Discovery of pulsars is one of the main goals for large radio telescopes. The Five-hundred-meter Aperture Spherical radio Telescope (FAST), that incorporates an L-band 19-beam receiver with a system temperature of about 20 K, is the most sensitive radio telescope utilized for discovering pulsars. We designed the snapshot observation mode for a FAST key science project, the Galactic Plane Pulsar Snapshot (GPPS) survey, in which every four nearby pointings can observe a cover of a sky patch of 0.1575 square degrees through beam-switching of the L-band 19-beam receiver. The integration time for each pointing is 300 seconds so that the GPPS observations for a cover can be made in 21 minutes. The goal of the GPPS survey is to discover pulsars within the Galactic latitude of ± 10° from the Galactic plane, and the highest priority is given to the inner Galaxy within ± 5°. Up to now, the GPPS survey has discovered 201 pulsars, including currently the faintest pulsars which cannot be detected by other telescopes, pulsars with extremely high dispersion measures (DMs) which challenge the currently widely used models for the Galactic electron density distribution, pulsars coincident with supernova remnants, 40 millisecond pulsars, 16 binary pulsars, some nulling and mode-changing pulsars and rotating radio transients (RRATs). The follow-up observations for confirmation of new pulsars have polarization-signals recorded for polarization profiles of the pulsars. Re-detection of previously known pulsars in the survey data also leads to significant improvements in parameters for 64 pulsars. The GPPS survey discoveries are published and will be updated at http://zmtt.bao.ac.cn/GPPS/.

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FDA proactively invests in tools to support innovation of emerging technologies, such as infectious disease next generation sequencing (ID-NGS). Here, we introduce FDA-ARGOS quality-controlled reference genomes as a public database for diagnostic purposes and demonstrate its utility on the example of two use cases. We provide quality control metrics for the FDA-ARGOS genomic database resource and outline the need for genome quality gap filling in the public domain. In the first use case, we show more accurate microbial identification of Enterococcus avium from metagenomic samples with FDA-ARGOS reference genomes compared to non-curated GenBank genomes. In the second use case, we demonstrate the utility of FDA-ARGOS reference genomes for Ebola virus target sequence comparison as part of a composite validation strategy for ID-NGS diagnostic tests. The use of FDA-ARGOS as an in silico target sequence comparator tool combined with representative clinical testing could reduce the burden for completing ID-NGS clinical trials.

Porcine reproductive and respiratory syndrome virus (PRRSV), an important pathogen that affects the pig industry, is a highly genetically diverse RNA virus. However, the phylogenetic and genomic recombination properties of this virus have not been completely elucidated. In this study, comparative analyses of all available genomic sequences of North American (NA)-type PRRSVs (n = 355, including 138 PRRSV genomes sequenced in this study) in China and the United States during 2014–2018 revealed a high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and the GP2 to GP3 regions. Lineage 1 (L1) PRRSV was found to be susceptible to recombination among PRRSVs both in China and the United States. The recombinant major parent between the 1991–2013 data and the 2014–2018 data showed a trend from complex to simple. The major recombination pattern changed from an L8 to L1 backbone during 2014–2018 for Chinese PRRSVs, whereas L1 was always the major backbone for US PRRSVs. Intralineage recombination hot spots were not as concentrated as interlineage recombination hot spots. In the two main clades with differential diversity in L1, NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, NADC34-like PRRSVs have been relatively stable in population genetic diversity for years. Systematic analyses of insertion and deletion (indel) polymorphisms of NSP2 divided PRRSVs into 25 patterns, which could generate novel references for the classification of PRRSVs. The results of this study contribute to a deeper understanding of the recombination of PRRSVs and indicate the need for coordinated epidemiological investigations among countries. IMPORTANCE Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant swine diseases. However, the phylogenetic and genomic recombination properties of the PRRS virus (PRRSV) have not been completely elucidated. In this study, we systematically compared differences in the lineage distribution, recombination, NSP2 polymorphisms, and evolutionary dynamics between North American (NA)-type PRRSVs in China and in the United States. Strikingly, we found high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and in the GP2 to GP3 region. Also, intralineage recombination hot spots were scattered across the genome between Chinese and US strains. Furthermore, we proposed novel methods based on NSP2 indel patterns for the classification of PRRSVs. Evolutionary dynamics analysis revealed that NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, suggesting that a dominant population may occur and cause an outbreak. Our findings offer important insights into the recombination of PRRSVs and suggest the need for coordinated international epidemiological investigations.