Superinfection exclusion creates spatially distinct influenza virus populations

Interactions between viruses during coinfections can influence viral fitness and population diversity, as seen in the generation of reassortant pandemic influenza A virus (IAV) strains. However, opportunities for interactions between closely related viruses are limited by a process known as superinfection exclusion (SIE), which blocks coinfection shortly after primary infection. Using IAVs, we asked whether SIE, an effect which occurs at the level of individual cells, could limit interactions between populations of viruses as they spread across multiple cells within a host. To address this, we first measured the kinetics of SIE in individual cells by infecting them sequentially with 2 isogenic IAVs, each encoding a different fluorophore. By varying the interval between addition of the 2 IAVs, we showed that early in infection SIE does not prevent coinfection, but that after this initial lag phase the potential for coinfection decreases exponentially. We then asked how the kinetics of SIE onset controlled coinfections as IAVs spread asynchronously across monolayers of cells. We observed that viruses at individual coinfected foci continued to coinfect cells as they spread, because all new infections were of cells that had not yet established SIE. In contrast, viruses spreading towards each other from separately infected foci could only establish minimal regions of coinfection before reaching cells where coinfection was blocked. This created a pattern of separate foci of infection, which was recapitulated in the lungs of infected mice, and which is likely to be applicable to many other viruses that induce SIE. We conclude that the kinetics of SIE onset segregate spreading viral infections into discrete regions, within which interactions between virus populations can occur freely, and between which they are blocked

Thresholds for adding degraded tropical forest to the conservation estate

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked

Thresholds for adding degraded tropical forest to the conservation estate

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked

Superinfection exclusion creates spatially distinct influenza virus populations

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Thresholds for adding degraded tropical forest to the conservation estate

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked

Thresholds for adding degraded tropical forest to the conservation estate.

Acknowledgements: This study was supported by funding to the Stability of Altered Forest Ecosystems Project by the Sime Darby Foundation. Research permission and site access were provided by the Maliau Basin Management Committee, the Sabah Foundation, Benta Wawasan, Sabah Softwoods, the Innoprise Foundation, the Sabah Forestry Department and the Sabah Biodiversity Centre. R.M.E. is supported by the NOMIS Foundation. Data collection was financed by Australian Research Council grant DP140101541; Bat Conservation International; the British Council Newton-Ungku Omar Fund 216433953; British Ecological Society grant 3256/4035; the Cambridge Trust; the Cambridge University Commonwealth Fund; the Czech Science Foundation (14-32302S); the European Research Council (281986); the European Social Fund and the Czech Republic (CZ.1.07/2.3.00/20.0064); the Fundamental Research Grant Scheme (FRG0302-STWN-1/ 2011), Ministry of Higher Education, Malaysia; FFWS CZU (IGA number A_26_22); the Jardine Foundation; Malaysia Industry Group for High Technology (216433953); the Ministry of Education, Youth and Sports of the Czech Republic (INTER-TRANSFER LTT19018); the Panton Trust; the Primate Society of Great Britain; ProForest; Royal Society of London grant RG130793; the Sime Darby Foundation; the S. T. Lee Fund; the Sir Philip Reckitt Educational Trust; the Tim Whitmore Fund; the Universiti Malaysia Sabah; the University of East Anglia; the University of Kent; the University of Florida Institute of Food and Agricultural Sciences; UK Research and Innovation Natural Environment Research Council grants NE/H011307/1, NE/K016253/1, NE/K016407/1, NE/K016148/1, NE/K0106261/1, NE/K015377/1, NE/L002515/1, NE/L002582/1 and NE/P00363X/1 and studentship 1122589; the Varley Gradwell Travelling Fellowship; and the World Wildlife Fund for Nature. Data collection was supported by R. Adzhar, A. Afendy, N. Arumugam, S. Benedick, V. Bignet, S. Butler, K. Graves, H. E. Hah, H. Heroin, A. Kendall, H. H. Mahsol, D. Mann, J. Miller, S. Milne, J. Mumford, D. Norman, H. Rossleykho, D. Shapiro, K. Sieving, J. Sugau, B. Udell, B. E. Yahya and M. A. Zakaria.Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked