Topics expected to influence personalized medicine (PM), where medical decisions, practices, and treatments are tailored to the individual patient, are reviewed. Lack of discrimination due to different biological conditions that express similar values of numerical variables (ambiguity) is regarded to be a major potential barrier for PM. This material explores possible causes and sources of ambiguity and offers suggestions for mitigating the impacts of uncertainties. Three causes of ambiguity are identified: (1) delayed adoption of innovations, (2) inadequate emphases, and (3) inadequate processes used when new medical practices are developed and validated. One example of the first problem is the relative lack of medical research on "compositional data" -the type that characterizes leukocyte data. This omission results in erroneous use of data abundantly utilized in medicine, such as the blood cell differential. Emphasis on data output ‒not biomedical interpretation that facilitates the use of clinical data‒ exemplifies the second type of problems. Reliance on tools generated in other fields (but not validated within biomedical contexts) describes the last limitation. Because reductionism is associated with these problems, non-reductionist alternatives are reviewed as potential remedies. Data structuring (converting data into information) is considered a key element that may promote PM. To illustrate a process that includes data-information-knowledge and decision-making, previously published data on COVID-19 are utilized. It is suggested that ambiguity may be prevented or ameliorated. Provided that validations are grounded on biomedical knowledge, approaches that describe certain criteria - such as non-overlapping data intervals of patients that experience different outcomes, immunologically interpretable data, and distinct graphic patterns - can inform, at personalized bases, earlier and/or with fewer observations.

To rapidly prognosticate and generate hypotheses on pathogenesis, leukocyte multi-cellularity was evaluated in SARS-CoV-2 infected patients treated in India or the United States (152 individuals, 384 temporal observations). Within hospital (< 90-day) death or discharge were retrospectively predicted based on the admission complete blood cell counts (CBC). Two methods were applied: (i) a "reductionist " one, which analyzes each cell type separately, and (ii) a "non-reductionist " method, which estimates multi-cellularity. The second approach uses a proprietary software package that detects distinct data patterns generated by complex and hypothetical indicators and reveals each data pattern's immunological content and associated outcome(s). In the Indian population, the analysis of isolated cell types did not separate survivors from non-survivors. In contrast, multi-cellular data patterns differentiated six groups of patients, including, in two groups, 95.5% of all survivors. Some data structures revealed one data point-wide line of observations, which informed at a personalized level and identified 97.8% of all non-survivors. Discovery was also fostered: some non-survivors were characterized by low monocyte/lymphocyte ratio levels. When both populations were analyzed with the non-reductionist method, they displayed results that suggested survivors and non-survivors differed immunologically as early as hospitalization day 1.

Biological classifications are made up of abstract classes created by biologists such as species, genera, families, and orders. Members of the lower species class are also members of the classes above it and this class inclusion is responsible for the fact that genera and families, for example, have more members than species and therefore require fewer properties to meet the qualification for membership. Class membership is the logical relation that allows a link to be established between physical organisms and conceptual constructs such as classes and taxa. A philosophical approach to science is useful for analyzing the ontology and epistemology of viruses and of living organisms, and it has led to a processual interpretation of organisms and viruses in terms of continuous self-generating processes of development and evolution. The need to distinguish between the antigenicity and immunogenicity of viral proteins is emphasized because confusion between these two concepts makes it very difficult for vaccinologists to develop vaccines.

The role played by studies of tobacco mosaic virus (TMV) in the development of virology is summarized. TMV was the first virus shown to be able to pass through a bacteria-retaining filter; it was also the first virus to be crystallized, to have its morphology and structure elucidated and its coat protein sequenced. Experiments done with TMV RNA in the 1950s established that viral nucleic acid is the carrier of viral infectivity. The mechanism of self-assembly and disassembly of TMV particles is described and the antigenic properties of virions and dissociated coat protein subunits are discussed. Studies of TMV have also led to various biotechnological applications which are briefly described.

