scholarly journals SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021

2021 ◽  
Vol 7 (11) ◽  
Author(s):  
Muhammad Bilal Sarwar ◽  
Muhammad Yasir ◽  
Nabil-Fareed Alikhan ◽  
Nadeem Afzal ◽  
Leonardo de Oliveira Martins ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Third Wave ◽  
Diagnostic Pcr ◽  
Travel History ◽  
Recent Transmission ◽  
Depth Analysis ◽  
Show Evidence ◽  
Alpha Variant ◽  
Surrounding Areas ◽  
The Uk

The SARS-CoV-2 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Indian sub-continent. Pakistan has one of the world’s largest populations, of over 200 million people and is experiencing a severe third wave of infections caused by SARS-CoV-2 that began in March 2021. In Pakistan, during the third wave until now only 12 SARS-CoV-2 genomes have been collected and among these nine are from Islamabad. This highlights the need for more genome sequencing to allow surveillance of variants in circulation. In fact, more genomes are available among travellers with a travel history from Pakistan, than from within the country itself. We thus aimed to provide a snapshot assessment of circulating lineages in Lahore and surrounding areas with a combined population of 11.1 million. Within a week of April 2021, 102 samples were sequenced. The samples were randomly collected from two hospitals with a diagnostic PCR cutoff value of less than 25 cycles. Analysis of the lineages shows that the Alpha variant of concern (first identified in the UK) dominates, accounting for 97.9 % (97/99) of cases, with the Beta variant of concern (first identified in South Africa) accounting for 2.0 % (2/99) of cases. No other lineages were observed. In depth analysis of the Alpha lineages indicated multiple separate introductions and subsequent establishment within the region. Eight samples were identical to genomes observed in Europe (seven UK, one Switzerland), indicating recent transmission. Genomes of other samples show evidence that these have evolved, indicating sustained transmission over a period of time either within Pakistan or other countries with low-density genome sequencing. Vaccines remain effective against Alpha, however, the low level of Beta against which some vaccines are less effective demonstrates the requirement for continued prospective genomic surveillance.

scholarly journals SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021

2021 ◽  
Author(s):  
Muhammad Bilal Sarwar ◽  
Muhammad Yasir ◽  
Nabil-Fareed Alikhan ◽  
Nadeem Afzal ◽  
Leonardo de Oliveria Martins ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Third Wave ◽  
Travel History ◽  
Recent Transmission ◽  
Depth Analysis ◽  
Show Evidence ◽  
Polymerase Chain ◽  
Alpha Variant ◽  
Surrounding Areas ◽  
The Uk

The SARS-CoV-2 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Indian sub-continent. Pakistan has one of the worlds largest populations, of over 200 million people and is experiencing a severe third wave of infections caused by SARS-CoV-2 beginning in March 2021. Currently very few SARS-CoV-2 genomes collected in Pakistan are available, with just 12 covering the third wave, 9 of which are from Islamabad. This highlights the need for more genome sequencing to allow surveillance of variants in circulation. In fact more genomes are available for travellers with a travel history from Pakistan, than from within the country itself. For an understanding of the circulating variants in Lahore and surrounding areas with a combined population of 11.1 million, 102 samples were sequenced, covering one week period from April 2021. The samples were randomly chosen from 2 hospitals with a diagnostic polymerase chain reaction (PCR) cutoff value of less than 25 cycles. Analysis of the lineages shows that B.1.1.7 (first identified in the UK, Alpha variant) dominates, accounting for 97.9% (97/99) of cases, with B.1.351 (first identified in South Africa, Beta variant) accounting for 2.0% (2/99) of cases. No other lineages were observed. In depth analysis of the B.1.1.7 lineages indicates multiple separate introductions and subsequent establishment within the region. Eight samples were identical to genomes observed in Europe (7 UK, 1 Switzerland), indicating recent transmission. Genomes of other samples show evidence that these have evolved, indicating sustained transmission over a period of time either within Pakistan or other countries with low density genome sequencing. Vaccines remain effective against B.1.1.7, however the low level of B.1.351 against which some vaccines are less effective demonstrates the requirement for continued prospective genomic surveillance.

