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This Week in PLOS: Oct 1, 2012

Arizona researchers look at clonal evolution in a treatment-refractory form of the rare sinus cavity cancer known as maxillary sinus carcinoma in a PLOS One study. Using a combination of tumor cell sorting by flow cytometry and array comparative genomic hybridization, the team tracked tumor cell populations in one individual — a 47-year-old man with maxillary sinus carcinoma — over time. Based on the genetic patterns identified in his surgically resected primary tumor and in tumors that appeared after the cancer's post-treatment recurrence and metastases, for instance, study authors uncovered a set of subclones harboring an amplicon that affects the KIT gene. "The evolution of these subclones was associated with distinct genetic aberrations and DNA ploidies," they write, adding that the new analysis "paves the way to understanding the development and progression of this disease."

An international research team used deep sequencing on patient blood samples to identify a new rabies-related virus suspected of causing a 2009 outbreak of hemorrhagic fever in the Democratic Republic of the Congo that affected three people. As they report in PLOS Pathogens, the researchers first saw the suspicious virus by Roche 454 pyrosequencing. Using ultra-deep Illumina sequencing, they then sequenced its genome and compared it with other known viral sequences. From their analyses so far, the group proposes that the virus, called the Bas-Congo virus, or BASV, falls into a divergent group within the rhabdovirus family, which also includes rabies virus and Chandipura virus. "Although the source of the virus remains unclear, our study findings suggest that BASV may be spread by human-to-human contact," they write, "and is an emerging pathogen associated with acute hemorrhagic fever in Africa." For more on the study, check out a related news story from our sister publication GenomeWeb Daily News.

In PLOS Genetics, the Max Planck Institute for Evolutionary Anthropology's Svante Pääbo and his colleagues explore gene expression profiles in the brain in relation to domestication in animals — an analysis that relied on messenger RNA sequencing of frontal cortex brain samples from wild animals and their related domestic counterparts. Based on their comparisons of genome-wide expression patterns in brain samples from wolves versus dogs, wild boars versus pigs, wild versus domesticated rabbits, wild versus domesticated guinea pigs, tame versus wild rats, and so on, the investigators concluded that each domestication event appears to involve shifts to somewhat different gene sets, arguing against a shared expression-based domestication program across animals. "The majority of brain gene expression changes in domesticated animals are specific to the given domestication event," the study authors explain, "suggesting that the causative variants of behavioral domestication traits may likewise be different."

The Scan

Pfizer-BioNTech Seek Full Vaccine Approval

According to the New York Times, Pfizer and BioNTech are seeking full US Food and Drug Administration approval for their SARS-CoV-2 vaccine.

Viral Integration Study Critiqued

Science writes that a paper reporting that SARS-CoV-2 can occasionally integrate into the host genome is drawing criticism.

Giraffe Species Debate

The Scientist reports that a new analysis aiming to end the discussion of how many giraffe species there are has only continued it.

Science Papers Examine Factors Shaping SARS-CoV-2 Spread, Give Insight Into Bacterial Evolution

In Science this week: genomic analysis points to role of human behavior in SARS-CoV-2 spread, and more.