More than 130,000 peer-reviewed studies have been published within one year after COVID-19 emerged in many countries. This large and rapidly growing field may overwhelm the synthesizing abilities of both researchers and policy-makers. To provide a sinopsis, prevent errors, and detect cognitive gaps that may require interdisciplinary research methods, the literature on COVID-19 is summarized, twice. The overall purpose of this study is to generate a dialogue meant to explain the genesis of and/or find remedies for omissions and contradictions. The first review starts in Biology and ends in Policy. Policy is chosen as a destination because it is the setting where cognitive integration must occur. The second review follows the opposite path: it begins with stated policies on COVID-19 and then their assumptions and disciplinary relationships are identified. The purpose of this interdisciplinary method on methods is to yield a relational and explanatory view of the field -one strategy likely to be incomplete but usable when large bodies of literature need to be rapidly summarized. These reviews identify nine inter-related problems, research needs, or omissions, namely: (1) nation-wide, geo-referenced, epidemiological data collection systems (open to and monitored by the public); (2) metrics meant to detect non-symptomatic cases -e.g., test positivity-; (3) cost-benefit oriented methods, which should demonstrate they detect silent viral spreaders even with limited testing; (4) new personalized tests that inform on biological functions and disease correlates, such as cell-mediated immunity, co-morbidities, and immuno-suppression; (5) factors that influence vaccine effectiveness; (6) economic predictions that consider the long-term consequences likely to follow epidemics that growth exponentially; (7) the errors induced by self-limiting and/or implausible paradigms, such as binary and reductionist approaches; (8) new governance models that emphasize problem-solving skills, social participation, and the use of scientific knowledge; and (9) new educational programs that utilize visual aids and audience-specific communication strategies. The analysis indicates that, to optimally address these problems, disciplinary and social integration is needed. By asking what is/are the potential cause(s) and consequence(s) of each issue, this methodology generates visualizations that reveal possible relationships as well as omissions and contradictions. While inherently limited in scope and likely to become obsolete, these shortcomings are avoided when this 'method on methods' is frequently practiced. Open-ended, inter-/trans-disciplinary perspectives and broad social participation may help researchers and citizens to construct, de-construct, and re-construct COVID-19 related research.

In addition to the well-established sense-antisense complementarity abundantly present in the nucleic acid world and serving as a basic principle of the specific double-helical structure of DNA, production of mRNA, and genetic code-based biosynthesis of proteins, sense-antisense complementarity is also present in proteins, where sense and antisense peptides were shown to interact with each other with increased probability. In nucleic acids, sense-antisense complementarity is achieved via the Watson-Crick complementarity of the base pairs or nucleotide pairing. In proteins, the complementarity between sense and antisense peptides depends on a specific hydropathic pattern, where codons for hydrophilic and hydrophobic amino acids in a sense peptide are complemented by the codons for hydrophobic and hydrophilic amino acids in its antisense counterpart. We are showing here that in addition to this pattern of the complementary hydrophobicity, sense and antisense peptides are characterized by the complementary order-disorder patterns and show complementarity in sequence distribution of their disorder-based interaction sites. We also discuss how this order-disorder complementarity can be related to protein evolution.

A workshop entitled: "Revisiting HIV inactivation, elite controllers, immunogenetics and new strategies for developing HIV vaccines" took place during a Eurovaccine Conference held in Rome in June 2016. The purpose of this workshop was to revisit old and new concepts and strategies in HIV vaccinology in the light of novel, and sometimes unexpected, data from recent preventative and therapeutic vaccine approaches that could guide future vaccine research. Panelists were asked to respond to five questions regarding key points and critical issues and problems in current HIV/AIDS vaccine research. Their responses are summarized.

Most attempts to develop synthetic peptide vaccines assume that it is possible to obtain effective vaccine immunogens by making short linear peptides adopt the structures observed when epitopes of pathogens are bound to neutralizing antibodies. Although more than a thousand synthetic peptides have been examined as potential prophylactic vaccines, only 125 peptides have progressed to phase I clinical trials, 30 have made it to phase II trials but not a single one has passed phase III trials and is currently marketed for human use. Reasons for this lack of success include 1) an excessive reliance on continuous epitopes as vaccine candidates, 2) an exaggerated confidence in the specificity of antibodies, 3) the failure to recognize that an operational bias is introduced when monoclonal antibodies are used to characterize epitopes and, 4) a tendency to underestimate the difference between antigenicity and immunogenicity. There clearly is a need to overcome these misconceptions if synthetic peptide vaccines are ever to become a reality.

The Third Cognitive Revolution poses particular challenges for biomedical research to adopt new knowledge. Interdisciplinary education at all levels would help to address these.

It is common parlance to refer to viral antigens and their epitopes as immunogens capable of producing antibodies (Abs) against the virus that harbours them. Words have an insiduous capacity to fashion our thinking and terms like immunogen and immunogenicity do suggest that epitopes are able to generate immune responses, although they only trigger in the host a series of reactions with B-cell receptors that eventually leads to the immune system (IS) producing a variety of antibodies. Although everyone in the field is well aware that antigens are different from immunogens, it seems that in many cases investigators do not use appropriate experimental tools for studying and controlling the immunogenicity of proteins rather than their antigenicity.

