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Classical epidemiological approaches have been limited in their ability to formally test hypotheses. Here, Dellicour et al. illustrate how phylodynamic and phylogeographic analyses can be leveraged for hypothesis testing in molecular epidemiology using West Nile virus in North America as an example.

The authors propose a nomenclature of SARS-CoV-2 lineages to assist research on epidemiology and decision-making during the COVID-19 pandemic. This nomenclature is based on the SARS-CoV-2 phylogeny and designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide. The authors develop a set of rules to produce a hierarchical four-level nomenclature of labels that is flexible and dynamic.

A 43-year dataset of rodents in the Hu region of China reveals how urbanization-induced changes to land-use configuration affect rodent community composition, including benefitting striped field mice, the primary local hosts of the zoonotic pathogen Hantaan virus.

This Perspective considers the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science.

In this study, the authors provide a global overview of SARS-CoV-2 genome sequencing, and estimate the proportion of cases sequenced and time to genome upload. They identify disparities and highlight the need to strengthen surveillance in lower and middle income countries.

Highly pathogenic avian influenza virus subtype H5 is an important pathogen of wild birds and poultry that has also caused infection in humans and other mammals. Here the authors use wild bird movement tracking data and virus genome sequences to quantify how seasonal bird migration facilitates global dispersal of the virus.

The rapid evolution of many important pathogens, particularly RNA viruses, means that their ecological and evolutionary dynamics occur on the same timescale. This Review discusses the insights into the transmission and epidemiology of viruses that have been provided by analyses of their evolutionary dynamics across a wide range of biological scales.

Highly pathogenic avian influenza viruses (HPAIV) can evolve via acquisition of polybasic cleavage sites, but the contribution of other mutations remains unclear. Here, the authors combine phylogenetic, statistical and structural approaches, and identify parallel mutations that are associated with HPAIV phenotype.

In this study, Aggarwal and colleagues perform prospective sequencing of SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge. They identify important factors that contributed to within university transmission and onward spread into the wider community.

The discovery of many new species of hepaciviruses and pegiviruses, which exhibit enormous genetic diversity, in wild rodent and bat populations might help us to understand the origins of the hepatitis C virus.

Analysis of SARS-CoV-2 genomes from around the world show that following initial importation largely from India, Delta spread in England was driven first by inter-regional travel and then by local population mixing.

Genetic and testing data from England show that the SARS-CoV-2 variant of concern B.1.1.7 has a transmission advantage over other lineages.

Sera from vaccinated individuals and some monoclonal antibodies show a modest reduction in neutralizing activity against the B.1.1.7 variant of SARS-CoV-2; but the E484K substitution leads to a considerable loss of neutralizing activity.

Chronic infection with SARS-CoV-2 leads to the emergence of viral variants that show reduced susceptibility to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma.

Statistical mapping techniques provide insights into the spread of two key arbovirus vectors in Europe and the United States, and predict the future distributions of both mosquitoes in response to accelerating urbanization, connectivity and climate change.

Brazil has one of the fastest-growing COVID-19 epidemics in the world. De Souza et al. report epidemiological, demographic and clinical findings for COVID-19 cases in the country during the first 3 months of the epidemic.

Other routes of infection are not the dominant contributor to the African epidemic.

The common vampire bat (Desmodus rotundus) is one of only three obligate blood-feeding mammals. By sequencing both its genome and gut metagenome, the authors provide a holistic view of the evolutionary adaptations that underlie this unusual diet.

A study of the evolution of the SARS-CoV-2 virus in England between September 2020 and June 2021 finds that interventions capable of containing previous variants were insufficient to stop the more transmissible Alpha and Delta variants.

Frequent dispersal and short-lived local transmission clusters fuelled the 2013–2016 Ebola virus epidemic in Guinea, Liberia and Sierra Leone.

The genomic profile and early transmission dynamics of the Omicron strain of SARS-CoV-2.

Evolutionary analysis of swine-origin H1N1 influenza A virus provides evidence that it was derived from several viruses circulating in swine and that it possesses genes from avian, swine and human origin. Furthermore, transmission to humans may have occurred several months before recognition of the current outbreak.