scholarly journals Cryptic speciation in the Warbling Vireo (Vireo gilvus)

The Auk ◽  
2021 ◽  
Author(s):  
Scott F Lovell ◽  
M Ross Lein ◽  
Sean M Rogers
Keyword(s):  
Contact Zone ◽  
Nuclear Dna ◽  
Biological Species ◽  
Valid Species ◽  
Migration Routes ◽  
Dna Evidence ◽  
Show Evidence ◽  
And Migration ◽  
Surrounding Areas ◽  
Taxonomic Groups

Abstract Eastern (Vireo gilvus gilvus) and western (V. g. swainsoni) forms of the Warbling Vireo have essentially allopatric breeding ranges across north-central North America, but come into contact in central Alberta, Canada. In 1986, Jon Barlow presented preliminary morphological and song evidence suggesting that the Warbling Vireo complex might comprise more than one valid species. However, to date, Barlow’s suggestion is supported by only limited DNA evidence, demonstration of molt and migration differences between the taxa, and anecdotal accounts of differences in song, morphology, plumage, and ecology. We analyzed variation in both mitochondrial and nuclear DNA in birds from Alberta and surrounding areas to determine the levels of genetic differentiation and hybridization occurring in the contact zone, and whether the two taxa warrant recognition as separate biological species. Our analyses reveal that Warbling Vireos in Alberta and the surrounding areas are separated into two well-defined, genetically differentiated, and monophyletic clades corresponding to previously recognized taxonomic groups. The two taxa come into contact in a narrow (~85 km) zone in Barrhead County, northwest of Edmonton, Alberta. They show evidence of limited hybridization. The distinct genetic differences are maintained in the contact zone, where individuals of the two taxa may occupy neighboring territories. Differences in spring arrival dates, molt schedules, and migration routes indicate that a migratory divide may play an important role in reproductive isolation. We suggest that the two taxa are distinct cryptic species: an eastern form, Vireo gilvus, and a western form, Vireo swainsoni.

scholarly journals Resituating the political in cultural intermediary work: Charity sector public relations and communication

2021 ◽  
pp. 136754942199423
Author(s):  
Anne M Cronin ◽  
Lee Edwards
Keyword(s):  
Public Relations ◽  
Power Relations ◽  
Party Politics ◽  
The Political ◽  
Depth Analysis ◽  
Cultural Intermediary ◽  
Cultural Intermediaries ◽  
The Uk ◽  
The Relationship

Drawing on a case study of public relations in the UK charity sector, this article argues that cultural intermediary research urgently requires a more sustained focus on politics and the political understood as power relations, party politics and political projects such as marketization and neoliberalism. While wide-ranging research has analysed how cultural intermediaries mediate the relationship between culture and economy, this has been at the expense of an in-depth analysis of the political. Using our case study as a prompt, we highlight the diversity of ways that the political impacts cultural intermediary work and that cultural intermediary work may impact the political. We reveal the tensions that underpin practice as a result of the interactions between culture, the economy and politics, and show that the tighter the engagement of cultural intermediation with the political sphere, the more tensions must be negotiated and the more compromised practitioners may feel.

scholarly journals Ectopic pregnancy: exploration of its global research architecture using density-equalising mapping and socioeconomic benchmarks

BMJ Open ◽  
2017 ◽  
Vol 7 (10) ◽  
pp. e018394 ◽  
Author(s):  
Dörthe Brüggmann ◽  
Jana Kollascheck ◽  
David Quarcoo ◽  
Michael H Bendels ◽  
Doris Klingelhöfer ◽  
...  
Keyword(s):  
Ectopic Pregnancy ◽  
Gdp Per Capita ◽  
Related Research ◽  
Depth Analysis ◽  
The Usa ◽  
Per Capita ◽  
The Uk ◽  
Research Architecture ◽  
Country Specific ◽  
Global Research