Virologists often use anthropomorphic metaphors to vividly describe the properties of viruses and this has led some virologists to claim that viruses are living microorganisms. The discovery of giant viruses that are larger and have a more complex genome than small bacteria has fostered the interpretation that viral factories, which are the compartments in virus-infected cells where the virus is being replicated, are able to transform themselves into a new type of living viral organism called a virocell. However, because of the widespread occurrence of horizontal gene transfer, endosymbiosis and hybridization in the evolution of viral genomes, it has not been possible to include metaphorical virocells in the so-called Tree of Life which itself is a metaphor. In the case of viruses that cause human diseases, the infection process is usually presented metaphorically as a war between host and virus and it is assumed that a virus such as the human immunodeficiency virus (HIV) is able to develop new strategies and mechanisms for escaping protective host immune responses. However, the ability of the virus to defeat the immune system is solely due to stochastic mutations arising from the error-prone activity of the viral enzyme reverse transcriptase. The following two types of metaphors will be distinguished: an intentionality metaphor commonly used for attributing goals and intentions to organisms and the living virus metaphor that considers viruses to be actually living organisms.

It is commonly assumed that neutralizing Mabs that bind to the HIV-1 Env glycoprotein are more specific reagents than anti-HIV-1 polyclonal antisera and that knowledge of the structure of these Mabs facilitates the rational design of effective HIV-1 vaccine immunogens. However, after more than ten years of unsuccessful experimentation using the structure-based reverse vaccinology approach, it is now evident that it is not possible to infer from the structure of neutralizing Mabs which HIV immunogens induced their formation nor which vaccine immunogens will elicit similar Abs in an immunized host. The use of Mabs for developing an HIV-1 vaccine was counterproductive because it overlooked the fact that the apparent specificity of a Mab very much depends on the selection procedure used to obtain it and also did not take into account that an antibody is never monospecific for a single epitope but is always polyspecific for many epitopes. When the rationale of the proponents of the unsuccessful rational design strategy is analyzed, it appears that investigators who claim they are designing a vaccine immunogen are only improving the binding reactivity of a single epitope-paratope pair and are not actually designing an immunogen able to generate protective antibodies. The task of a designer consists in imagining what type of immunogen is likely to elicit a protective immune response but in the absence of knowledge regarding which features of the immune system are responsible for producing a functional neutralizing activity in antibodies, it is not feasible to intentionally optimize a potential immunogen candidate in order to obtain the desired outcome. The only available option is actually to test possible solutions by trial-and-error experiments until the preset goal is perhaps attained. Rational design and empirical approaches in HIV vaccine research should thus not be opposed as alternative options since empirical testing is an integral part of a so-called design strategy.

The concept of antibody specificity is analyzed and shown to reside in the ability of an antibody to discriminate between two antigens. Initially, antibody specificity was attributed to sequence differences in complementarity determining regions (CDRs), but as increasing numbers of crystallographic antibody‐antigen complexes were elucidated, specificity was analyzed in terms of six antigen‐binding regions (ABRs) that only roughly correspond to CDRs. It was found that each ABR differs significantly in its amino acid composition and tends to bind different types of amino acids at the surface of proteins. In spite of these differences, the combined preference of the six ABRs does not allow epitopes to be distinguished from the rest of the protein surface. These findings explain the poor success of past and newly proposed methods for predicting protein epitopes. Antibody polyspecificity refers to the ability of one antibody to bind a large variety of epitopes in different antigens, and this property explains how the immune system develops an antibody repertoire that is able to recognize every antigen the system is likely to encounter. Antibody heterospecificity arises when an antibody reacts better with another antigen than with the one used to raise the antibody. As a result, an antibody may sometimes appear to have been elicited by an antigen with which it is unable to react. The implications of antibody polyspecificity and heterospecificity in vaccine development are pointed out. Copyright © 2014 John Wiley & Sons, Ltd.

