L-325 Sagebrush Habitat Mitigation Project: Final Compensation Area Monitoring Report

This document provides a review and status of activities conducted in support of the Fluor Daniel Hanford Company (Fluor), now Mission Support Alliance (MSA), Mitigation Action Plan (MAP) for Project L-325, Electrical Utility Upgrades (2007). Three plantings have been installed on a 4.5-hectare mitigation area to date. This review provides a description and chronology of events, monitoring results, and mitigative actions through fiscal year (FY) 2012. Also provided is a review of the monitoring methods, transect layout, and FY 2012 monitoring activities and results for all planting years. Planting densities and performance criteria stipulated in the MAP were aimed at a desired future condition (DFC) of 10 percent mature sagebrush (Artemisia tridentata ssp wyomingensis) cover. Current recommendations for yielding this DFC are based upon a conceptual model planting of 1000 plants/ha (400/ac) exhibiting a 60-percent survival rate after 5 monitoring years (DOE 2003). Accordingly, a DFC after 5 monitoring years would not be less than 600 plants/ha (240/ac). To date, about 8700 sagebrush plants have been grown and transplanted onto the mitigation site. Harsh site conditions and low seedling survival have resulted in an estimated 489 transplants/ha on the mitigation site, which is 111 plants/ha short of the target DFC. Despite this apparent shortcoming, 71, 91, and 24 percent of the surviving seedlings planted in FY 2007 and FY 2008 and FY 2010, respectively, showed signs of blooming in FY 2012. Blooming status may be a positive indication of future sagebrush recruitment, and is therefore a potential source for reaching the target DFC of 600 plants/ha on this mitigation site over time. Because of the difficulty establishing small transplants on this site, we propose that no additional plantings be considered for this mitigation area and to rely upon the potential recruitment by established seedlings to achieve the mitigation commitment set forth in the MAP of 600 plants/ha

Survey of Revegetated Areas on the Fitzner/Eberhardt Arid Lands Ecology Reserve: Status and Initial Monitoring Results

During 2010, the U.S. Department of Energy (DOE), Richland Operations Office removed a number of facilities and debris from the Fitzner/Eberhardt Arid Lands Ecology Reserve (ALE), which is part of the Hanford Reach National Monument (HRNM). Revegetation of disturbed sites is necessary to stabilize the soil, reduce invasion of these areas by exotic weeds, and to accelerate re-establishment of native plant communities. Seven revegetation units were identified on ALE based on soils and potential native plant communities at the site. Native seed mixes and plant material were identified for each area based on the desired plant community. Revegetation of locations affected by decommissioning of buildings and debris removal was undertaken during the winter and early spring of 2010 and 2011, respectively. This report describes both the details of planting and seeding for each of the units, describes the sampling design for monitoring, and summarizes the data collected during the first year of monitoring. In general, the revegetation efforts were successful in establishing native bunchgrasses and shrubs on most of the sites within the 7 revegetation units. Invasion of the revegetation areas by exotic annual species was minimal for most sites, but was above initial criteria in 3 areas: the Hodges Well subunit of Unit 2, and Units 6 and 7

Acoustic Telemetry Studies of Juvenile Chinook Salmon Survival at the Lower Columbia Projects in 2006

The Portland District of the U.S. Army Corps of Engineers contracted with the Pacific Northwest National Laboratory (PNNL) to conduct three studies using acoustic telemetry to estimate detection probabilities and survival of juvenile Chinook salmon at three hydropower projects on the lower Columbia River. The primary goals were to estimate detection and survival probabilities based on sampling with JSATS equipment, assess the feasibility of using JSATS for survival studies, and estimate sample sizes needed to obtain a desired level of precision in future studies. The 2006 JSATS arrays usually performed as well or better than radio telemetry arrays in the JDA and TDA tailwaters, and underperformed radio arrays in the BON tailwater, particularly in spring. Most of the probabilities of detection on at least one of all arrays in a tailwater exceeded 80% for each method, which was sufficient to provide confidence in survival estimates. The probability of detection on one of three arrays includes survival and detection probabilities because fish may die or pass all three arrays undetected but alive

Survival of Juvenile Chinook Salmon Passing the Bonneville Dam Spillway in 2007

The U.S. Army Corps of Engineers Portland District (CENWP) funds numerous evaluations of fish passage and survival on the Columbia River. In 2007, the CENWP asked Pacific Northwest National Laboratory to conduct an acoustic telemetry study to estimate the survival of juvenile Chinook salmon passing the spillway at Bonneville Dam. This report documents the study results which are intended to be used to improve the conditions juvenile anadromous fish experience when passing through the dams that the Corps operates on the river

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16–20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement

Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Background The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, Rt, for the two incidence estimates. Findings From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the Rt of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, Rt fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

A first update on mapping the human genetic architecture of COVID-19

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