The Effect of Site Characteristics on the Reproductive Output of Lesser Celandine (Ranunculus ficaria)

Ranunculus ficaria L., an ephemeral perennial invasive plant brought over from Europe, is becoming widespread throughout the Northeastern United States. This herbaceous buttercup is able to create extensive dense mats that limit native species growth. Taking advantage of an early growing season and rapid reproduction rates, this species can create dense monocultures, which threatens native communities and ecosystems. Elimination of native spring ephemerals results in decreased biodiversity. A better understanding of how R. ficaria responds to site characteristics is needed to prioritize management efforts toward high-risk sites.Ranunculus ficaria abundance and reproductive output (seed, bulbil and tuber production rates) were examined in plots spanning a disturbance gradient away from a river. Site characteristics (PAR, aspect, soil pH, soil moisture, texture and nutrient content) were investigated to examine their role in plant performance. I hypothesized that soil characteristics (pH and nutrient availability) drive R. ficaria plant performance; specifically I expected higher biomass and reproductive output to be associated with higher soil pH. I also expected reproductive output and R. ficaria biomass would be highest in moist floodplain at intermediate distances from rivers.Many soil nutrients and characteristics were significantly related to biomass and reproductive output; specifically phosphorus, calcium and LTI (Lime Test Index) all showed significantly positive relationships with plant biomass and bulbil counts, while soil pH was significantly positively related to biomass. Bulbil and tuber counts were significantly higher in soils of high percent silt. These findings suggest that soil characteristics (pH, texture) and nutrients (P, Ca) are strongly linked to plant performance, supporting my hypothesis. Reproductive output and R. ficaria biomass were not significantly greater at intermediate distances from rivers, in contrast to my hypothesis. A plant performance model was generated using object-based image analysis with the aim of creating an accurate classification of sites in terms of suitability for R. ficaria performance. A large scale field survey was used to assess model predictions, which were found be 68 % accurate. Overall, this study was able to expand on the current limited understanding of R. ficaria, which can prove helpful in aiding management to reduce population size and spread

Soil Characteristics Drive Ficaria verna Abundance and Reproductive Output

Lesser celandine (Ficaria verna Huds.), an invasive plant from Europe, is becoming widespread in river valleys throughout the northeastern United States and the Pacific Northwest. Its high rate of asexual bulbil and tuber production creates dense infestations threatening native spring ephemerals. Ficaria verna abundance and reproductive output (seeds, bulbils, and tubers) were examined in invaded transects spanning a disturbance gradient away from a river. Site characteristics (photosynthetically active radiation [PAR], soil pH, moisture, texture, and nutrients) were quantified to examine their roles in plant abundance and reproduction. A larger-scale study examined random transects not specifically chosen based on F. verna infestations. Soil characteristics and slope were hypothesized to drive F. verna abundance and reproduction; we also hypothesized that reproductive output and biomass would be highest at intermediate distances from rivers, where disturbances are infrequent. Ficaria verna abundance and reproductive output varied considerably by site; soil characteristics, rather than landscape placement, appeared to drive plant abundance and reproduction. Lower percent sand was associated with significantly higher F. verna stem density and bulbil and tuber production. CEC was significantly negatively related to F. verna biomass and tuber counts. In the larger-scale survey, slope and PAR were significantly negatively related to F. verna presence and percent cover, respectively. Overall, these findings suggest that soil texture and slope can help explain higher abundance and reproductive outputs. However, reproductive output and biomass were not significantly greater at intermediate distances, contrary to expectations. We did not observe any seed production in any of the plots, although we did see a few plants with seeds outside our study area in the second year, demonstrating a near-complete reliance on asexual reproduction in these populations. This study expands on the current limited understanding of F. verna and can help management by identifying areas likely to support dense infestations

Soil Characteristics Drive Ficaria verna Abundance and Reproductive Output

Lesser celandine (Ficaria verna Huds.), an invasive plant from Europe, is becoming widespread in river valleys throughout the northeastern United States and the Pacific Northwest. Its high rate of asexual bulbil and tuber production creates dense infestations threatening native spring ephemerals. Ficaria verna abundance and reproductive output (seeds, bulbils, and tubers) were examined in invaded transects spanning a disturbance gradient away from a river. Site characteristics (photosynthetically active radiation [PAR], soil pH, moisture, texture, and nutrients) were quantified to examine their roles in plant abundance and reproduction. A larger-scale study examined random transects not specifically chosen based on F. verna infestations. Soil characteristics and slope were hypothesized to drive F. verna abundance and reproduction; we also hypothesized that reproductive output and biomass would be highest at intermediate distances from rivers, where disturbances are infrequent. Ficaria verna abundance and reproductive output varied considerably by site; soil characteristics, rather than landscape placement, appeared to drive plant abundance and reproduction. Lower percent sand was associated with significantly higher F. verna stem density and bulbil and tuber production. CEC was significantly negatively related to F. verna biomass and tuber counts. In the larger-scale survey, slope and PAR were significantly negatively related to F. verna presence and percent cover, respectively. Overall, these findings suggest that soil texture and slope can help explain higher abundance and reproductive outputs. However, reproductive output and biomass were not significantly greater at intermediate distances, contrary to expectations. We did not observe any seed production in any of the plots, although we did see a few plants with seeds outside our study area in the second year, demonstrating a near-complete reliance on asexual reproduction in these populations. This study expands on the current limited understanding of F. verna and can help management by identifying areas likely to support dense infestations

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

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 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

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

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant