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Human papillomavirus type 16 (HPV16) is the most common cause of cervical cancer, but most infections are transient with lesions not progressing to cancer. There is a lack of specific biomarkers for early cancer risk stratification. This study aimed to explore the intrahost HPV16 genomic variation in longitudinal samples from HPV16-infected women with different cervical lesion severity (normal, low-grade, and high-grade). The TaME-seq deep sequencing protocol was used to generate whole genome HPV16 sequences of 102 samples collected over time from 40 individuals. Single nucleotide variants (SNVs) and intrahost SNVs (iSNVs) were identified in the viral genomes. A majority of individuals had a unique set of SNVs and these SNVs were stable over time. Overall, the number of iSNVs and APOBEC3-induced iSNVs were significantly lower in high-grade relative to normal and low-grade samples. A significant increase in the number of APOBEC3-induced iSNVs over time was observed for normal samples when compared to high-grade. Our results indicates that the lower incidence of iSNVs and APOBEC3-induced iSNVs in high-grade lesions may have implications for novel biomarkers discoveries, potentially aiding early stratification of HPV-induced cervical precancerous lesions., (© 2024 The Authors. Journal of Medical Virology published by Wiley Periodicals LLC.)

Conservation translocations often inherently involve a risk of genetic diversity loss, and thus loss of adaptive potential, but this risk is rarely quantified or monitored through time. The reintroduction of beavers to Scotland, via the Scottish Beaver Trial in Knapdale, is an example of a translocation that took place in the absence of genetic data for the founder individuals and resulted in a small and suspected to be genetically depauperate population. In this study we use a high-density SNP panel to assess the genetic impact of that initial translocation and the effect of subsequent reinforcement translocations using animals from a different genetic source to the original founders. We demonstrate that the initial translocation did, indeed, lead to low genetic diversity ( H o  = 0.052) and high mean kinship (KING-robust = 0.159) in the Knapdale population compared to other beaver populations. We also show that the reinforcement translocations have succeeded in increasing genetic diversity ( H o  = 0.196) and reducing kinship (KING robust = 0.028) in Knapdale. As yet, there is no evidence of admixture between the two genetic lineages that are now present in Knapdale and such admixture is necessary to realise the full genetic benefits of the reinforcement and for genetic reinforcement and then rescue to occur; future genetic monitoring will be required to assess whether this has happened. We note that, should admixture occur, the Knapdale population will harbour combinations of genetic diversity not currently seen elsewhere in Eurasian beavers, posing important considerations for the future management of this population. We consider our results in the wider context of beaver conservation throughout Scotland and the rest of Britain, and advocate for more proactive genetic sampling of all founders to allow the full integration of genetic data into translocation planning in general., Competing Interests: The authors declare no conflict of interest., (© 2023 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Background: Previously developed TaME-seq method for deep sequencing of HPV, allowed simultaneous identification of the human papillomavirus (HPV) DNA consensus sequence, low-frequency variable sites, and chromosomal integration events. The method has been successfully validated and applied to the study of five carcinogenic high-risk (HR) HPV types (HPV16, 18, 31, 33, and 45). Here, we present TaME-seq2 with an updated laboratory workflow and bioinformatics pipeline. The HR-HPV type repertoire was expanded with HPV51, 52, and 59. As a proof-of-concept, TaME-seq2 was applied on SARS-CoV-2 positive samples showing the method's flexibility to a broader range of viruses, both DNA and RNA., Results: Compared to TaME-seq version 1, the bioinformatics pipeline of TaME-seq2 is approximately 40× faster. In total, 23 HPV-positive samples and seven SARS-CoV-2 clinical samples passed the threshold of 300× mean depth and were submitted to further analysis. The mean number of variable sites per 1 kb was ~ 1.5× higher in SARS-CoV-2 than in HPV-positive samples. Reproducibility and repeatability of the method were tested on a subset of samples. A viral integration breakpoint followed by a partial genomic deletion was found in within-run replicates of HPV59-positive sample. Identified viral consensus sequence in two separate runs was > 99.9% identical between replicates, differing by a couple of nucleotides identified in only one of the replicates. Conversely, the number of identical minor nucleotide variants (MNVs) differed greatly between replicates, probably caused by PCR-introduced bias. The total number of detected MNVs, calculated gene variability and mutational signature analysis, were unaffected by the sequencing run., Conclusion: TaME-seq2 proved well suited for consensus sequence identification, and the detection of low-frequency viral genome variation and viral-chromosomal integrations. The repertoire of TaME-seq2 now encompasses seven HR-HPV types. Our goal is to further include all HR-HPV types in the TaME-seq2 repertoire. Moreover, with a minor modification of previously developed primers, the same method was successfully applied for the analysis of SARS-CoV-2 positive samples, implying the ease of adapting TaME-seq2 to other viruses., (© 2023. The Author(s).)

Persistent infection with Human Papillomavirus (HPV) is responsible for almost all cases of cervical cancers, and HPV16 and HPV18 associated with the majority of these. These types differ in the proportion of viral minor nucleotide variants (MNVs) caused by APOBEC3 mutagenesis as well as integration frequencies. Whether these traits extend to other types remains uncertain. This study aimed to investigate and compare genomic variability and chromosomal integration in the two phylogenetically distinct Alpha-7 and Alpha-9 clades of carcinogenic HPV types. The TaME-seq protocol was employed to sequence cervical cell samples positive for HPV31, HPV33 or HPV45 and combine these with data from a previous study on HPV16 and HPV18. APOBEC3 mutation signatures were found in Alpha-9 (HPV16/31/33) but not in Alpha-7 (HPV18/45). HPV45 had significantly more MNVs compared to the other types. Alpha-7 had higher integration frequency compared to Alpha-9. An increase in integration frequency with increased diagnostic severity was found for Alpha-7. The results highlight important differences and broaden our understanding of the molecular mechanisms behind cervical cancer induced by high-risk HPV types from the Alpha-7 and Alpha-9 clades., Competing Interests: Declaration of competing interest We have no competing interests to declare., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Alpine and arctic bird populations have shown an unmistakable decrease over the last three decades, and the need for conservation is highly necessary. We investigated the use of five privately-owned dogs (Canis lupus familiaris) as a non-invasive tool to determine the presence of rock ptarmigan (Lagopus muta), through sniffing out faecal pellets, using a yes/no training regime. We carried out 36 double-blind experimental trials per dog and hypothesised that dogs could discriminate the rock ptarmigan from similar species, such as black grouse (Tetrao tetrix), western capercaillie (T. urogallus) and willow grouse (L. lagopus). Our dogs detected differences between the avian species with an average accuracy of 65.9%, sensitivity of 66.7% and specificity of 65.3%. We showed that privately-owned dogs have the potential to be used as biodetectors for conservational work within controlled laboratory conditions for declining species, but overall, only one dog was considered proficient enough. We concluded that dogs could be used as a non-invasive tool to detect the rock ptarmigan, and with further field training and testing, operate in the field for detection surveys., Competing Interests: All authors declare that they have no competing non-financial or financial interest.

The Arabian tahr ( Arabitragus jayakari ) occurs only in the mountains of northern Oman and the United Arab Emirates. The species is classified as Endangered due to its small declining population. In this study, we combined genetic and landscape ecology techniques in order to inform landscape scale conservation and genetic management of Arabian tahr. Using 540 base pairs of mitochondrial control region in a dataset of 53 samples, we found eight haplotypes, which fell into two haplogroups. Population genetic analysis using a panel of 14 microsatellite loci also showed a weak, but significant division. Analyses of landscape connectivity supported the genetic results showing poor connectivity between populations in the far south of the study area and those in the north. The most likely location of corridors connecting Arabian tahr populations were identified. Many corridors between tahr populations are impeded by multi-lane highways and restoration of these connections is required to maintain population viability of Arabian tahr. Owing to limited genetic samples outside of Wadi Sareen, further sampling is needed to elucidate both mtDNA and the nuclear structure of Arabian tahr more fully. Our study provides a toolkit that may be used for future genetic and connectivity monitoring of the Arabian tahr population., Competing Interests: Conflicts of interestOn behalf of all authors, the corresponding author states that there is no conflict of interest., (© The Author(s) 2020.)

