A team from China describes dengue virus (DENV) genomic epidemiological features found in the country's Guangdong province for a paper in PLOS Neglected Tropical Diseases. The researchers did whole-genome sequencing on 114 DENV isolates from serotypes 1-4, which were collected in 21 cities between 2013 and 2017, using the sequence data to search for informative variants and signs of recombination, and to untangle phylogenetic relationships between the isolates. Their results revealed multiple phylogenetic clusters, for example, along with recurrent recombination events affecting the non-structural protein-coding gene NS3, a gene previously implicated in viral replication. "Phylogenetic analyses revealed that dengue fever was not endemic in Guangdong, which was indirectly supported by our recombination analyses," the authors report, noting that these and other data "will facilitate the development of more effective epidemiological surveillance strategies for dengue infection."
For a paper in PLOS One, researchers from the US and Brazil search for suspicious viral isolates in blood plasma samples from nearly 800 individuals from Brazil who displayed dengue fever-related symptoms but tested negative for DENV, Zika virus, and several other known viruses. Using viral sequence enrichment, amplification, and sequencing, the team tested more than 100 pooled plasma samples from 781 individuals, identifying several new and known viruses. Within the Parvoviridae family, for example, they unearthed new chapparvovirus and ambidensovirus isolates, which were assessed in more detail using genome sequence and other data. "Further testing the human tropism of the human plasma-associated parvovirus and densovirus reported here will require detection of specific antibody responses, viral amplification in human cells, and/or the detection of viral RNA in cells of infected tissues," they note.
A University of Ryukyus- and University of Tokyo-led team takes a look at ancient human plaque samples from Japan, searching for clues to individuals' diets during the 18th and 19th century with targeted sequencing. As they report in PLOS One, the researchers relied on rice-specific PCR primers and meta-barcoded sequencing approaches to target plant, animal, and fungal sequences in ancient dental calculi samples from 13 humans at a site from Japan's Edo period. Along with rice sequences, which turned up in more than half of the samples, the authors picked up sequences corresponding to fungal and plant taxa, including lettuce, Japanese chestnut, barley or wheat, tea, and tobacco. "The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past," they write, "and can complement other analytical methods such as microparticle analysis and stable isotope analysis."