Variation in predicted COVID‐19 risk among lemurs and lorises

Melin, Amanda D.; Orkin, Joseph D.; Janiak, Mareike C.; Valenzuela, Alejandro; Kuderna, Lukas F. K.; 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; Harris, R. Alan; Gut, Marta; Gut, Marta; Lizano, Esther; Nadler, Tilo; Zinner, Dietmar; Lê, Minh Đức; Manu, Shivakumara; Rabarivola, Clément; Zaramody, Alphonse; Andriaholinirina, Nicole; Johnson, Steig E.; Jarvis, Erich D.; Fédrigo, Olivier; Wu, Dong‐Dong; Farh, Kyle Kai‐How; Rogers, Jeffrey; Marquès‐Bonet, Tomàs; Navarro, Arcadi; Juan, David; Arora, Paramjit S.; Higham, James P.

doi:10.1002/ajp.23255

Cited by 7 publications

(11 citation statements)

References 55 publications

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“…For example, it is now known that African and Asian monkeys and apes, as well as some lemurs, share similar 12 ACE-2 genes as humans involved in virus binding, while monkeys in the Americas appear less susceptible to COVID-19 infection (Damas et al, 2020;Melin et al, 2020Melin et al, , 2021. To date, no primate species have been reported to experience natural COVID-19 outbreaks or high mortality rates in the wild (Ramon et al, 2023), though in many regions where primates are endemic, local community rates of COVID-19 are not well documented (Delahay et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…Since its emergence in 2019, the development of vaccines has reduced the risks of severe disease resulting from COVID‐19 infection (e.g., Kim et al, 2021), the virus has mutated to become less deadly, though more contagious, in humans (e.g., Liao et al, 2022; Rudan et al, 2022), and more information has emerged regarding nonhuman primate susceptibility to infection (e.g., Fan et al, 2022). For example, it is now known that African and Asian monkeys and apes, as well as some lemurs, share similar 12 ACE‐2 genes as humans involved in virus binding, while monkeys in the Americas appear less susceptible to COVID‐19 infection (Damas et al, 2020; Melin et al, 2020, 2021). To date, no primate species have been reported to experience natural COVID‐19 outbreaks or high mortality rates in the wild (Ramon et al, 2023), though in many regions where primates are endemic, local community rates of COVID‐19 are not well documented (Delahay et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

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Primate field research during a pandemic: Lessons learned from the SARS‐CoV‐2 outbreak

Jack,

Kulick

2023

American J Primatol

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The COVID‐19 pandemic abruptly halted most primate field research in early 2020. While international travel bans and regional travel restrictions made continuing primate field research impossible early on in the pandemic, ethical concerns of transmitting the virus from researchers to primates and surrounding human communities informed decisions regarding the timing of resuming research. Between June and September 2020, we surveyed field primatologists regarding the impacts of the pandemic on their research. We received 90 completed surveys from respondents residing in 21 countries, though most were from the United States and Canada. These data provide a valuable window into the perspectives and actions taken by researchers during the early stages of the pandemic as events were still unfolding. Only 2.4% of projects reported continuing research as usual, 33.7% continued with some decrease in productivity, 42.2% reported postponing research projects, and 21.7% reported canceling projects or postponing research indefinitely. Respondents most severely impacted by the pandemic were those establishing new field sites and graduate students whose projects were postponed or canceled due to pandemic‐related shutdowns. Fears about increased poaching, the inability to pay local assistants, frozen research funds, declining habituation, disruptions to data collection, and delays in student projects were among the top concerns of respondents. Nearly all the projects able to continue research in any capacity during the early months of the pandemic were run by or employed primate habitat country primatologists. This finding is a major lesson learned from the pandemic; without habitat country scientists, primate research is not sustainable.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Primate field research during a pandemic: Lessons learned from the SARS‐CoV‐2 outbreak

Jack,

Kulick

2023

American J Primatol

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“…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).…”

Section: Nhps Are Susceptible To Coronaviruses and Potentially Anthro...mentioning

confidence: 99%

“…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).…”

Section: Nhps Are Susceptible To Coronaviruses and Potentially Anthro...mentioning

confidence: 99%

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

Mathavarajah

Melin

Dellaire

2021

American J Primatol

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In most of our lifetimes, we have not faced a global pandemic such as the novel coronavirus disease 2019. The world has changed as a result. However, it is not only humans who are affected by a pandemic of this scale. Our closest relatives, the non‐human primates (NHPs) who encounter researchers, sanctuary/zoo employees, and tourists, are also potentially at risk of contracting the virus from humans due to similar genetic susceptibility. “Anthropozoonosis”—the transmission of diseases from humans to other species—has occurred historically, resulting in infection of NHPs with human pathogens that have led to disastrous outbreaks. Recent studies have assessed the susceptibility of NHPs and predict that catarrhine primates and some lemurs are potentially highly susceptible to infection by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) virus. There is accumulating evidence that a new factor to consider with the spread of the virus is fecal‐oral transmission. The virus has been detected in the watersheds of countries with underdeveloped infrastructure where raw sewage enters the environment directly without processing. This may expose NHPs, and other animals, to SARS‐CoV‐2 through wastewater contact. Here, we address these concerns and discuss recent evidence. Overall, we suggest that the risk of transmission of SARS‐CoV‐2 via wastewater is low. Nonetheless, tracking of viral RNA in wastewater does provide a unique testing approach to help protect NHPs at zoos and wildlife sanctuaries. A One Health approach going forward is perhaps the best way to protect these animals from a novel virus, the same way that we would protect ourselves.

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“…Highly contiguous, complete, and accurate genome assemblies are fundamental to associating genotypes with phenotypes [19, 22]; genome-based evolution [19] and speciation studies [22]; analyzing repeat-organization and function [28]; population genetics [33]; and, ultimately, biomedical research [29, 47]. 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 [24, 40, 31].…”

Section: Introductionmentioning

confidence: 99%

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

Ludwig

Dibrov

Myers

et al. 2022

Preprint

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Highly contiguous genome assemblies are essential for genomic research. Chromosome-scale assembly is feasible with the modern sequencing techniques in principle, but in practice, scaffolding errors frequently occur, leading to incorrect number and sizes of chromosomes. Relating the observed chromosome sizes from karyotype images to the generated assembly scaffolds offers a method for detecting these errors.Here, we present KICS, a semi-automated approach for estimating relative chromosome sizes from karyotype images and their subsequent comparison to the corresponding assembly scaffolds. The method relies on threshold-based image segmentation and uses the computed areas of the chromosome-related connected components as a proxy for the actual chromosome size. We demonstrate the validity and practicality of our approach by applying it to karyotype images of humans and various amphibians, birds, fish, insects, mammals, and plants. We found a strong linear relationship between pixel counts and the DNA content of chromosomes. Averaging estimates from eight human karyotype images, KICS predicts most of the chromosome sizes within an error margin of just 6 Mb.Our method provides additional means of validating genome assemblies at low costs. An interactive implementation of KICS is available at https://github.com/mpicbg-csbd/napari-kics.

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Variation in predicted COVID‐19 risk among lemurs and lorises

Cited by 7 publications

References 55 publications

Primate field research during a pandemic: Lessons learned from the SARS‐CoV‐2 outbreak

Primate field research during a pandemic: Lessons learned from the SARS‐CoV‐2 outbreak

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

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

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