A Critical Analysis of the Evidence for the SARS-CoV-2 Origin Hypotheses.

When humans experience a new, devastating viral infection such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), significant challenges arise. How should individuals as well as societies respond to the situation? One of the primary questions concerns the origin of the SARS-CoV-2 virus that infected and was transmitted efficiently among humans, resulting in a pandemic. At first glance, the question appears straightforward to answer. However, the origin of SARS-CoV-2 has been the topic of substantial debate primarily because we do not have access to some relevant data. At least two major hypotheses have been suggested: a natural origin through zoonosis followed by sustained human-to-human spread or the introduction of a natural virus into humans from a laboratory source. Here, we summarize the scientific evidence that informs this debate to provide our fellow scientists and the public with the tools to join the discussion in a constructive and informed manner. Our goal is to dissect the evidence to make it more accessible to those interested in this important problem. The engagement of a broad representation of scientists is critical to ensure that the public and policy-makers can draw on relevant expertise in navigating this controversy.

Virology under the Microscope-a Call for Rational Discourse.

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.

Review of authorship for COVID-19 research conducted during the 2020 first-wave epidemic in Africa reveals emergence of promising African biomedical research and persisting asymmetry of international collaborations.

OBJECTIVES: The contribution of African authors to the biomedical literature is small. We evaluated the African and non-African scientific production published in the international literature on the COVID-19 in Africa during the first year of the epidemic (2020). METHODS: Papers on COVID-19 in Africa were extracted from the Medline (PubMed) database for bibliometric analysis including the proportions of three leading and last authors by study type, study country, authors' and laboratories/institutions' countries of affiliation and journal ranking. RESULTS: A total of 160 articles fulfilling the inclusion criteria were analysed. The majority (91.3%) was produced by half (53.7%) of African countries, with important regional disparities, and generally without sources of funding mentioned. The majority (>85.0) of authors in lead positions (first, second, third and last authors) were Africans. Only a small number (8.7%) of studies on COVID-19 in Africa were carried out by laboratories not on the African continent (mainly Europe, USA and China) and generally received funding. The last and first authors were more frequently of non-African origin in journals with an Impact Factor ranking ≥1, and more frequently of African origin in journals with a lower ranking (< 1). The first and last non-African authors tended to report their studies in high ranking ≥1 journals. CONCLUSIONS: Our study demonstrates that the emergence of promising African research capable of publishing in indexed but low-impact factor medical journals and reveals the persistence of a North-South asymmetry in international cooperation in biomedical research with Africa.

The quality of systematic reviews and other synthesis in the time of COVID-19.

COVID-19 research has been produced at an unprecedented rate and managing what is currently known is in part being accomplished through synthesis research. Here we evaluated how the need to rapidly produce syntheses has impacted the quality of the synthesis research. Thus, we sought to identify, evaluate and map the synthesis research on COVID-19 published up to 10 July 2020. A COVID-19 literature database was created using pre-specified COVID-19 search algorithms carried out in eight databases. We identified 863 citations considered to be synthesis research for evaluation in this project. Four-hundred and thirty-nine reviews were fully assessed with A MeaSurement Tool to Assess systematic Reviews (AMSTAR-2) and rated as very low-quality (n = 145), low-quality (n = 80), medium-quality (n = 208) and high-quality (n = 151). The quality of these reviews fell short of what is expected for synthesis research with key domains being left out of the typical methodology. The increase in risk of bias due to non-adherence to systematic review methodology is unknown and prevents the reader from assessing the validity of the review. The responsibility to assure the quality is held by both producers and publishers of synthesis research and our findings indicate there is a need to equip readers with the expertise to evaluate the review conduct before using it for decision-making purposes.

A Productive Scholar's Guide to Respectful, Responsible Inquiry During the COVID-19 Pandemic: Moving Forward.

