• Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

      Damas, Joana; Hughes, Graham M.; Keough, Kathleen C.; Painter, Corrie A.; Persky, Nicole S.; Corbo, Marco; Hiller, Michael; Koepfli, Klaus-Peter; Pfenning, Andreas R.; Zhao, Huabin; et al. (2020)
      The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency <0.001) variants in 10/25 binding sites. In addition, we found significant signals of selection and accelerated evolution in the ACE2 coding sequence across all mammals, and specific to the bat lineage. Our results, if confirmed by additional experimental data, may lead to the identification of intermediate host species for SARS-CoV-2, guide the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.
    • Conservation implications of inaccurate estimation of cryptic population size: Inaccurate estimation of cryptic population size

      Katzner, T. E.; Ivy, Jamie A.; Bragin, E. A.; Milner-Gulland, E.J.; DeWoody, J. A. (2011)
      ...Estimating population size is central to species‐oriented conservation and management. However, in spite of recent development in monitoring protocols, there are gaps in our ability to accurately and quickly estimate numbers of individuals present, especially for the cryptic and often non‐breeding components of structured vertebrate populations. Yet knowing the size and growth trajectory of all stage classes of a population is critical for species conservation. Here we use data from 2 years of non‐invasive genetic sample collection from the cryptic, non‐breeding component of an endangered bird of prey population to evaluate the impact of variability in population estimates on demographic models that underpin conservation efforts....
    • The fishes of Genome 10K

      Bernardi, Giacomo; Wiley, Edward O.; Mansour, Hicham; Miller, Michael R.; Orti, Guillermo; Haussler, David; O'Brien, Stephen J.; Ryder, Oliver A.; Venkatesh, Byrappa (2012)
      The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes....