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Although shrews are one of the largest groups of mammals little is known about their role in the evolution and transmission of viral pathogens including coronaviruses. We captured 266 Asian house shrews () in Jiangxi and Zhejiang provinces, China, during 2013-2015. Coronavirus (CoV) RNA was detected in 24 Asian house shrews, with an overall prevalence of 9.02%. Complete viral genome sequences were successfully recovered from the RNA positive samples. The newly discovered shrew CoV fell into four lineages reflecting their geographic origins, indicative of largely allopatric evolution. Notably, these viruses were most closely related to alphacoronaviruses, but sufficiently divergent that they should be considered a novel member of the genus , which we denote Wénchéng shrew virus (WESV). Phylogenetic analysis revealed that WESV was a highly divergent member of the alphacoronaviruses and, more dramatically, that the S gene of WESV fell in a cluster that was genetically distinct from that of known coronaviruses. The divergent position of WESV suggests that coronaviruses have a long association with Asian house shrews. In addition, the genome of WESV contains a distinct NS7 gene that exhibits no sequence similarity to any known viruses. Together, these data suggest that shrews are natural reservoirs for coronaviruses and may have played an important and long-term role in CoV evolution. The subfamily contains several notorious human and animal pathogens, including severe acute respiratory syndrome coronavirus, Middle East respiratory syndrome coronavirus, and porcine epidemic diarrhea virus. Because of their genetic diversity and phylogenetic relationships it has been proposed that the alphacoronaviruses likely have their ultimate ancestry in those viruses residing in bats. Here, we described a novel alphacoronavirus (Wénchéng shrew virus, WESV) that was sampled from Asian house shrews in China. Notably, WESV is a highly divergent member of the alphacoronaviruses and possesses an S gene that is genetically distinct from that of all known coronaviruses. In addition, the genome of WESV contains a distinct NS7 gene that exhibits no sequence similarity to any known viruses. Together, these data suggest that shrews are important and long-standing hosts for coronaviruses that merit additional research and surveillance.

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To better understand the genetic diversity, host associations and evolution of coronaviruses (CoVs) in China we analyzed a total of 696 rodents encompassing 16 different species sampled from Zhejiang and Yunnan provinces. Based on reverse transcriptase PCR-based CoV screening of fecal samples and subsequent sequence analysis of the RdRp gene, we identified CoVs in diverse rodent species, comprising Apodemus agrarius, Apodemus chevrieri, Apodemus latronum, Bandicota indica, Eothenomys cachinus, E. miletus, Rattus andamanesis, Rattus norvegicus, and R. tanezumi. CoVs were particularly commonplace in Apodemus chevrieri, with a detection rate of 12.44% (24/193). Genetic and phylogenetic analysis revealed the presence of three groups of CoVs carried by a range of rodents that were closely related to the Lucheng Rn rat coronavirus (LRNV), China Rattus coronavirus HKU24 (ChRCoV_HKU24) and Longquan Rl rat coronavirus (LRLV) identified previously. One newly identified A. chevrieri-associated virus closely related to LRNV lacked an NS2 gene. This virus had a similar genetic organization to AcCoV-JC34, recently discovered in the same rodent species in Yunnan, suggesting that it represents a new viral subtype. Notably, additional variants of LRNV were identified that contained putative nonstructural NS2b genes located downstream of the NS2 gene that were likely derived from the host genome. Recombination events were also identified in the ORF1a gene of Lijiang-71. In sum, these data reveal the substantial genetic diversity and genomic complexity of rodent-borne CoVs, and extend our knowledge of these major wildlife virus reservoirs.

The agricultural intensification and the subsequent habitat changes in agroecosystem can strongly affect biological control services. We here examine the influence of inter-annual landscape change in wheat field area on interactions of cereal aphids and their natural enemies, as well as the efficacy of biological control using data collected from a 4-year experiment in Northwest China. Two hypotheses were tested. (i) Population densities decline following an inter-annual expansion of wheat crop proportion cover due to dilution and crowding effects. (ii) Species that are specialists or at higher trophic levels are more sensitive to bottomup disturbance by inter-annual change in percent cover of wheat crop. Results showed the population densities of one cereal aphid (Macrosiphum avenae), one parasitic wasp (Aphidius avenae), two specialist predators (ladybirds: Hippodamia variegata and H. tredecimpunctata) and one hyperparasitic wasp (Pachyneuron aphidis) declined following the expansion of wheat crop areas, supporting the predictions of inter-annual dilution and crowding effects. In contrast, the populations of one cereal aphid (Schizaphis graminum), one parasitic wasp (A. gifuensis), two generalist predators (spiders: Pardosa astrigera; carabid beetles: Chlaenius pallipes), and two hyperparasitic wasps (Asaphes suspensus, and Alloxysta sp.) did not respond to inter-annual landscape change. The two hypotheses were partially supported but with noticeable exceptions, and the bio-control efficiency declined with the increase of the proportion cover of wheat field in agricultural landscape. Overall, different responses of cereal aphids and their natural enemies make it difficult but still possible to optimize inter-annual landscape change for enhancing the parasitism rate and predator-prey ratio. ZusammenfassungDie Intensivierung der Landwirtschaft und die daraus folgenden Änderungen der Habitate in Agrarökosystemen können die biologische Schädlingsbekämpfung stark beeinflussen. Wir untersuchen hier den Einfluss der jährlichen Änderungen des Flächenanteils von Weizenfeldern in der Landschaft auf die Interaktionen zwischen Getreideblattläusen und ihren natürlichen Feinden sowie auf die Effektivität der biologischen Schädlingsbekämpfung. Wir nutzten Daten aus einem vierjährigen Experiment im Nordwesten Chinas. Zwei Hypothesen wurden getestet: (1) Nach einer Ausweitung des Flächenanteils der Weizenfelder gehen die Populationsdichten zurück als Folge von Verdünnungs-und Konzentrationseffekten. (2) Spezialisten und

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A single reaction coordinate is designed to perform umbrella sampling for the water-chain-assist transmembrane permeation processes of ions and highly polar groups. In these permeation processes, there are three types of configuration changes including deformation of both leaflets of the lipid bilayer, formation of a water chain across the bilayer, and translocation of the ion through the bilayer. Due to the complexity of the permeation process, multiple reaction coordinates and expensive high dimensional free energy calculations have been used in previous studies. Our single reaction coordinate can be used to obtain sample data of the entire permeation process, which significantly reduces the computational cost in free energy calculations. We show that one-dimensional umbrella sampling along the new reaction coordinate can be used to obtain continuous sample data roughly along the minimum free energy path (MFEP) on the phase plane of the two components of the new reaction coordinate. Along the MFEP, a one-dimensional bin-segmentation of the sample data is then used to calculate the potential of mean force accurately by the newly developed free energy analysis method: weighted least-square analysis method (Welsam). Our work not only proposes a useful reaction coordinate to obtain sample data for water-chain assist transmembrane permeation processes but also establishes a general methodology for one-dimensional free energy calculations with bin-segmentation along the transition path in multiple dimensional phase space.

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