An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia

Souilmi, Yassine; Lauterbur, M. Elise; Tobler, Raymond; Huber, Christian D.; Johar, Angad; Moradi, Shayli Varasteh; Johnston, Wayne A.; Krogan, Nevan J.; Alexandrov, Kirill; Enard, David

doi:10.1016/j.cub.2021.05.067

Cited by 80 publications

(103 citation statements)

References 72 publications

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“…Throughout history, infectious diseases have imposed strong selection pressures on humans 1 – 3 . In particular, viral pandemics, including ones caused by coronaviruses, have occurred repeatedly over the last century, and probably throughout human history 4 – 7 . Clinical variability in response to infection, viral or otherwise, can be explained, at least in some individuals, by human genetic factors 8 .…”

Section: Mainmentioning

confidence: 99%

A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection

et al. 2021

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SARS-CoV-2 infections display tremendous interindividual variability, ranging from asymptomatic infections to life-threatening disease. Inborn errors of, and autoantibodies directed against, type I interferons (IFNs) account for about 20% of critical COVID-19 cases among SARS-CoV-2-infected individuals. By contrast, the genetic and immunological determinants of resistance to infection per se remain unknown. Following the discovery that autosomal recessive deficiency in the DARC chemokine receptor confers resistance to Plasmodium vivax , autosomal recessive deficiencies of chemokine receptor 5 (CCR5) and the enzyme FUT2 were shown to underlie resistance to HIV-1 and noroviruses, respectively. Along the same lines, we propose a strategy for identifying, recruiting, and genetically analyzing individuals who are naturally resistant to SARS-CoV-2 infection.

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Section: Mainmentioning

confidence: 99%

A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection

et al. 2021

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“…Recent studies have investigated genetic susceptibility to SARS-CoV-2 and reported that genetic errors and gene loci are associated with approximately 20% of life-threatening COVID-19 cases, most of which are involved in two immune signaling pathways—i.e., the interferon-mediated antiviral signaling and chemokine-mediated inflammatory signaling pathways [ 5 ]. Interestingly, Souilmi et al showed a strong genomic signature in the East Asian population, likely due to ancient coronavirus epidemics that may have emerged more than 20,000 years ago, involving gene variants encoding virus-interacting proteins (VIPs), which may imply a difference in genetic susceptibility to SARS-CoV-2 infection [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

Correlation between α1-Antitrypsin Deficiency and SARS-CoV-2 Infection: Epidemiological Data and Pathogenetic Hypotheses

Vianello

Guarnieri

Braccioni

et al. 2021

JCM

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The most common hereditary disorder in adults, α1-antitrypsin deficiency (AATD), is characterized by reduced plasma levels or the abnormal functioning of α1-antitrypsin (AAT), a major human blood serine protease inhibitor, which is encoded by the SERine Protein INhibitor-A1 (SERPINA1) gene and produced in the liver. Recently, it has been hypothesized that the geographic differences in COVID-19 infection and fatality rates may be partially explained by ethnic differences in SERPINA1 allele frequencies. In our review, we examined epidemiological data on the correlation between the distribution of AATD, SARS-CoV-2 infection, and COVID-19 mortality rates. Moreover, we described shared pathogenetic pathways that may provide a theoretical basis for our epidemiological findings. We also considered the potential use of AAT augmentation therapy in patients with COVID-19.

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“…Supporting a broad host competency, SARS-CoV-2 has also infected a broad range of hosts, including various carnivores, bats, non-human primates, and rodents [15][16][17], and is likely capable of infecting many more [18] (Figure 1C). Other historical emergences may have gone undocumented [19][20][21].…”

Section: Highlightsmentioning

confidence: 99%

“…In the past two decades, coronaviruses have emerged more than once per decade. Even if earlier times were less favorable for viral emergence, a lower rate maintained over the many thousands of years of pre-modern history would still have resulted in many emerging viruses [19,21]. If these emerging viruses persisted, even at low rates, there would be many endemic coronaviruses around today.…”

Section: Trends Trends In In Immunology Immunologymentioning

confidence: 99%

Why are there so few (or so many) circulating coronaviruses?

Rice

Douek

McDermott

et al. 2021

Trends in Immunology

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Despite vast diversity in non-human hosts and conspicuous recent spillover events, only a small number of coronaviruses have been observed to persist in human populations. This puzzling mismatch suggests substantial barriers to establishment. Here, we detail hypotheses that might contribute to explain the low numbers of endemic coronaviruses, despite their considerable evolutionary and emergence potential. We assess the possible explanations ranging from issues of ascertainment, historically lower opportunities for spillover, aspects of human demographic changes, as well as features of pathogen biology and pre-existing adaptive immunity to related viruses. We describe how successful emergent viral species must triangulate transmission, virulence, and host immunity to maintain circulation. Characterizing factors that might shape the limits of viral persistence can delineate promising research directions to better understand the combinations of pathogens and contexts most likely to lead to spillover.

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An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia

Abstract: Highlights d Ancient viral epidemics can be identified through adaptation in host genomes d Genomes in East Asia bear the signature of an 25,000-yearold viral epidemic d Functional analysis supports an ancient corona-or related virus epidemic

Cited by 80 publications

References 72 publications

A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection

A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection

Correlation between α1-Antitrypsin Deficiency and SARS-CoV-2 Infection: Epidemiological Data and Pathogenetic Hypotheses

Why are there so few (or so many) circulating coronaviruses?

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