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Phytophthora cinnamomi is a pathogenic oomycete that causes plant dieback disease across a range of natural ecosystems and in many agriculturally important crops on a global scale. An annotated draft genome sequence is publicly available (JGI Mycocosm) and suggests 26,131 gene models. In this study, soluble mycelial, extracellular (secretome), and zoospore proteins of P. cinnamomi were exploited to refine the genome by correcting gene annotations and discovering novel genes. By implementing the diverse set of sub-proteomes into a generated proteogenomics pipeline, we were able to improve the P. cinnamomi genome annotation. Liquid chromatography mass spectrometry was used to obtain high confidence peptides with spectral matching to both the annotated genome and a generated 6-frame translation. Two thousand seven hundred sixty-four annotations from the draft genome were confirmed by spectral matching. Using a proteogenomic pipeline, mass spectra were used to edit the P. cinnamomi genome and allowed identification of 23 new gene models and 60 edited gene features using high confidence peptides obtained by mass spectrometry, suggesting a rate of incorrect annotations of 3% of the detectable proteome. The novel features were further validated by total peptide support, alongside functional analysis including the use of Gene Ontology and functional domain identification. We demonstrated the use of spectral data in combination with our proteogenomics pipeline can be used to improve the genome annotation of important plant diseases and identify missed genes. This study presents the first use of spectral data to edit and manually annotate an oomycete pathogen.

COVID-19 vaccines are likely to be scarce for years to come. Many countries, from India to the U.K., have demonstrated vaccine nationalism. What are the ethical limits to this vaccine nationalism? Neither extreme nationalism nor extreme cosmopolitanism is ethically justifiable. Instead, we propose the fair priority for residents (FPR) framework, in which governments can retain COVID-19 vaccine doses for their residents only to the extent that they are needed to maintain a noncrisis level of mortality while they are implementing reasonable public health interventions. Practically, a noncrisis level of mortality is that experienced during a bad influenza season, which society considers an acceptable background risk. Governments take action to limit mortality from influenza, but there is no emergency that includes severe lockdowns. This “flu-risk standard” is a nonarbitrary and generally accepted heuristic. Mortality above the flu-risk standard justifies greater governmental interventions, including retaining vaccines for a country's own citizens over global need. The precise level of vaccination needed to meet the flu-risk standard will depend upon empirical factors related to the pandemic. This links the ethical principles to the scientific data emerging from the emergency. Thus, the FPR framework recognizes that governments should prioritize procuring vaccines for their country when doing so is necessary to reduce mortality to noncrisis flu-like levels. But after that, a government is obligated to do its part to share vaccines to reduce risks of mortality for people in other countries. We consider and reject objections to the FPR framework based on a country: (1) having developed a vaccine, (2) raising taxes to pay for vaccine research and purchase, (3) wanting to eliminate economic and social burdens, and (4) being ineffective in combating COVID-19 through public health interventions.

Once effective coronavirus disease 2019 (COVID-19) vaccines are developed, they will be scarce. This presents the question of how to distribute them fairly across countries. Vaccine allocation among countries raises complex and controversial issues involving public opinion, diplomacy, economics, public health, and other considerations. Nevertheless, many national leaders, international organizations, and vaccine producers recognize that one central factor in this decision-making is ethics (1, 2). Yet little progress has been made toward delineating what constitutes fair international distribution of vaccine. Many have endorsed “equitable distribution of COVID-19…vaccine” without describing a framework or recommendations (3, 4). Two substantive proposals for the international allocation of a COVID-19 vaccine have been advanced, but are seriously flawed. We offer a more ethically defensible and practical proposal for the fair distribution of COVID-19 vaccine: the Fair Priority Model. The Fair Priority Model is primarily addressed to three groups. One is the COVAX facility—led by Gavi, the World Health Organization (WHO), and the Coalition for Epidemic Preparedness Innovations (CEPI)—which intends to purchase vaccines for fair distribution across countries (5). A second group is vaccine producers. Thankfully, many producers have publicly committed to a “broad and equitable” international distribution of vaccine (2). The last group is national governments, some of whom have also publicly committed to a fair distribution (1). These groups need a clear framework for reconciling competing values, one that they and others will rightly accept as ethical and not just as an assertion of power. The Fair Priority Model specifies what a fair distribution of vaccines entails, giving content to their commitments. Moreover, acceptance of this common ethical framework will reduce duplication and waste, easing efforts at a fair distribution. That, in turn, will enhance producers' conf