Morphological and metric description of a rare Mesolithic deciduous tooth from Trail Creek Caves, Alaska

This study describes a morphologic and metric examination of a rare human deciduous maxillary left central incisor from Trail Creek, Alaska, radiocarbon dated to 8085 ±40 BP, from ancient Beringia. The tooth is compared to the maxillary incisors from the deciduous dentition of USR1 from central Alaska. Genetic analysis of the Trail Creek child as well as the USR1 child showed that they both belonged to an ancient eastern Beringian population that remained isolated in present-day Alaska during the late Pleistocene and early Holocene. The tooth was measured using a sliding calliper and the morphology of the tooth described directly from macroscopic evaluation as well as from a 3D surface scan. Based on tooth development the age of the Trail Creek child corresponds to an age of 1-1.5 years. The sex of the child cannot be positively assessed purely based on tooth morphology, but tooth size indicates a female which was confirmed from the genetic analysis. The tooth showed the basal morphology for deciduous maxillary central incisors known already from late Pleistocene and early Holocene without marked shovel shape

Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery

Viral infections cause many different diseases stemming both from well-characterized viral pathogens but also from emerging viruses, and the search for novel viruses continues to be of great importance. High-throughput sequencing is an important technology for this purpose. However, viral nucleic acids often constitute a minute proportion of the total genetic material in a sample from infected tissue. Techniques to enrich viral targets in high-throughput sequencing have been reported, but the sensitivity of such methods is not well established. This study compares different library preparation techniques targeting both DNA and RNA with and without virion enrichment. By optimizing the selection of intact virus particles, both by physical and enzymatic approaches, we assessed the effectiveness of the specific enrichment of viral sequences as compared to non-enriched sample preparations by selectively looking for and counting read sequences obtained from shotgun sequencing. Using shotgun sequencing of total DNA or RNA, viral targets were detected at concentrations corresponding to the predicted level, providing a foundation for estimating the effectiveness of virion enrichment. Virion enrichment typically produced a 1000-fold increase in the proportion of DNA virus sequences. For RNA virions the gain was less pronounced with a maximum 13-fold increase. This enrichment varied between the different sample concentrations, with no clear trend. Despite that less sequencing was required to identify target sequences, it was not evident from our data that a lower detection level was achieved by virion enrichment compared to shotgun sequencing

<i>Propionibacterium acnes: </i>disease-causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing

Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions but is also a proven contaminant of human clinical samples and surgical wounds. Its significance as a pathogen is consequently a matter of debate. In the present study, we investigated the presence of P. acnes DNA in 250 next-generation sequencing data sets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were subjected to either microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun sequencing. We detected high proportions of P. acnes DNA in enriched samples, particularly skin tissue-derived and other tissue samples, with the levels being higher in enriched samples than in shotgun-sequenced samples. P. acnes reads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show that P. acnes can be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. The possibility of contamination from the patient or other sources, including laboratory reagents or environment, should therefore always be considered carefully when P. acnes is detected in clinical samples. We advocate that detection of P. acnes always be accompanied by experiments validating the association between this bacterium and any clinical condition

Cutavirus in cutaneous malignant melanoma

A novel human protoparvovirus related to human bufavirus and preliminarily named cutavirus has been discovered. We detected cutavirus in a sample of cutaneous malignant melanoma by using viral enrichment and high-throughput sequencing. The role of cutaviruses in cutaneous cancers remains to be investigated

Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads

From Illumina sequencing of DNA from brain and liver tissue from the lion, Panthera leo, and tumor samples from the pike-perch, Sander lucioperca, we obtained two assembled sequence contigs with similarity to known retroviruses. Phylogenetic analyses suggest that the pike-perch retrovirus belongs to the epsilonretroviruses, and the lion retrovirus to the gammaretroviruses. To determine if these novel retroviral sequences originate from an endogenous retrovirus or from a recently integrated exogenous retrovirus, we assessed the genetic diversity of the parental sequences from which the short Illumina reads are derived. First, we showed by simulations that we can robustly infer the level of genetic diversity from short sequence reads. Second, we find that the measures of nucleotide diversity inferred from our retroviral sequences significantly exceed the level observed from Human Immunodeficiency Virus infections, prompting us to conclude that the novel retroviruses are both of endogenous origin. Through further simulations, we rule out the possibility that the observed elevated levels of nucleotide diversity are the result of co-infection with two closely related exogenous retroviruses.Full Tex

Metagenomic analysis reveals previously undescribed bat coronavirus strains in Eswatini

We investigated the prevalence of coronaviruses in 44 bats from four families in northeastern Eswatini using high-throughput sequencing of fecal samples. We found evidence of coronaviruses in 18% of the bats. We recovered full or near-full-length genomes from two bat species: Chaerephon pumilus and Afronycteris nana, as well as additional coronavirus genome fragments from C. pumilus, Epomophorus wahlbergi, Mops condylurus, and Scotophilus dinganii. All bats from which we detected coronaviruses were captured leaving buildings or near human settlements, demonstrating the importance of continued surveillance of coronaviruses in bats to better understand the prevalence, diversity, and potential risks for spillover.The National Science Foundation Graduate Research Fellowship; a National Science Foundation Graduate Research Opportunities Worldwide grant; Innovation Fund Denmark; a Student Research Grant from Bat Conservation International; a University of Florida Biodiversity Institute Fellowship; the Zuckerman STEM Leadership Program and an NIH Grant.http://link.springer.com/journal/10393hj2022Mammal Research InstituteZoology and Entomolog

Ancient human genomes and environmental DNA from the cement attaching 2,000 year-old head lice nits

Over the past few decades there has been an increased demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult for ethical reasons, and previous methods of breaking the skull to access the petrous bone are often forbidden for curatorial reasons, together with teeth which may be missing or too precious to sample. However, most ancient humans carried head lice, and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice eggs (nits) to the hair of ancient Argentinian mummies, 1,500–2,000 years old. The cement also preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel Cell Polyomavirus. We also show that human DNA obtained from nit cement can equal human genome assessment from tooth DNA, can increase assessment from petrous bone by two-fold, and by four-fold DNA over bloodmeal of adult lice a millennium younger. Genome-wide analyses from nit cement DNA also enables identification of the population genetic affinities of ancient humans. In metric studies of the sheaths, the length of the cement tube negatively correlated with the age of the specimens, while hair linear distance between nit and scalp informed about environmental conditions at the time before death. Ectoparasitic lice sheaths on hair, feathers, skins, or mummified remains can offer an alternative, non-destructive source of high-quality ancient DNA from a variety of host taxa and reveal details of their historical environment