North American Variants Research Articles

DEVELOPMENT OF A RAPID SNP PCR ASSAY TO DIFFERENTIATE BETWEEN EUROPEAN AND NORTH AMERICAN HAPLOTYPES OF ECHINOCOCCUS MULTILOCULARIS.

Herein we describe a single nucleotide polymorphism-specific polymerase chain reaction (PCR) assay to rapidly detect and differentiate variants belonging to the European and North American lineages of Echinococcus multilocularis in clinical samples. This is an extremely relevant and applicable test in North America because the range of E. multilocularis continues to expand across the continent and because of a rise in prevalence in wildlife, domestic animals, and humans. The endemic North American (NA) and introduced European (EU) variants are believed to have different pathogenic potentials, with the EU variants being more infective and pathogenic than the NA variants. The rise of the EU variants of E. multilocularis increases the risk of spillover from wildlife to humans because of its increased potential for infectivity. Current PCR-based diagnostics can detect E. multilocularis deoxyribonucleic acid (DNA), but DNA sequencing is required to identify the specific variant. Our assay provides a straightforward conventional PCR method to differentiate the NA and EU variants, and we suggest this same approach could be used for the diagnosis of other parasites or variants that are genetically very similar. As surveillance continues for E. multilocularis across North America, identifying the different genetic variants from different geographic regions will become essential to understanding the current epidemiological shift that the parasite is experiencing, as well as informing public health decisions in affected areas.

Identification of HPV16 Lineages in South African and Mozambican Women with Normal and Abnormal Cervical Cytology.

Human papillomavirus 16 (HPV16) is an oncogenic virus responsible for the majority of invasive cervical cancer cases worldwide. Due to genetic modifications, some variants are more oncogenic than others. We analysed the HPV16 phylogeny in HPV16-positive cervical Desoxyribonucleic Acid (DNA) samples collected from South African and Mozambican women to detect the circulating lineages. Polymerase chain reaction (PCR) amplification of the long control region (LCR) and 300 nucleotides of the E6 region was performed using HPV16-specific primers on HPV16-positive cervical samples collected in women from South Africa and Mozambique. HPV16 sequences were obtained through Next Generation Sequencing (NGS) methods. Geneious prime and MEGA 11 software were used to align the sequences to 16 HPV16 reference sequences, gathering the A, B, C, and D lineages and generating the phylogenetic tree. Single nucleotide polymorphisms (SNPs) in the LCR and E6 regions were analysed and the phylogenetic tree was generated using Geneious Prime software. Fifty-eight sequences were analysed. Of these sequences, 79% (46/58) were from women who had abnormal cervical cytology. Fifteen SNPs in the LCR and eight in the E6 region were found to be the most common in all sequences. The phylogenetic analysis determined that 45% of the isolates belonged to the A1 sublineage (European variant), 34% belonged to the C1 sublineage (African 1 variant), 16% belonged to the B1 and B2 sublineage (African 2 variant), two isolates belonged to the D1-3 sublineages (Asian-American variant), and one to the North American variant. The African and European HPV16 variants were the most common circulating lineages in South African and Mozambican women. A high-grade squamous intraepithelial lesion (HSIL) was the most common cervical abnormality observed and linked to European and African lineages. These findings may contribute to understanding molecular HPV16 epidemiology in South Africa and Mozambique.

Descriptive epidemiology of variants of infectious salmon anaemia virus in four Atlantic salmon farms in Newfoundland and Labrador, Canada.

An incursion of infectious salmon anaemia virus (ISAV) was detected in 2020 in southern Newfoundland, Canada. This resulted in an outbreak affecting four marine farms stocking Atlantic salmon (Salmo salar L.) vaccinated against ISAV. This study provides the first description of epidemiologic characteristics of an ISAV outbreak in 2020 and 2021, and detected ISAV variants at the population level. Fish kidneys were screened for ISAV by real-time RT-PCR and non-negative samples were submitted for genotyping and further diagnostic testing. Nine distinct ISAV variants were identified: five European and three North American (NA) HPRΔ ISAV, and one NA-HPR0 ISAV variant. A notable finding was the concurrent detection of both an HPR0 and an HPRΔ ISAV variant in one individual fish. In two farms, both European and NA variants were simultaneously detected, while in the other two farms either NA or European variants were identified, but not both together. Generally, mortality increases followed rises in ISAV prevalence and cycle threshold values on RT-PCR decreased with time. Epidemiologic descriptions of ISAV outbreaks in Atlantic Canada contributes to the understanding of local disease dynamics and identification of changes thereof. Such insights are essential for the strengthening of disease management plans.

