Variation in predicted COVID-19 risk among lemurs and lorises
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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.
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SciScore for 10.1101/2021.02.03.429540: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources , scaffold 13170, (gene identified via BLAST). BLASTsuggested: (BLASTX, RRID:SCR_001653)Gene Alignments: We mapped reads from whole-genome sequence (WGS) data to the closest available annotated reference assembly from among the set of partially unpublished (unp.) references (Daubentonia madagascariensis, ( WGSsuggested: NoneBriefly, after removing adapter sequences using cutadapt, we mapped the reads using bwa mem and processed and sorted alignments using samtools. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)We then aligned these 66 amino acid sequences using MAFFT with default settings … SciScore for 10.1101/2021.02.03.429540: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources , scaffold 13170, (gene identified via BLAST). BLASTsuggested: (BLASTX, RRID:SCR_001653)Gene Alignments: We mapped reads from whole-genome sequence (WGS) data to the closest available annotated reference assembly from among the set of partially unpublished (unp.) references (Daubentonia madagascariensis, ( WGSsuggested: NoneBriefly, after removing adapter sequences using cutadapt, we mapped the reads using bwa mem and processed and sorted alignments using samtools. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)We then aligned these 66 amino acid sequences using MAFFT with default settings with those extracted from publicly available genomes (Melin et al., 2020). MAFFTsuggested: (MAFFT, RRID:SCR_011811)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Additional limitations include that our study examined variation at sites identified to be critical for SARS-CoV-2 viral binding, but did not assess the impact of residues that are not in direct contact with the virus and which may still affect binding allosterically. In addition, we did not examine genetic variation or model the function of the protease (TMPRSS2) that facilitates viral entry post binding (Hoffman et al. 2020), which is anticipated to impact disease progression. We also emphasize that our approach investigates the likely initial susceptibility of species to SARS-CoV-2 infection. The severity of viral infection responses may differ between species and is related to variation in immune and other responses (Lukassen et al., 2020). Nonetheless, the results of in vivo infection studies conducted on haplorrhine primates and other mammals strongly support the predictions of protein-protein interaction models about the susceptibility of different species to SARS-CoV-2 and the development of COVID-19-like symptoms (Blair et al., 2020; Lu et al., 2020; Rockx et al., 2020; Shan et al., 2020; Shi et al., 2020), supporting the applicability of our results. An additional tangible contribution of our study is that it provides novel sequence data that can be used in site-directed mutagenesis to recreate taxon-specific ACE2 proteins for cellular assays (Guy et al., 2005). At the same time, results predicting high susceptibility among a large number of genera are sufficiently ...
Results from TrialIdentifier: No clinical trial numbers were referenced.
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Results from JetFighter: We did not find any issues relating to colormaps.
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