As a result of the COVID-19 pandemic of 2020, schools across the country have pivoted to providing a range of instructional opportunities including remote, hybrid, and modified in-person options with a commitment to keeping our society safe and supporting our nations' youth in continuing their education. One byproduct of this most challenging situation has been the interruption of scientific inquiry in many fields, including educational research. Using a framework of self-leadership, in this feature article, we provide reflections to guide discussion among scholars involved in school-based research during and after the COVID-19 pandemic. Based on lessons learned in our own mentee-mentor relationships and from our collective experiences, the purpose of this article is to offer considerations primarily for early-career scholars, but also to engage dialogue among mid- and late-career scholars to promote school-based inquiry in this defining moment in history, at a time when educators are concerned with mitigating learning loss. We focus on (a) revisiting and refining programmatic lines of inquiry, (b) crafting articles to disseminate lessons learned from research conducted to date-including those with lost time points, (c) retooling in a focused area of inquiry (e.g., methodology), (d) conceptualizing future studies featuring procedures that do-and do not-allow for interpersonal contact, and (e) appreciating and acknowledging individuals who have facilitated inquiry. We conclude with a note of encouragement and call to action for future educational research.

Triaging ethical issues in the coronavirus pandemic: how to prioritize bioethics research during public health emergencies.

Much of the ethical discourse concerning the coronavirus pandemic has focused on the allocation of scarce resources, be it potentially beneficial new treatments, ventilators, intensive care beds, or oxygen. Somewhat ironically, the more important ethical issues may lie elsewhere, just as the more important medical issues do not concern intensive care or treatment for COVID-19 patients, but rather the diversion towards these modes of care at the expense of non-Covid patients and treatment. In this article I explore how ethicists can and should prioritize which ethical issues to deal with, and develop a method of triage for identification and prioritization of ethical issues both in the next public health emergency and in bioethics more widely.

[Scientific research in times of pandemics.] / La ricerca scientifica in tempi di pandemia.

When a pandemic occurs, scientific research moves fast in order to achieve readily results, such as effective therapies to fight the SARS-CoV-2 and vaccines. But this high-speed science, engaged by the emergency and characterized by the explosion of online publications in preprint form not subject to scrutiny by peer reviewers, carries some risks. And it represents a challenge to maintain research integrity and to comply with those globally recognized standard principles of fairness. Competition and the pressure to publish immediately - a way of encouraging rapid data sharing - can favor the dissemination of incomplete if not erroneous results obtained from partial studies, which feed false news, such as the benefits of a drug, and illusory hopes. It is commonly through press releases that "speed science" disseminates information to an audience that wants to be informed and reassured. Financial and political interests often mix with the urgency to find solutions. Covid-19 has highlighted in particular the risk of a politicization of science at the expense of transparency.

The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.

The 2021 Nucleic Acids Research database Issue contains 189 papers spanning a wide range of biological fields and investigation. It includes 89 papers reporting on new databases and 90 covering recent changes to resources previously published in the Issue. A further ten are updates on databases most recently published elsewhere. Seven new databases focus on COVID-19 and SARS-CoV-2 and many others offer resources for studying the virus. Major returning nucleic acid databases include NONCODE, Rfam and RNAcentral. Protein family and domain databases include COG, Pfam, SMART and Panther. Protein structures are covered by RCSB PDB and dispersed proteins by PED and MobiDB. In metabolism and signalling, STRING, KEGG and WikiPathways are featured, along with returning KLIFS and new DKK and KinaseMD, all focused on kinases. IMG/M and IMG/VR update in the microbial and viral genome resources section, while human and model organism genomics resources include Flybase, Ensembl and UCSC Genome Browser. Cancer studies are covered by updates from canSAR and PINA, as well as newcomers CNCdatabase and Oncovar for cancer drivers. Plant comparative genomics is catered for by updates from Gramene and GreenPhylDB. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been substantially updated, revisiting nearly 1000 entries, adding 90 new resources and eliminating 86 obsolete databases, bringing the current total to 1641 databases. It is available at https://www.oxfordjournals.org/nar/database/c/.

The carnage of substandard research during the COVID-19 pandemic: a call for quality.

Worldwide there are currently over 1200 research studies being performed on the topic of COVID-19. Many of these involve children and adults over age 65 years. There are also numerous studies testing investigational vaccines on healthy volunteers. No research team is exempt from the pressures and speed at which COVID-19 research is occurring. And this can increase the risk of honest error as well as misconduct. To date, 33 papers have been identified as unsuitable for public use and either retracted, withdrawn, or noted with concern. Asia is the source of most of these manuscripts (n=19; 57.6%) with China the largest Asian subgroup (n=11; 57.9%). This paper explores these findings and offers guidance for responsible research practice during pandemics.