Degradation of p53 by HPV16-E6 variants isolated from cervical cancer specimens of Moroccan women.

Cervical cancer is the second most diagnosed cancer in Moroccan women. The main etiological factor for developing cervical cancer is the persistent infection with HPV16. Genetic studies have reported the occurrence of amino acid variations within the E6 oncoprotein that promotes host cell transformation by targeting p53 for degradation. To verify the biological effects of E6 polymorphisms towards p53 degradation, HPV16-E6 prototype and 7 variants isolated from cervical cancer biopsies of Moroccan women were evaluated for their activities by transient expression assays using pcDNA3.1-E6 constructs in C33A cell line. Expression of E6 genes in transfected cells was detected with reverse transcription PCR (RT-PCR), then, p53 levels were evaluated by western blot analysis. Significant dissimilarities in p53 degradation activities of HPV16-E6 prototype and intratypic variants were noticed. As compared to the prototype, the highest p53 degradation were exhibited by the African variants Af2-a/r, Af1-d/G295 and Af2-a/G285 (p<0.001), followed by the European variants E- C442/G350 and E-G350/r (p<0.01), then, the North American variant NA1-b/r (p<0.05). The inter-variant differences were statistically significant between Af2-a/r variant and the North American variants NA1-b/r and NA1 (p<0.05). Thus, the Af2-a/r variant was significantly more active in degrading p53 in our in vitro experiments (p<0.0001). Our findings support the fact that HPV16-E6 variations have a biological impact on degrading p53, and so, represent a significant carcinogenic potential for developing cervical cancer.

Emergence of European and North American mutant variants of SARS-CoV-2 in South-East Asia.

The SARS‐CoV‐2 coronavirus is responsible for the current COVID‐19 pandemic, with an ongoing toll of over 5 million infections and 333 thousand deaths worldwide within the first 5 months. Insight into the phylodynamics and mutation variants of this virus is vital to understanding the nature of its spread in different climate conditions. The incidence rate of COVID‐19 is increasing at an alarming pace within subtropical South‐East Asian nations with high temperatures and humidity. To understand this spread, we analysed 444 genome sequences of SARS‐CoV‐2 available on the GISAID platform from six South‐East Asian countries. Multiple sequence alignments and maximum‐likelihood phylogenetic analyses were performed to analyse and characterize the non‐synonymous (NS) mutant variants circulating in this region. Global mutation distribution analysis showed that the majority of the mutations found in this region are also prevalent in Europe and North America, and the concurrent presence of these mutations at a high frequency in other countries indicates possible transmission routes. Unique spike protein and non‐structural protein mutations were observed circulating within confined area of a given country. We divided the circulating viral strains into four major groups and three subgroups on the basis of the most frequent NS mutations. Strains with a unique set of four co‐evolving mutations were found to be circulating at a high frequency within India, specifically. Group 2 strains characterized by two co‐evolving NS mutants which alter in RdRp (P323L) and spike (S) protein (D614G) were found to be common in Europe and North America. These European and North American variants have rapidly emerged as dominant strains within South‐East Asia, increasing from a 0% prevalence in January to an 81% by May 2020. These variants may have an evolutionary advantage over their ancestral types and could present a large threat to South‐East Asia for the coming winter.

Mammalian pathogenicity and transmissibility of a reassortant Eurasian avian-like A(H1N1v) influenza virus associated with human infection in China (2015)

Swine-origin (variant) H1 influenza A viruses associated with numerous human infections in North America in recent years have been extensively studied in vitro and in mammalian models to determine their pandemic potential. However, limited information is available on Eurasian avian-like lineage variant H1 influenza viruses. In 2015, A/Hunan/42443/2015 virus was isolated from a child in China with a severe infection. Molecular analysis revealed that this virus possessed several key virulence and human adaptation markers. Similar to what was previously observed in C57BL/6J mice, we report here that in the BALB/c mouse model, A/Hunan/42443/2015 virus caused more severe morbidity and higher mortality than did North American variant H1 virus isolates. Furthermore, the virus efficiently replicated throughout the respiratory tract of ferrets and exhibited a capacity for transmission in this model, underscoring the need to monitor zoonotic viruses that cross the species barrier as they continue to pose a pandemic threat.

Identification of human papillomavirus type 16 variants circulating in the Calabria region by sequencing and phylogenetic analysis of HPV16 from cervical smears

Sequence analysis of HPV16 isolates reveals the presence of genome variants with characteristic mutations. The HPV16 variants have different geographical distribution and diverge into four phylogenetic lineages (A, B, C and D) and 16 sub-lineages: A1, A2, A3 (previously known as European variants), A4 (Asian variant), B1, B2, B3, B4, C1, C2, C3, and C4 (African variants), D1 (North-American variant), D2, D3 (Asian-American variants) and D4. Population studies showed that infections with viruses belonging to specific HPV16 sublineages confer different risks of viral persistence and cancer. In this study, 39 HPV16-positive cervical smears from European women living in Calabria (Italy) were analyzed for the presence of HPV16 variants. Cervical DNA extracts were processed by PCR to amplify L1, the Long Control Region (LCR), E6 and E7, which were sequenced. The sequences were concatenated and the 3169 nucleotides long fragments were characterized by BLAST and phylogenetic analysis. A total of 96 Single Nucleotide Polymorphism (SNPs) were detected, 29 of which mapping in the L1, 45 in the LCR, 15 in the E6 and 7 in the E7. The most common SNP was the T350G (29/39 samples, 74.4%), causing the L83 V amino acid change in the E6. Most of the HPV16 isolates (89.7%) had 99% of nucleotide (nt) identity to members of the A1 and A2 sublineages, while 4 isolates had 99% nt identity to members of the B2, B4, C1 and D4 sublineages. In conclusion, viruses belonging to the A1, A2, B2, B4, C1 and D4 HPV16 sublineages were found to circulate in the Calabria region.

Isolation of a Bohle-like iridovirus from boreal toads housed within a cosmopolitan aquarium collection.

A captive 'survival assurance' population of 56 endangered boreal toads Anaxyrus boreas boreas, housed within a cosmopolitan collection of amphibians originating from Southeast Asia and other locations, experienced high mortality (91%) in April to July 2010. Histological examination demonstrated lesions consistent with ranaviral disease, including multicentric necrosis of skin, kidney, liver, spleen, and hematopoietic tissue, vasculitis, and myriad basophilic intracytoplasmic inclusion bodies. Initial confirmation of ranavirus infection was made by Taqman real-time PCR analysis of a portion of the major capsid protein (MCP) gene and detection of iridovirus-like particles by transmission electron microscopy. Preliminary DNA sequence analysis of the MCP, DNA polymerase, and neurofilament protein (NFP) genes demonstrated highest identity with Bohle iridovirus (BIV). A virus, tentatively designated zoo ranavirus (ZRV), was subsequently isolated, and viral protein profiles, restriction fragment length polymorphism analysis, and next generation DNA sequencing were performed. Comparison of a concatenated set of 4 ZRV genes, for which BIV sequence data are available, with sequence data from representative ranaviruses confirmed that ZRV was most similar to BIV. This is the first report of a BIV-like agent outside of Australia. However, it is not clear whether ZRV is a novel North American variant of BIV or whether it was acquired by exposure to amphibians co-inhabiting the same facility and originating from different geographic locations. Lastly, several surviving toads remained PCR-positive 10 wk after the conclusion of the outbreak. This finding has implications for the management of amphibians destined for use in reintroduction programs, as their release may inadvertently lead to viral dissemination.

