4.7 Review

Disease-causing human viruses: novelty and legacy

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Review Microbiology

Ecology, evolution and spillover of coronaviruses from bats

Manuel Ruiz-Aravena et al.

Summary: Bats are known to carry a variety of coronaviruses and have been identified as prime reservoir hosts for emerging viruses. Since the first SARS epidemic in 2002, the understanding of bats as key hosts of coronaviruses has rapidly advanced. There are critical knowledge gaps regarding bat coronaviruses, and filling these gaps may help prevent the next pandemic.

NATURE REVIEWS MICROBIOLOGY (2022)

Article Immunology

Novel Canine Coronavirus Isolated from a Hospitalized Patient With Pneumonia in East Malaysia

Anastasia N. Vlasova et al.

Summary: This study identified a novel canine-feline recombinant alphacoronavirus isolated from a child with pneumonia, suggesting recent zoonotic transmission and emphasizing the public health threat of animal CoVs. Better surveillance is needed to monitor these viruses and their potential impact on human health.

CLINICAL INFECTIOUS DISEASES (2022)

Editorial Material Medicine, General & Internal

A Novel International Monkeypox Outbreak

Amesh Adalja et al.

ANNALS OF INTERNAL MEDICINE (2022)

Article Multidisciplinary Sciences

Climate change increases cross-species viral transmission risk

Colin J. Carlson et al.

Summary: At least 10,000 virus species have the potential to infect humans. However, changes in climate and land use may lead to viral sharing among different species of wild mammals, increasing the risk of zoonotic diseases. Using simulations, researchers found that future viral sharing could occur in high elevation areas, biodiversity hotspots, and regions with high human population density in Asia and Africa. Bats, due to their ability to disperse, are the main contributors to novel viral sharing and are likely to facilitate future disease emergence in humans.

NATURE (2022)

Article Biochemistry & Molecular Biology

Evolutionary History of Endogenous Human Herpesvirus 6 Reflects Human Migration out of Africa

Amr Aswad et al.

Summary: This study used advanced sequencing technology and mining of public human genome datasets to comprehensively understand the evolution of HHV-6, revealing that heritable integration of HHV-6 has existed since human migrations out of Africa. The research also showed that circulating and integrated HHV-6A and HHV-6B have distinct evolutionary histories and characteristics.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Multidisciplinary Sciences

Independent infections of porcine deltacoronavirus among Haitian children

John A. Lednicky et al.

Summary: Since 2003, coronaviruses have caused three major epidemics, including the ongoing SARS-CoV-2 pandemic. The emergence of coronaviruses in human species has been associated with zoonotic transmissions from animal reservoirs, emphasizing the propensity of such pathogens to spill over and adapt to new species.

NATURE (2021)

Article Infectious Diseases

Genomic-informed pathogen surveillance in Africa: opportunities and challenges

Seth C. Inzaule et al.

Summary: The article highlights the importance of enhancing disease surveillance and management in Africa, discusses the opportunities and challenges of integrating pathogen genomics into public health surveillance systems, and provides recommendations such as establishing networks, training experts, and developing policies.

LANCET INFECTIOUS DISEASES (2021)

Article Multidisciplinary Sciences

Ten millennia of hepatitis B virus evolution

Arthur Kocher et al.

Summary: Hepatitis B virus (HBV) has been infecting humans for millennia, originating between similar to 20,000 and 12,000 years ago. It was present in European and South American hunter-gatherers during the early Holocene, and later replaced by a lineage disseminated by early farmers after the European Neolithic transition.

SCIENCE (2021)

Article Multidisciplinary Sciences

Climate predicts geographic and temporal variation in mosquito-borne disease dynamics on two continents

Jamie M. Caldwell et al.

Summary: Climate has complex effects on population dynamics and vector-borne diseases, with seemingly opposing effects in different contexts. Models incorporating laboratory-measured physiological traits of mosquitoes can predict outbreak characteristics in diverse settings, yet with variable accuracy. The effects of climate on disease dynamics are highly dependent on specific contexts, such as population demographics and environmental factors.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia

Supaporn Wacharapluesadee et al.

Summary: A study identified a SARS-CoV-2-related coronavirus (SC2r-CoV), RacCS203, in Rhinolophus acuminatus bats from Thailand, with 91.5% genome similarity to SARS-CoV-2, and demonstrated that sera obtained from bats and Malayan pangolin can neutralize SARS-CoV-2.

NATURE COMMUNICATIONS (2021)

Review Virology

Interspecies Jumping of Bat Coronaviruses

Antonio C. P. Wong et al.

