Variation in predicted COVID‐19 risk among lemurs and lorises

• Published in: American Journal of Primatology 2021-06, Vol.83 (6), p.e23255-n/a
• Main Authors: Melin, Amanda D., Orkin, Joseph D., Janiak, Mareike C., Valenzuela, Alejandro, Kuderna, Lukas, Marrone, Frank, Ramangason, Hasinala, Horvath, Julie E., Roos, Christian, Kitchener, Andrew C., Khor, Chiea Chuen, Lim, Weng Khong, Lee, Jessica G. H., Tan, Patrick, Umapathy, Govindhaswamy, Raveendran, Muthuswamy, Alan Harris, R., Gut, Ivo, Gut, Marta, Lizano, Esther, Nadler, Tilo, Zinner, Dietmar, Le, Minh D., Manu, Sivakumara, Rabarivola, Clément J., Zaramody, Alphonse, Andriaholinirina, Nicole, Johnson, Steig E., Jarvis, Erich D., Fedrigo, Olivier, Wu, Dongdong, Zhang, Guojie, Farh, Kyle Kai‐How, Rogers, Jeffrey, Marques‐Bonet, Tomas, Navarro, Arcadi, Juan, David, Arora, Paramjit S., Higham, James P.
• Format: Article
• Language: English
• Subjects: ACE2; ACE2 gene; Affinity; Amino acids; Angiotensin; Angiotensin-converting enzyme 2; Avahi; Binding; Conservation; Coronaviruses; COVID-19; Disruption; Endangered; Endangered species; Extinction; Gene sequencing; Genera; Health risks; High risk; Infections; Interaction models; Monkeys & apes; Primates; Propithecus; Proteins; Rare species; Receptors; Risk; Sequences; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Species extinction; Susceptibility; Variability; Variants; Variation; Viral diseases; Viruses
• ISSN: 0275-2565; 1098-2345
• DOI: 10.1002/ajp.23255

The novel coronavirus SARS‐CoV‐2, which in humans leads to the disease COVID‐19, has caused global disruption and more than 2 million fatalities since it first emerged in late 2019. As we write, infection rates are at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary target of SARS‐CoV‐2 is the cellular receptor angiotensin‐converting enzyme‐2 (ACE2). Recent sequence analyses of the ACE2 gene predict that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results while finding additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS‐CoV‐2 infection. Troublingly, some species, including the rare and endangered aye‐aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID‐19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS‐CoV‐2. Research Highlights We used predominantly unpublished ACE2 gene sequences from 71 individuals across 51 species of strepsirrhines, to predict the infection risk presented by the SARS‐CoV‐2 coronavirus to different species of lemurs and lorises. We converted the ACE2 gene sequences to protein sequences, and used protein‐protein interaction modeling to predict how amino acid residue differences between species are predicted to increase or decrease the binding affinity of the receptor to the virus. We found great variation among strepsirrhines in their predicted binding affinity for SARS‐CoV‐2, with some groups, including members of the genera Daubentonia, Avahi, and Propithecus, predicted to be at high risk. We use our data to highlight the risks posed by t