The island biogeography theory is one of the major theories in ecology, and its applicability to natural systems is well documented. The core model of the theory, the equilibrium model of island biogeography, predicts that species diversity on an island is positively related to the size of the island, but negatively related by the island's distance to the mainland. In recent years, ecologists have begun to apply this model when investigating genetic diversity, arguing that genetic and species diversity might be influenced by similar ecological processes. However, most studies have focused on oceanic islands, but knowledge on how the theory applies to islands located on the mainland (e.g., mountain islands, forest islands) is scarce. In this study, we examined how the size and degree of isolation of mountain islands would affect the genetic diversity of an alpine bird, the rock ptarmigan ( Lagopus muta ). Within our study area, we defined the largest contiguous mountain area as the mainland, while smaller mountains surrounding the mainland were defined as islands. We found that the observed heterozygosity ( H o ) was significantly higher, and the inbreeding coefficient ( F is ) significantly lower, on the mainland compared to islands. There was a positive significant relationship between the unbiased expected heterozygosity ( H n.b. ) and island size (log km 2 ), but a negative significant relationship between H o and the cost distance to the mainland. Our results are consistent with the equilibrium model of island biogeography and show that the model is well suited for investigating genetic diversity among islands, but also on islands located on the mainland., Competing Interests: None declared.

Amphibians are particularly sensitive to landscape fragmentation. Potential barriers between breeding sites can negatively influence the dispersal of individuals and increase genetic structure between populations. In this study, we genotyped 10 microsatellites for 334 marbled newts (Triturus marmoratus) at 11 different locations in Western France. Samples were collected in different regions with contrasting agricultural landscapes (low and high proportion of arable land in the north and south, respectively). We found a strong genetic structure between the northern and southern sampling sites. Isolation by distance was recorded after 62 km, but within the northern region, little or no genetic structure was detected over large distances (up to 114 km). Genetic structure at shorter distance (43 km) was found between sites situated in landscapes with larger amounts of arable lands. A significant positive relationship was found between the pairwise genetic distance (F st ) between sites and the amount of arable land together with the distance between sites. Our results suggest that the Loire River might act as a corridor for the marbled newt, while arable land might act as a barrier. Finally, although a large city is located between sampling sites, no effect was detected on population structure.

Objective: The genetic markers designed for this study can facilitate future genetic studies on the rock ptarmigan (Lagopus muta). To our knowledge no microsatellite markers have ever been developed specifically for this species before. These new microsatellite markers will be useful for population genetics studies and for future conservation projects., Results: Using Next Generation Sequencing 6252 potential microsatellite sequences were found. Sixteen nonpalindromic tetranucleotide microsatellites and their respective primers were selected. The markers were tested on both the rock ptarmigan and the willow grouse (L. lagopus). The number of alleles varied between 2 and 18 for the rock ptarmigan, and between 3 and 13 for the willow grouse. Expected heterozygosity was in the range 0.1244-0.8692 and 0.1358-0.8722 for the rock ptarmigan and the willow grouse, respectively.

This open study evaluated the influence of renal function on the pharmacokinetics of ranitidine (50 mg i.v. infusion given over 6 min). Five groups, each of 8 subjects, 1 with normal renal function and 4 with different degrees of renal impairment were studied. Renal function was assessed in each patient by 51Cr-EDTA (glomerular filtration rate, GFR), creatinine clearance (GFR) and N-methylnicotinamide clearance (reflecting glomerular and tubular function). Sixteen blood samples (5 ml) taken up to 48 h post dose from each subject were analysed for plasma ranitidine concentrations by reversed phase HPLC. Patient groups with renal impairment had significantly increased AUC infinity and t1/2 with corresponding decreases in CLp and lambda z when compared with normal subjects. There was also a significant increase in tmax but not in Cmax. There was a high linear correlation between the degree of renal impairment and ranitidine clearance. In patients with GFR < or = 20 ml min-1, the AUC infinity mean ratio (compared with normal subjects) was up to 4.6 while for patients with GFR 20-50 ml min-1, the average AUC infinity ratio was 2.6. It is recommended that the dose of ranitidine is halved in patients with GFR < or = 20 ml min-1.

A case of primary polycythaemia presenting with severe chorea is reported and compared with previous cases. The aetiological factors of the chorea are discussed and the importance of early diagnosis stressed.