ObjectiveAbout 2% of all pregnancies are complicated by the implantation of the zygote outside the uterine cavity and termed ectopic pregnancy. Whereas a multitude of guidelines exists and related research is constantly growing, no thorough assessment of the global research architecture has been performed yet. Hence, we aim to assess the associated scientific activities in relation to geographical and chronological developments, existing research networks and socioeconomic parameters.DesignRetrospective, descriptive study.SettingOn the basis of the NewQIS platform, scientometric methods were combined with novel visualising techniques such as density-equalising mapping to assess the scientific output on ectopic pregnancy. Using the Web of Science, we identified all related entries from 1900 to 2012.Results8040 publications were analysed. The USA and the UK were dominating the field in regard to overall research activity (2612 and 723 publications), overall citation numbers and country-specific H-Indices (US: 80, UK: 42). Comparison to economic power of the most productive countries demonstrated that Israel invested more resources in ectopic pregnancy-related research than other nations (853.41 ectopic pregnancy-specific publications per 1000 billlion US$ gross domestic product (GDP)), followed by the UK (269.97). Relation to the GDP per capita index revealed 49.3 ectopic pregnancy-specific publications per US$1000 GDP per capita for the USA in contrast to 17.31 for the UK. Semiqualitative indices such as country-specific citation rates ranked Switzerland first (24.7 citations per ectopic pregnancy-specific publication), followed by the Scandinavian countries Finland and Sweden. Low-income countries did not exhibit significant research activities.ConclusionsThis is the first in-depth analysis of global ectopic pregnancy research since 1900. It offers unique insights into the global scientific landscape. Besides the USA and the UK, Scandinavian countries and Switzerland can also be regarded as leading nations with regard to their relative socioeconomic input.

scholarly journals Young relicts and old relicts: a novel palaeoendemic vertebrate from the Australian Central Uplands

2016 ◽  
Vol 3 (10) ◽  
pp. 160018 ◽  
Author(s):  
Paul M. Oliver ◽  
Peter J. McDonald
Keyword(s):  
Late Miocene ◽  
Arid Zone ◽  
Dominant Role ◽  
Morphological Data ◽  
New Taxon ◽  
Isolated Populations ◽  
Show Evidence ◽  
Molecular Phylogenetic ◽  
Surrounding Areas ◽  
Close Relatives

Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus Oedura from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected Oedura cincta has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the early Pliocene. A new taxon (described herein) diverged from all extant Oedura much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including Oedura cincta ), gene flow with other parts of Australia probably occurred until at least the very late Miocene or Pliocene. There are, however, a small number of palaeoendemic taxa—often ecologically specialized forms—that show evidence of having persisted since earlier intensification of aridity in the late Miocene.

scholarly journals Investigation of Arctic ozone depletion sampled over midlatitudes during the Egrett Campaign of spring/summer 2000

2004 ◽  
Vol 4 (1) ◽  
pp. 141-168 ◽  
Author(s):  
D. E. M. Ross ◽  
J. A. Pyle ◽  
N. R. P. Harris ◽  
J. D. McIntyre ◽  
G. A. Millard ◽  
...  
Keyword(s):  
Ozone Depletion ◽  
Lower Stratosphere ◽  
Transport Model ◽  
Chemical Transport Model ◽  
Middle Latitudes ◽  
Halogen Chemistry ◽  
Show Evidence ◽  
Research Aircraft ◽  
Chemical Cycle ◽  
The Uk

Abstract. A unique halocarbon dataset has been obtained using the Australian high altitude research aircraft, the Grob G520T Egrett, during May–June 2000 with GC instrument (DIRAC), which has been previously deployed on balloon platforms. The halocarbon data generally shows a good anticorrelation with ozone data obtained simultaneously from commercial sensors. On 5 June 2000, at 380 K, the Egrett entered a high latitude tongue of air over the UK CFC-11 and O3 data obtained on the flight show evidence of this feature. The dataset has been used, in conjunction with a 3D chemical transport model, to infer ozone depletion encountered in the midlatitude lower stratosphere during the flight. We calculate that ozone is depleted by 20% relative to its winter value in the higher latitude airmass. A suite of ozone loss tracers in the model have been used to track ozone depletion according to location relative to the vortex and chemical cycle responsible. The model, initialised on 9 December, indicates that 50% of the total chemical ozone destruction encountered in June in the middle latitudes occurred between the 90–70° N equivalent latitude band and that 70% was due to halogen chemistry.

