Comment

Decades of coronavirus research and intense studies of SARS-CoV-2 since the beginning of the COVID-19 pandemic have led to an unprecedented level of knowledge of coronavirus biology and pathogenesis, yet many outstanding questions remain. Here, we discuss knowledge gaps and research priorities in the field.

Invasive fungal diseases are on the increase globally. The World Health Organization fungal priority pathogens list highlights fungi of critical or high importance to human health and provides pathways for action. The report calls for improved surveillance (diagnostics and antifungal resistance monitoring), research and innovation (implementation research) and public-health interventions.

Although numerous tick-borne viruses are seemingly apathogenic in humans, a number of emerging tick-borne viruses have been recently identified to possess human-infection potential, with more yet to be discovered. Here, we call for greater research efforts to better delineate their precise disease burden and threats posed to global public health.

Sewage surveillance could provide information on the resistance situation in the underlying population and on environmental transmission risks. There are opportunities to make such surveillance data more informative and actionable, but there are also challenges.

Global COVID-19 vaccine equity remains aspirational for much of the world. But the emergence of rapidly evolving SARS-CoV-2 variants provides new opportunities to correct past public policies, support local vaccine production and combat rising anti-vaccine aggression.

The biofilm community has historically been very successful in aggregating scientists from very diverse fields. Now, we must harness innovative technologies across disciplines to illuminate the biofilm microenvironment and create in vitro models that accurately recapitulate natural environments.

The ongoing monkeypox outbreak in non-endemic countries is likely to be a consequence of the failure to curtail the spread of the disease in endemic regions of Africa despite decades of constant outbreaks. A globally driven one health approach to prevention and treatment of the disease is essential to control present and future outbreaks.

The comparatively milder infections with the Omicron variant and higher levels of population immunity have raised hopes for a weakening of the pandemic. We argue that the lower severity of Omicron is a coincidence and that ongoing rapid antigenic evolution is likely to produce new variants that may escape immunity and be more severe.

The magnitude of immune evasion of Omicron raises the question whether it should be considered as a distinct SARS-CoV-2 serotype. Here, we discuss lines of evidence in support or against the concept of SARS-CoV-2 serotypes, and the implications of this classification.

The International Committee on Systematics of Prokaryotes (ICSP) has recently altered long-standing phylum names and given no guidance for taxonomy of uncultured or imperfectly cultured archaea and bacteria, disrupting progress towards a universal system of microbial taxonomy. Inclusion of new members into ICSP may help it to keep up to date.

The SARS-CoV-2 pandemic has seen a notable global reduction in influenza cases of both influenza A and B viruses. In particular, the B/Yamagata lineage has not been isolated from April 2020 to August 2021, suggesting that this influenza lineage may have become extinct, which may provide opportunities for improving availability and effectiveness of influenza vaccines.

Humankind relies on host–microbe symbioses and the ecosystems they form for diverse services, including food and health. It is important to understand how symbioses will fare in a world facing rapid global change and how adaptation and resilience of symbioses can be aided to secure their services for future generations.

In settings with limited resources and a wide range of possible etiologies, molecular technologies offer an effective solution for infectious disease diagnostics, because they are agile, fast and flexible. Health systems that routinely use molecular diagnostics will achieve economies of scale, maximize limited expertize and rapidly respond to new threats.

The integrative environment-health sciences including One Health, Conservation Medicine, EcoHealth and Planetary Health embody the transdisciplinary synthesis needed to understand the multitude of factors that underpin emerging infections and their management. Future successes in confronting and resolving the complex causal basis of disease emergence to generate robust, systems-oriented risk reduction strategies that preserve both human health as well as promoting sustainable futures represent the ‘Moon Shot’ for the integrative environment-health sciences.

A global assessment of the structure and function of the crop microbiome is urgently needed for the development of effective and rationally designed microbiome technologies for sustainable agriculture. Such an effort will provide new knowledge on the key ecological and evolutionary interactions between plant species and their microbiomes that can be harnessed for increasing agriculture productivity.

Coronavirus disease 2019 may have a complex long-term impact on antimicrobial resistance (AMR). Coordinated strategies at the individual, health-care and policy levels are urgently required to inform necessary actions to reduce the potential longer-term impact on AMR and on access to effective antimicrobials.

To harness the potential of microbiome science across the broad range of relevant disciplines, new approaches to data infrastructure and transdisciplinary collaboration are necessary. The National Microbiome Data Collaborative is a new initiative to support microbiome data exploration and discovery through a collaborative, integrative data science ecosystem.

To control antimicrobial resistance (AMR) will require approaches to develop, share and preserve antibiotics that are scaled to the scientific, economic and ethical dimensions of the crisis. The three cooperative, interdisciplinary, international councils proposed in this Comment by Carl Nathan exemplify what this will require.

Resistance to the current first-line antimalarials threatens the control of malaria caused by Plasmodium falciparum and underscores the urgent need for new drugs with novel modes of action. Small-Saunders, Hagenah and Fidock present the argument that the parasite’s chloroquine resistance transporter (PfCRT) constitutes a promising target to combat multidrug-resistant malaria.

Faecal microbiota transplant (FMT) is now accepted as an effective treatment for Clostridioides difficile infections. With the increasing number of FMT treatments and clinical trials for other indications there is an urgent need for standardized regulations to ensure patient safety and focused development of safer, rationally designed, microbiota-based medicines.