Summary: In the past two decades, there have been several interspecies jumping events of coronaviruses (CoV) between bats and other animals, resulting in major epidemics/pandemics and high fatality rates. The discovery of SARS-related CoVs in bats and civets, as well as genomic studies, have confirmed the transmission routes from bats to civets to humans. The MERS epidemic, with dromedaries as the reservoir, also highlights the potential risks of interspecies jumping events.

VIRUSES-BASEL (2021)

Article Biochemistry & Molecular Biology

Identifying and prioritizing potential human-infecting viruses from their genome sequences

Nardus Mollentze et al.

Summary: By developing machine learning models, we can identify candidate zoonotic pathogens based on host range features encoded in viral genomes, providing a rapid and cost-effective approach for evidence-driven virus surveillance and facilitating research on the biological and ecological characteristics of viruses.

PLOS BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Genome of Pesxtera Muierii skull shows high diversity and low mutational load in pre-glacial Europe

Emma Svensson et al.

Summary: Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced, showing similarities to modern-day Europeans but indicating they are not direct ancestors. All EUP European hunter-gatherers display high genetic diversity, and despite having the lowest diversity ever observed among Europeans, the pathogenic variant load was relatively constant from EUP to modern times.

CURRENT BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Discovery of Novel Herpes Simplexviruses in Wild Gorillas, Bonobos, and Chimpanzees Supports Zoonotic Origin of HSV-2

Joel O. Wertheim et al.

Summary: Research discovered that herpes simplexviruses from African apes are more closely related to HSV-2, indicating a potential shared evolutionary event between humans and gorillas. Through molecular clock-based hypothesis testing, multiple cross-species transmission events were identified, with the most recent one occurring between humans and bonobos.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Medicine, General & Internal

Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease

Placide Mbala-Kingebeni et al.

Summary: During the Ebola virus disease outbreak in the Democratic Republic of Congo, a young man developed EVD, recovered after receiving monoclonal antibody treatment, but later experienced a relapse, transmitted the virus, and ultimately died.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

Article Biochemistry & Molecular Biology

Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses

Hong Zhou et al.

Summary: A study in Yunnan province, China, found the existence of bat coronaviruses related to both SARS-CoV-2 and SARS-CoV, with RpYN06 virus being the closest relative of SARS-CoV-2. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species, with the largest hot-spots extending from South Laos and Vietnam to southern China. The study highlights the remarkable diversity of bat coronaviruses at the local scale.
Review Biochemistry & Molecular Biology

The origins of SARS-CoV-2: A critical review

Edward C. Holmes et al.

Summary: This article critically reviews the current scientific evidence to help clarify the origin of SARS-CoV-2. Recent debate has centered around two competing ideas: a laboratory escape scenario and zoonotic emergence.
Letter Infectious Diseases

Variola virus DNA in skeletal remains, 17th to 18th centuries, southeastern France

Avril Meffray et al.

CLINICAL MICROBIOLOGY AND INFECTION (2021)

Article Biochemistry & Molecular Biology

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

Yassine Souilmi et al.

Summary: Evolutionary analyses of human genomic datasets have revealed adaptive events involving coronaviruses and other viruses that likely occurred over 20,000 years ago in the ancestors of East Asian populations. The study highlights the importance of evolutionary information in predicting future pandemics, pointing to East Asia as a geographical origin of modern coronavirus epidemics and emphasizing that adaptation to ancient viral pressures in specific human populations does not imply genetic susceptibility differences.

CURRENT BIOLOGY (2021)

Article Biochemistry & Molecular Biology

A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses

Mahan Ghafari et al.

Summary: This study provides a predictive mechanistic model to explain the rate decay phenomenon of viruses and successfully applies it to re-estimate the date of diversification of hepatitis C virus genotypes, as well as the origin time of the most recent common ancestor of sarbecoviruses. By studying the evolutionary processes of viruses, it offers a new perspective for us to understand the origins of these viruses.

CURRENT BIOLOGY (2021)

Letter Medicine, General & Internal

Science, not speculation, is essential to determine how SARS-CoV-2 reached humans

Charles H. Calisher et al.

LANCET (2021)

Article Multidisciplinary Sciences

Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks

Alpha Kabinet Keita et al.

Summary: The 2021 Ebola virus outbreak in Guinea was found to be a resurgence from the previous outbreak, rather than a new spillover event from an animal reservoir. This highlights the need for long-term medical and social care for survivors to reduce the risk of re-emergence and prevent further stigmatization.