scholarly journals Transmission of Multidrug/Rifampicin-Resistant Mycobacterium Tuberculosis in Chongqing, China: A Retrospective Observational Study Using Whole-Genome Sequencing

2021 ◽  
Author(s):  
Bing Zhao ◽  
Chunfa Liu ◽  
Jiale Fan ◽  
Aijing Ma ◽  
Wencong He ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Resistance Mutations ◽  
Treatment Information ◽  
Recent Transmission ◽  
Drugs Analysis ◽  
Lineage 2 ◽  
And Cluster Analysis

Abstract Background: Multidrug/rifampicin-resistant tuberculosis (MDR/RR-TB) is a global barrel for ‘Stop TB plan’. China has the second highest MDR/RR-TB burden in whole world wide. Understanding the transmission dynamic is facilitated for disease control. Methods: Whole genome sequencing (WGS) data from patients of Chongqing tuberculosis control institute were used for phylogenetic classifications, resistance predictions, and cluster analysis as indicator for recent transmission (RT). Factors associated with MDR/RR-TB were defined by a logistic regression model. Results: A total of 223 cases of MDR/RR-TB were recorded between Jan 1, 2018 and Dec 31, 2020, and 200 cases obtained relevant treatment information. The patients who are older than 55 year old were more likely to suffering from death. 178 MDR/RR strains were obtained WGS data, 152 were classified as lineage 2 strains. 80 (44.9%, 80 of 178) strains were in 20 genomic clusters that differed by 12 or fewer single nucleotide polymorphisms (SNPs), indicating RT. Patients who were infected with lineage 2 strains is a significant factor driving the epidemic towards MDR/RR-TB. Resistance mutations of first-line tuberculosis drugs analysis found that 79 (98.8%) of all 80 strains defined as RT have same mutations among each clusters totally. 55% (44 of 80) of the MDR/RR-TB strains accumulated additional drug resistance mutations along the transmission chain, especially fluoroquinolones (FQs) (63.6%, 28 of 44). Conclusions: The age is the most significant factor that causes death of MDR/RR-TB patients. RT of MDR/RR strains is not only drove the MDR/RR-TB epidemic, but also accumulated more serious resistance along the transmission chains.

scholarly journals Effect of Delta variant on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK

2021 ◽  
Author(s):  
Koen B. Pouwels ◽  
Emma Pritchard ◽  
Philippa C. Matthews ◽  
Nicole Stoesser ◽  
David W. Eyre ◽  
...  
Keyword(s):  
Natural Infection ◽  
Absolute Difference ◽  
Community Based ◽  
Symptomatic Infection ◽  
The United Kingdom ◽  
Viral Burden ◽  
Alpha Variant ◽  
The Uk ◽  
Prior Infection ◽  
Similar Peak

AbstractThe effectiveness of the BNT162b2 and ChAdOx1 vaccines against new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections requires continuous re-evaluation, given the increasingly dominant B.1.617.2 (Delta) variant. In this study, we investigated the effectiveness of these vaccines in a large, community-based survey of randomly selected households across the United Kingdom. We found that the effectiveness of BNT162b2 and ChAdOx1 against infections (new polymerase chain reaction (PCR)-positive cases) with symptoms or high viral burden is reduced with the B.1.617.2 variant (absolute difference of 10–13% for BNT162b2 and 16% for ChAdOx1) compared to the B.1.1.7 (Alpha) variant. The effectiveness of two doses remains at least as great as protection afforded by prior natural infection. The dynamics of immunity after second doses differed significantly between BNT162b2 and ChAdOx1, with greater initial effectiveness against new PCR-positive cases but faster declines in protection against high viral burden and symptomatic infection with BNT162b2. There was no evidence that effectiveness varied by dosing interval, but protection was higher in vaccinated individuals after a prior infection and in younger adults. With B.1.617.2, infections occurring after two vaccinations had similar peak viral burden as those in unvaccinated individuals. SARS-CoV-2 vaccination still reduces new infections, but effectiveness and attenuation of peak viral burden are reduced with B.1.617.2.

scholarly journals Genomic analysis of an outbreak of bovine tuberculosis in a man-made multi-host species system: a call for action on wildlife in Brazil

2021 ◽  
Author(s):  
Daiane A. R. Lima ◽  
Cristina K. Zimpel ◽  
José Salvatore Patané ◽  
Taiana T. Silva-Pereira ◽  
Rodrigo N. Etges ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Genome Sequencing ◽  
Mycobacterium Bovis ◽  
Bovine Tuberculosis ◽  
Genomic Analysis ◽  
Whole Genome ◽  
System A ◽  
Recent Transmission ◽  
And Control ◽  
Tuberculin Tests

We report on a 15-year-long outbreak of bovine tuberculosis (bTB) in wildlife from a Brazilian safari park. A timeline of diagnostic events and whole-genome sequencing (WGS) of 21 Mycobacterium bovis isolates from deer and llamas were analyzed. Accordingly, from 2003 to 2018, at least 16 animals, from 8 species, died due to TB, which is likely an underestimated number. In three occasions since 2013, the deer presented positive tuberculin tests, leading to the park closure and culling of all deer. WGS indicated that multiple M. bovis strains were circulating, with at least three founding introductions since the park inauguration in 1977. Recent transmission events between nearby farms and the park were not found based on WGS. Lastly, by discussing socio-economic and environmental factors escaping current regulatory gaps that were determinant of this outbreak, we pledge for the development of a plan to report and control bTB in wildlife in Brazil.

scholarly journals Quality Assessment of Some Freshwater Resources Located in Bucharest and Surrounding Areas. III. Case Study: Trophic Status Assessment of Mogosoaia, Herastrau and Pantelimon Lakes

2019 ◽  
Vol 70 (11) ◽  
pp. 3778-3782
Author(s):  
Violeta Monica Radu ◽  
Petra Ionescu ◽  
Gyorgy Deak ◽  
Alexandru Anton Ivanov ◽  
Elena Diacu ◽  
...  
Keyword(s):  
Quality Assessment ◽  
Trophic Status ◽  
Phosphorus Content ◽  
Anthropogenic Activities ◽  
Quality Parameters ◽  
Nitrogen And Phosphorus ◽  
High Accumulation ◽  
Freshwater Resources ◽  
Depth Analysis ◽  
Surrounding Areas

The aim of this paper is the evaluation of the trophic status of three lakes riparian to the Colentina River, namely Mogosoaia, Herastrau, Pantelimon, as Part III of an extended study on evaluation of the freshwater resources quality in Bucharest and surrounding areas [1, 2], supplementing the general quality assessment based on indices and indexes presented in Part I with a more in depth analysis of nutrient speciation and partitioning between water and upper sedimentary layers. Water and sediment samples were taken from the inlet and outlet areas of each lake in two sampling campaigns in July 2016 and September 2016. Some of the nutrient related water quality parameters presented in Part I of this series have been used here, together with the analysis of total nitrogen and total phosphorus content in sediments, to assess the general trophic state of the lakes and to highlight the relationships between the nitrogen and the phosphorus content from water and sediments.The studied lakes were found to be eutrophic, Mogosoaia and Pantelimon being in the most advanced state. A significant amount of nitrogen and phosphorus was detected in all sediments analysed, constituting a high accumulation of nutrients from anthropogenic activities. Actions to improve local sanitation infrastructure and to prevent anaerobic leakage of nutrients from sedimentary deposits are recommended.

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