictions were lifted. Mutational spectra may be a powerful tool to infer niches of established and emergent pathogens

A lung-specific mutational signature enables inference of viral and bacterial respiratory niche.

Exposure to different mutagens leaves distinct mutational patterns that can allow inference of pathogen replication niches. We therefore investigated whether SARS-CoV-2 mutational spectra might show lineage-specific differences, dependent on the dominant site(s) of replication and onwards transmission, and could therefore rapidly infer virulence of emergent variants of concern (VOCs). Through mutational spectrum analysis, we found a significant reduction in G>T mutations in the Omicron variant, which replicates in the upper respiratory tract (URT), compared to other lineages, which replicate in both the URT and lower respiratory tract (LRT). Mutational analysis of other viruses and bacteria indicates a robust, generalizable association of high G>T mutations with replication within the LRT. Monitoring G>T mutation rates over time, we found early separation of Omicron from Beta, Gamma and Delta, while mutational patterns in Alpha varied consistent with changes in transmission source as social restrictions were lifted. Mutational spectra may be a powerful tool to infer niches of established and emergent pathogens