Post-international travel quarantine has been widely implemented to mitigate SARS-CoV-2 transmission, but the impacts of such policies are unclear. Here, the authors used linked genomic and contact tracing data to assess the impacts of a 14-day quarantine on return to England in summer 2020.

Genome sequencing of Zika virus samples from infected patients and Aedes aegypti mosquitoes in Florida shows that the virus was probably introduced into the United States on multiple occasions, and that the Caribbean is the most likely source.

Virus genomes reveal the establishment of Zika virus in Brazil and the Americas, and provide an appropriate timeframe for baseline (pre-Zika) microcephaly in different regions.

Analysis of spatial heterogeneity of crowding in China and Italy, together with COVID-19 case data, show that cities with higher crowding have longer epidemics and higher attack rates after the first epidemic wave.

HIV infection can be partially regulated by the host immune system; however whether B cells contribute to this response is unclear. Huanget al. show that transient depletion of B cells can result in an increase in HIV viral load suggesting that these immune cells do participate in the control of HIV infection.

The SARS-CoV-2 Delta variant has spread rapidly worldwide. Here, the authors characterise a single chain of transmission of Delta in China, and find evidence that it is more infectious and replicates faster during early infection compared to early pandemic lineages.

The Omicron variant evades vaccine-induced neutralization but also fails to form syncytia, shows reduced replication in human lung cells and preferentially uses a TMPRSS2-independent cell entry pathway, which may contribute to enhanced replication in cells of the upper airway. Altered fusion and cell entry characteristics are linked to distinct regions of the Omicron spike protein.

During the last Ebola virus outbreak in West Africa, a large amount of viral genomic data was obtained. Here, Dellicour et al. use phylodynamic approaches to assess effect of intervention strategies such as border closures.

Glycosylation plays a key role in shielding of immunogenic epitopes on viral spike (S) proteins. Here Watanabe et al. report that glycans of coronavirus SARS and MERS S proteins are heterogeneously distributed and do not form an efficacious high-density global shield which would ensure efficient immune evasion.

This study describes a new method that improves the sensitivity of viral detection compared with next-generation sequencing and enables the detection of emerging flaviviruses not specifically targeted a priori. Metagenomic sequencing with spiked primer enrichment is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making it applicable for diagnostic laboratory and field use.

Current influenza vaccine approaches largely focus on highly variable epitopes with high immunogenicity or epitopes of low variability that often have low immunogenicity. Here, Thompson et al. identify a highly immunogenic epitope of limited variability in the head ___domain of the H1 haemagglutinin and show protection from diverse H1N1 strains in mice.

Analysis of individual-level patient records from Brazil reveals that the extensive shocks in COVID-19 mortality rates are associated with pre-pandemic geographic inequities as well as shortages in healthcare capacity during the pandemic.

Current debate on the selection of strains for the influenza vaccine highlights the need for epidemiological understanding of human influenza A virus. This paper analyses genomic sequences from global viral isolates, and hypothesizes that the virus follows a 'sink-source' model, where new lineages keep arising from some areas and dying out in other areas.

Genomic characterization of the SARS-CoV-2 Omicron lineages BA.4 and BA.5, responsible for the fifth COVID-19 pandemic wave in South Africa, shows continued viral diversification and provides insights into the potential mechanisms underlying the ability of the new lineages to outcompete their predecessors.

A group convened and led by the Virus Evolution Working Group of the World Health Organization reports on its deliberations and announces a naming scheme that will enable clear communication about SARS-CoV-2 variants of interest and concern.

In this Review, the authors describe how phylogenetic and phylodynamic methods provide insight into viral evolution, focusing on the SARS-CoV-2 pandemic. The approaches reveal routes and timings of transmission events, and they can assess the effectiveness of various intervention measures aimed at controlling the virus.

High-coverage sequencing of 79 (wild and captive) individuals representing all six non-human great ape species has identified over 88 million single nucleotide polymorphisms providing insight into ape genetic variation and evolutionary history and enabling comparison with human genetic diversity.