NATURE (2021)

Article Multidisciplinary Sciences

Genomic history of human monkey pox infections in the Central African Republic between 2001 and 2018

Nicolas Berthet et al.

Summary: The study aimed to sequence the full genome of 10 MPXV isolates collected during CAR epidemics from 2001 to 2018 to determine their phylogenetic relationships among previously described MPXV lineages in Central Africa. The results showed that the 10 CAR isolates belong to lineages closely related to those found in the DRC, suggesting transmissions from wild animals living in the rainforest. This highlights the importance of understanding the socio-economic situation, armed conflicts, and ecological disturbances in CAR, which may increase the risk of zoonotic spillover.

SCIENTIFIC REPORTS (2021)

Article Biology

Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Axel A. Guzman-Solis et al.

Summary: The introduction of new pathogens after European colonization led to a dramatic population decline of Indigenous inhabitants in the Americas. Research on ancient viruses from individuals buried during epidemics in Mexico City enriches the discussion on the etiology of infectious diseases during the Colonial period, providing direct molecular evidence of ancient viruses being transported to the Americas through the transatlantic slave trade.
Article Virology

Intrahost speciations and host switches played an important role in the evolution of herpesviruses

Anderson F. Brito et al.

Summary: As more herpesviral sequences became available, incongruences between host and viral phylogenies became more evident, with host switching and intrahost speciation being more common.

VIRUS EVOLUTION (2021)

Article Biochemistry & Molecular Biology

You Will Never Walk Alone: Codispersal of JC Polyomavirus with Human Populations

Diego Forni et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biochemistry & Molecular Biology

Recent Out-of-Africa Migration of Human Herpes Simplex Viruses

Diego Forni et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Infectious Diseases

Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics

Bram Vrancken et al.

PLOS NEGLECTED TROPICAL DISEASES (2020)

Article Immunology

Forty years with coronaviruses

Susan R. Weiss

JOURNAL OF EXPERIMENTAL MEDICINE (2020)

Review Microbiology

The continued threat of emerging flaviviruses

Theodore C. Pierson et al.

NATURE MICROBIOLOGY (2020)

Letter Biochemistry & Molecular Biology

The proximal origin of SARS-CoV-2

Kristian G. Andersen et al.

NATURE MEDICINE (2020)

Article Multidisciplinary Sciences

Evidence of human occupation in Mexico around the Last Glacial Maximum

Ciprian F. Ardelean et al.

NATURE (2020)

Article Multidisciplinary Sciences

The timing and effect of the earliest human arrivals in North America

Lorena Becerra-Valdivia et al.

NATURE (2020)

Review Biochemistry & Molecular Biology

The Recovery, Interpretation and Use of Ancient Pathogen Genomes

Sebastian Duchene et al.

CURRENT BIOLOGY (2020)

Article Multidisciplinary Sciences

Measles virus and rinderpest virus divergence dated to the sixth century BCE

Ariane Duex et al.

SCIENCE (2020)

Article Biology

Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox

Giada Ferrari et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2020)

Article Multidisciplinary Sciences

Origin and cross-species transmission of bat coronaviruses in China

Alice Latinne et al.

NATURE COMMUNICATIONS (2020)

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Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age

Barbara Muehlemann et al.

SCIENCE (2020)

Article Virology

Arenavirus genomics: novel insights into viral diversity, origin, and evolution

Chiara Pontremoli et al.

CURRENT OPINION IN VIROLOGY (2019)

Article Biochemistry & Molecular Biology

Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates

Jade Vincent Membrebe et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Review Genetics & Heredity

Ancient pathogen genomics as an emerging tool for infectious disease research

Maria A. Spyrou et al.

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Article Biochemistry & Molecular Biology

How host genetics dictates successful viral zoonosis

Cody J. Warren et al.

PLOS BIOLOGY (2019)

Article Multidisciplinary Sciences

Using hominin introgression to trace modern human dispersals

Joao C. Teixeira et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Infectious Diseases

Outbreak of human monkeypox in Nigeria in 2017-18: a clinical and epidemiological report

Adesola Yinka-Ogunleye et al.

LANCET INFECTIOUS DISEASES (2019)

Review Microbiology

Prisoners of war - host adaptation and its constraints on virus evolution

Peter Simmonds et al.

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Origin and evolution of pathogenic coronaviruses

Jie Cui et al.

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Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

L. E. Kafetzopoulou et al.

SCIENCE (2019)

Review Immunology

Chikungunya virus in Asia - Pacific: a systematic review

B. M. C. Randika Wimalasiri Yapa et al.

EMERGING MICROBES & INFECTIONS (2019)

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A 5700 year-old human genome and oral microbiome from chewed birch pitch

Theis Z. T. Jensen et al.

