Variation in predicted COVID-19 risk among lemurs and lorises

Abstract

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts 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 and finds 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.

SARS‐CoV‐2 and wastewater: What does it mean for non‐human primates?

“…A similar approach has also been applied by others to predict which NHP species are potentially susceptible to the SARS-CoV-2. For example, in two similar studies, catarrhine primates (African and Asian apes and monkeys) and some strepsirrhines (specifically, some lemurs) were predicted to be highly susceptible to the virus (Melin et al, 2020(Melin et al, , 2021, although missense variants within populations may alter susceptibility for some individuals. For example, a common missense variant is present in West African/Caribbean green monkey (Chlorocebus sabaeus) populations and it is predicted to reduce the affinity of SARS-CoV-2 binding to ACE2, thus affecting susceptibility (Schmitt et al, 2020).…”

“…A better understanding of the missense variants in wild primate populations will help us model the susceptibility and infection dynamics of SARS-CoV-2. In potentially better news, platyrrhines (monkeys in the Americas) and many strepsirrhines carry ACE2 receptors with mutations that reduce SARS-CoV-2 binding, suggesting that species from these clades have lower susceptibility relative to other primates (Melin et al, 2020(Melin et al, , 2021. However, as a group primates have higher predicted risk than many other mammals (Damas et al, 2020).…”

Year without End: Primatology in 2020

“…)—show potentially high risk of susceptibility to SARS‐CoV‐2 (Melin et al. 2021). These vulnerable taxa are of particular concern due to the conservation concerns for strepsirrhine primates in Madagascar: an epidemic of a potentially fatal and contagious disease like COVID‐19 would be disastrous for the long‐term survival of many of these taxa (Melin et al.…”

“…In humans, there is very little variation in ACE2 and TMPRSS2 , suggesting very little genetic variation leading to population‐specific differences in susceptibility. Melin et al.’s (2021) work on strepsirrhines found ACE2 residues to be conserved among conspecific individuals, with a sampling range of four to seventeen individuals within multiply sampled taxa. My own work with colleagues to model ACE2 and TMPRSS2 variation in a large sample of wild and captive savanna monkeys ( Chlorocebus spp.)…”

Estimating chromosome sizes from karyotype images enables validation of de novo genome assemblies

“…Highly contiguous, complete, and accurate genome assemblies are fundamental to associating genotypes with phenotypes [1,2]; genome-based evolution [1] and speciation studies [2]; analyzing repeat-organization and function [3]; population genetics [4]; and, ultimately, biomedical research [5,6]. De novo assemblies can achieve chromosome-length scaffolds using third-generation long sequencing reads combined with additional sequencing data for scaffolding such as Bionano optical maps or Hi-C chromatin interaction maps [7][8][9].…”