HPV16 E6 variants: Frequency, association with HPV types and in silico analysis of the identified novel variants

High-risk human papillomavirus (HPV) types, specifically HPV 16 E6 variants are involved in viral persistence and the development of cervical lesions. India contributes to 1/3rd of the global cervical cancer deaths; however, information on E6 variants in the Indian population is limited. Information on these variants is essential for successful implementation of cervical cancer immunization programs. The E6 variants and their possible biological implications to the outcome of infection were studied in women attending the Tata Memorial Hospital, Mumbai, India. Cervical cancer patients with HPV 16 as a single infection (n = 33), co-infection with another HPV type (n = 20) or with multiple types (n = 10) were examined for HPV16 E6 variants using PCR and sequence analysis. The variants were identified using the prototype sequence (HPV 16R) belonging to the European lineage. The results revealed that the European T350G was the most common variant (50%) followed by the European prototype (40.3%) and the North-American (N = 3; 4.8%). The European prototype was significantly more frequent in patients infected with HPV16 alone (P < 0.05, C.I. 1.2-13.6), while the European T350G variants were seen in women with co-infections. The North-American lineage was found in women infected with HPV16 and 33. Three novel variants were identified of which two were non-synonymous. Phylogenetic analysis revealed that the variant F69L + L83V is not related to any of these lineages, while the variant M137L + L83V is closely related to the North American variant. This study found a difference in the prevalence of E6 variants compared to earlier Indian studies and their association with type of infection.

CUIDADO DA VIDA E CUIDADO DE SI: SOBRE A INDIVIDUALIZAÇÃO BIOPOLÍTICA CONTEMPORÂNEA

No curso de 1979, intitulado Naissance de la biopolitique, Michel Foucault propõe que o neoliberalismo contemporâneo, principalmente na sua variante norteamericana, seja lido como uma das mais expressivas configurações da governamentalidade biopolítica de nossa época. O artigo analisa se o cuidado da vida e sua articulação com a constituição do indivíduo como livre empreendedor de si mesmo, observável nessa biopolítica, podem ser considerados desdobramentos contemporâneos do “cuidado de si”, conceito nuclear nos últimos escritos de Foucault. Sugere-se que o cuidado de si, entendido como princípio de inquietude permanente cujo escopo é a transformação de si mesmo e a criação de novas maneiras de ser e de viver, permite apontar duas conclusões: a primeira delas, que o cuidado neoliberal da vida é inseparável da gestão da liberdade dos indivíduos; a segunda, que o autogoverno neoliberal, considerado pelo cálculo do investimento econômico em si mesmo, é algo do qual convém desprender-se.

Development of high-resolution melting (HRM) analysis for population studies of Fascioloides magna (Trematoda: Fasciolidae), the giant liver fluke of ruminants

The high-resolution melting (HRM) technique was successfully optimized as fast and effective method for population study of digenetic fluke, Fascioloides magna (Trematoda: Fasciolidae), originally North American liver parasite of free-living and domestic ruminants. Previously selected variable region (439bp) of mitochondrial cytochrome c oxidase subunit I (cox1) of 249 fluke individuals from enzootic European and North American regions were sequenced and mutually compared. The sequence analysis of partial cox1 revealed presence of seven structurally different haplotypes. Based on the sequence structure and alignments of six of them (Ha1-Ha6), three internal probes were designed and applied in HRM-based haplotype determination of all F. magna specimens. HRM analysis, performed with three designed probes, resulted in classification of samples into the seven haplogroups, equally with their assortment according to the sequence analysis. The representative of the haplotype, which was not involved in probe design (Ha7), was characterized by a unique melting curve shape as well. This provided an evidence of optimally settled conditions in HRM assay and indicated a probability of successful discrimination of novel haplotypes in future population studies on F. magna. The successful optimization of HRM method stands for an opportunity of detection of genetically unknown North American variants of F. magna and promises its application as fast and cheap screening technique for phylogeography studies of the giant liver fluke on its original continent.

Heterobasidion annosum and H. parviporum in the Southern Rocky Mountains and Adjoining States.

Collections of Heterobasidion spp. from Nebraska, Colorado, Arizona, and New Mexico were identified based on the sequence of the internal transcribed spacer region of the ribosomal DNA. The North American variant of Heterobasidion annosum sensu stricto was found on Pinus ponderosa and Juniperus virginiana in central Nebraska, southern Colorado, central Arizona, and southern New Mexico. The North American variant of H. parviporum was found on Abies concolor and Picea engelmannii in southern Colorado and central New Mexico. The pathogens were not found in a survey of conifer forests in Wyoming and the Black Hills of South Dakota. Historical records of annosus root disease are reviewed by host group to gain more insight into the potential distributions of the respective pathogens. An apparent lack of overlap in host range suggests that substitution of tree species may be a useful management approach in some cases.

Recent Approaches in English to Brazilian Racial Ideologies: Ambiguity, Research Methods, and Semiotic Ideologies.A Review Essay

Social scientists usually agree that it is difficult, if not impossible, to conceive of the United States without invoking race. The same is often assumed of the Americas' second most populous nation, Brazil, albeit for different reasons. Throughout much of the twentieth century, debates about Brazil's apparent exceptionalism turned on claims about an ostensibly ambiguous blackwhite color line and assertions that its ideologies are somehow more mutable, more multifaceted, and hence less riven by descent-based and legallysanctioned distinctions than North American variants. In fact, the twentiethcentury construction of the Brazilian nation has drawn in critical ways on such idealized, often contradictory, engagements with mixtures that supposedly gird a hybrid brownness known as racial democracy. This seductive yet problematic story of a nation made modem through miscegenation has been popularized by a number of influential thinkers, most notably Gilberto Freyre, a Franz Boas-trained public intellectual and scion of a planter family. Freyre, as part of an elite response to European and North American denigrations of Brazil's mixed-race populace, argued famously in his

Sequencing of Peach Latent Mosaic Viroid Variants from Nine North American Peach Cultivars Shows that This RNA Folds into a Complex Secondary Structure

We sequenced 34 new peach latent mosaic viroid (PLMVd) variants isolated from nine different peach cultivars. This study provides the widest view of PLMVd diversity reported to date and includes the original characterization of North American variants, which cannot be differentiated from European sequences. PLMVd appears as a species in which each isolate is a complex mixture of RNAs. Analysis of base-pair covariations supports the hypothesis that PLMVd folds into a complex branched structure with the potential of including three new pseudoknots. The resulting “globular-like” structure is in contrast to the rod-like one adopted by most other viroids.

Anglo-American Legal History in Review

Elisabeth A. Cawthon and David E. Narrett, eds. Essays on English Law andthe American Experience: The Walter Prescott Webb Memorial Lectures.Arlington: The University of Texas, 1994. Pp. xiv + 135.Joyce Lee Malcolm. To Keep and Bear Arms: The Origins of an Anglo-American Right. Cambridge, MA: Harvard University Press, 1994. Pp. xii +177 and notes and index.The comparative approach offers a great deal for the study of Anglo-American legal history. Given the English origins of American law and so-ciety, it might even be argued that a comparative methodology is a naturalfor studies focused on the evolution and development of law and legalsystems in North America and Great Britain. However, while the benefits ofsuch a method seem apparent, there are relatively few studies which activelyemploy a comparative approach. Further, when authors do adopt a com-parative method, more often than not they are encouraged to look to Englishinstitutions for sources, clues, and explanations as to later North Americanvariants. Rarely are the comparisons to be found running in the opposite di-rection. These two books, Elisabeth Cawthon and David Narrett's editedcollection of essays produced by the Walter Prescott Webb Memorial Lec-tures, and Joyce Lee Malcolm's study of the right to bear arms fall withinthat tradition of locating the English origins of American rights and obliga-tions. While both works demonstrate the significant contribution that comparative study can offer, they are also marked by the inherent difficulties ofundertaking such an approach.

Health and Safety Reform: A Review of Four Different Approaches

New Zealand reformed its approach to occupational health and safety in 1992, with the passage of the Health and Safety in Employment Act and the Accident, Rehabilitation, Compensation, and Insurance Act. These legislative changes were not, for the most part, informed by a thorough review of the variaus policy options. This paper provides part of such a review by assessing the effectiveness of four different approaches to occupational health and safety. The first three approaches examined are found to have major deficiencies. The market approach of compen sating dangerous work with wage premiums is criticized, because workers nor mally lack the bargaining power to secure pay concessions or hazard prevention measures. The regulatory approach of setting startdards to limit hazard levels or to prescribe safe production methods is faulted for being difficult to errforce and difficult to apply to most hazards. The accident compensation approach of experi ence-rating employer levies to employee claims is also faulted for failing to tightly link employer costs to unsafe conditions. In contrast, the fourth approach of giving workers the right to refuse unsafe work is lauded for its advantages in both detecting hazards and providing incentives for their prevention and rectification. However, improvements on the North American variants of the right to refuse unsafe work are suggested to allow workers to refuse to work in a greater variety of unsafe circumstances without fear of being disciplined.