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Undersampling Genomes has Biased Time and Rate Estimates Throughout the Tree of Life

Julie Marin et al.

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Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans

Barbara Muehlemann et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

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The Global Virome Project

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Re-visiting the evolution, dispersal and epidemiology of Zika virus in Asia

John H-O Pettersson et al.

EMERGING MICROBES & INFECTIONS (2018)

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Origin and dispersal of Hepatitis E virus

Diego Forni et al.

EMERGING MICROBES & INFECTIONS (2018)

Article Ecology

Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico

Ashild J. Vagene et al.

NATURE ECOLOGY & EVOLUTION (2018)

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Pandemics: spend on surveillance, not prediction

Edward C. Holmes et al.

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Ancient hepatitis B viruses from the Bronze Age to the Medieval period

Barbara Muhlemann et al.

NATURE (2018)

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Emergence of Monkeypox as the Most Important Orthopoxvirus Infection in Humans

Nikola Sklenovska et al.

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Bayesian molecular dating: opening up the black box

Lindell Bromham et al.

BIOLOGICAL REVIEWS (2018)

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Transmission between Archaic and Modern Human Ancestors during the Evolution of the Oncogenic Human Papillomavirus 16

Ville N. Pimenoff et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemistry & Molecular Biology

Ancient Recombination Events between Human Herpes Simplex Viruses

Sonia Burrel et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Multidisciplinary Sciences

Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes

Yang Liu et al.

NATURE (2017)

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Host and viral traits predict zoonotic spillover from mammals

Kevin J. Olival et al.

NATURE (2017)

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Tracing the peopling of the world through genomics

Rasmus Nielsen et al.

NATURE (2017)

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Worldwide circulation of HSV-2 x HSV-1 recombinant strains

David M. Koelle et al.

SCIENTIFIC REPORTS (2017)

Review Infectious Diseases

Environmental and Social Change Drive the Explosive Emergence of Zika Virus in the Americas

Sofia Ali et al.

PLOS NEGLECTED TROPICAL DISEASES (2017)

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17th Century Variola Virus Reveals the Recent History of Smallpox

Ana T. Duggan et al.

CURRENT BIOLOGY (2016)

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Time-Dependent Rate Phenomenon in Viruses

Pakorn Aiewsakun et al.

JOURNAL OF VIROLOGY (2016)

Article Multidisciplinary Sciences

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Swapan Mallick et al.

NATURE (2016)

Article Biology

Closing the gap between rocks and clocks using total-evidence dating

Fredrik Ronquist et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2016)

Article Virology

Hepacivirus cross-species transmission and the origins of the hepatitis C virus

Oliver G. Pybus et al.

CURRENT OPINION IN VIROLOGY (2016)

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Measles

Paul A. Rota et al.

NATURE REVIEWS DISEASE PRIMERS (2016)

Article Biochemistry & Molecular Biology

Rates of Vaccine Evolution Show Strong Effects of Latency: Implications for Varicella Zoster Virus Epidemiology

Lucy A. Weinert et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

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Origin of HTLV-1 in Hunters of Nonhuman Primates in Central Africa

Mirdad Kazanji et al.

JOURNAL OF INFECTIOUS DISEASES (2015)

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Using HSV-1 Genome Phylogenetics to Track Past Human Migrations

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Letter Medicine, General & Internal

Variola Virus in a 300-Year-Old Siberian Mummy

Philippe Biagini et al.

NEW ENGLAND JOURNAL OF MEDICINE (2012)

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Origins of HIV and the AIDS Pandemic

Paul M. Sharp et al.

COLD SPRING HARBOR PERSPECTIVES IN MEDICINE (2011)

Review Biology

The evolution of HIV-1 and the origin of AIDS

Paul M. Sharp et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2010)

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Major increase in human monkeypox incidence 30 years after smallpox vaccination campaigns cease in the Democratic Republic of Congo

Anne W. Rimoin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

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Origins of major human infectious diseases

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A tale of two clades: monkeypox viruses

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JOURNAL OF GENERAL VIROLOGY (2005)

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Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

SYW Ho et al.

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The molecular population genetics of HIV-1 group O

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GENETICS (2004)

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Tracing the origin and history of the HIV-2 epidemic

P Lemey et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

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The DNA sequence of the simian varicella virus genome

WL Gray et al.

VIROLOGY (2001)

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Timing the ancestor of the HIV-1 pandemic strains

B Korber et al.

SCIENCE (2000)