Using the SIV model in Chinese macaques, the group headed by Jean-Marie Andrieu in Paris and Wei Lu in Montpellier were able to suppress the initial activation of SIV- positive CD4+ T-lymphocytes in vivo which is the crucial step that allows SIV to initiate replication and to establish infection. They used an oral vaccine made of inactivated SIVmac239 associated with a common commensal bacterium of the digestive tract known as Lactobacillus plantarum which is known to induce immunological tolerance to foreign antigens. In contrast to what happens with all anti-viral vaccines, this oral tolerogenic vaccine elicited neither anti-SIV antibodies nor cytotoxic T-lymphocytes but induced instead a previously unrecognized class of SIV- specific, non-cytolytic CD8+ T-regulatory cells which prevented SIV+ CD4+ T-cell activation and suppressed SIV replication. By blocking SIV reverse transcription in CD4+ T-cells, the initial burst of virus replication was prevented and the vaccinated macaques were protected from infection. Of the 16 vaccinated macaques that were challenged intra-rectally 3 to 14 months later with the homologous SIV strain as well as with the heterologous strainSIV-B670, 15 were solidly protected from SIV challenge. Since CD4+ T-cell activation drives both the initial SIV and HIV-1 replication in macaques and humans respectively, it is plausible that such a tolerogenic vaccine may also be effective against HIV-1 in humans and this will be certainly be investigated in the near future, either as a preventive or therapeutic vaccine. This remarkable and totally unexpected breakthrough was obtained by an investigator-driven research that was not funded by the usual governmental and large scale organizations that support most of the ongoing HIV vaccine research world-wide. It was sponsored by a private benefactor who funded the project to the tune of 13 million Euros. This illustrates once again that success in basic vaccine research is unpredictable and that “risky” projects based on unorthodox thinking may deserve as much funding as the “safe” projects that are often prefer red because they abide by current fashionable paradigms.

The Executive Committee of the International Committee on Taxonomy of Viruses (ICTV) has recently decided to modify the current definition of virus species (Code of Virus Classification and Nomenclature Rule 3.21) and will soon ask the full ICTV membership (189 voting members) to ratify the proposed controversial change. In this discussion paper, 14 senior virologists, including six Life members of the ICTV, compare the present and proposed new definition and recommend that the existing definition of virus species should be retained. Since the pros and cons of the proposal posted on the ICTV website are not widely consulted, the arguments are summarized here in order to reach a wider audience.

This review describes the structure-based reverse vaccinology approach aimed at developing vaccine immunogens capable of inducing antibodies that broadly neutralize HIV-1. Some basic principles of protein immunochemistry are reviewed and the implications of the extensive polyspecificity of antibodies for vaccine development are underlined. Although it is natural for investigators to want to know the cause of an effective immunological intervention, the classic notion of causality is shown to have little explanatory value for a system as complex as the immune system, where any observed effect always results from many interactions between a large number of components. Causal explanations are reductive because a single factor is singled out for attention and given undue explanatory weight on its own. Other examples of the negative impact of reductionist thinking on HIV vaccine development are discussed. These include (1) the failure to distinguish between the chemical nature of antigenicity and the biological nature of immunogenicity, (2) the belief that when an HIV-1 epitope is reconstructed by rational design to better fit a neutralizing monoclonal antibody (nMab), this will produce an immunogen able to elicit Abs with the same neutralizing capacity as the Ab used as template for designing the antigen, and (3) the belief that protection against infection can be analyzed at the level of individual molecular interactions although it has meaning only at the level of an entire organism. The numerous unsuccessful strategies that have been used to design HIV-1 vaccine immunogens are described and it is suggested that the convergence of so many negative experimental results justifies the conclusion that reverse vaccinology is unlikely to lead to the development of a preventive HIV-1 vaccine. Immune correlates of protection in vaccines have not yet been identified because this will become feasible only retrospectively once an effective vaccine exists. The finding that extensive antibody affinity maturation is needed to obtain mature anti-HIV-1 Abs endowed with a broad neutralizing capacity explains why antigens designed to fit matured Mabs are not effective vaccine immunogens since these are administered to naive recipients who possess only B-cell receptors corresponding to the germline version of the matured Abs.

Copyright: © 2012 Van Regenmortel MHV. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Since 1987, more than 30 candidate HIV-1 vaccines have advanced to human clinical trials, of which some were large-scale phase IIb and III trials [1-3]. Of all these trials, only the Thai Phase III RV144 trial, based on a recombinant canarypox-HIV vector prime and recombinant HIV-1 envelope gp120 subunit protein, showed modest protection against HIV-1 infection [4]. This result came as a surprise because the RV144 trial, which had initially been fiercely condemned as illconceived and unjustified [5-7], instilled a new feeling of optimism into the field, because it suggested that developing a preventive HIV-1 vaccine may after all be feasible. Three years later, it seems appropriate to devote a special issue of the Journal of AIDS and Clinical Research to review what progress has been made in the search for a preventive HIV-1 vaccine.