The Old Guard of Virology Warn About the Ways of the New Guard and Their Molecular Toys

In July 2001, virologist Charles Calisher, along with 13 other illustrious names in virology, wrote an open letter published in the August/Sept issue of Emerging Infectious Disease. In it, they highlighted many of the concerns the “old guard” of virology had with the “new guard.” These virologists felt that the established tried and true methods of virology were getting lost in the new molecular technology. This letter was spotlighted in an issue of Science which happened to contain some revealing quotes from Calisher. I provided some highlights from the article below along with images of the article for reference:

Old Guard Urges Virologists To Go Back to Basics

“When the dot-com bubble burst, many wondered how the old way of doing business–face to face—could have been written off so prematurely. Now, some say that in science, too, infatuation with modern technology has gone too far. In an impassioned plea published last week, a group of veteran virologists argues that the genetic techniques that have revolutionized their field can’t answer some of the most urgent and basic questions.

The message to the younger generation, with its sleek polymerase chain reaction (PCR) robots, DNA sequencers, and high-speed computers: Without bricks-and-mortar virology, it will be much harder to understand and fight the next dangerous class that comes along.

“We may be old farts, but I think we have something important to say,” says Charles Calisher, 64, a virologist at Colorado State University in Fort Collins, who drafted the paper. Slated to be printed in the July/August issue of Emerging Infectious Diseases, it was posted online(*) last week.

Calisher has been worrying for years about the wholesale takeover by modern lab toys, fearing that the genetic code they spit out sheds much less light on a class’s workings than “classic” methods. Many senior scientists (some quite a bit younger) share his views: The 14 signatories include some of the most illustrious names in U.S. virology. Together, they have many decades of experience chasing exotic classes across the globe.”

“Nowadays, scientists can detect a virus simply by searching for and amplifjhg snippels of its DNA in human or animal samples. Indeed, they have identified and described quite a few new viruses without ever isolating them.

“Although all that is terrific, says Calisher, a string of DNA letters in a data bank tells little or nothing about how a virus multiplies, which animals carry it, how it makes people sick, or whether antibodies to other viruses might protect against it. Just studying sequences, Calisher says, is “like trying to say whether somebody has bad breath by looking at his fingerprints.

“And techniques such as cloning and PCR are indispensable for studying viruses that are impossible to isolate.”

https://www.google.com/amp/s/fdocuments.in/amp/document/virology-old-guard-urges-virologists-to-go-back-to-basics.html

When I originally wrote about this letter back in August 2020, all I could find was the PDF of the 2001 Science article but not the actual letter itself. Within the article was a link to the CDC site supposedly containing Calisher’s letter. Unfortunately, when I tried accessing the link, the page no longer existed (surprise surprise). I was content back then just going off of the revealing quotes from Calisher in the Science article. However, I have always been curious what Calisher and the other virologists actually said.

Fortunately, since August 2020, I have learned a few tricks when attempting to track down difficult to find articles. I’m not the most tech savvy guy in the world so I’m sure others would have come up with this letter much faster than myself. Presented below is the entirety of Charles Calisher and his group of virologists plea to the new guard.

Keep in mind while reading this, Calisher and Co. wholeheartedly believe in the old ways of “virus isolation.” However, their definition of isolation is not the same as what the majority think of when hearing the word. These “viruses” do not come directly from humans but from cell cultured supernatant which is derived from a process that is very much the opposite of isolation. Also notice, purification of “virus” particles is never mentioned once.

For a brief overview of what virologists claim as isolation, see this link:

What Do Virologists Mean by Isolation?

Without further ado, Calisher and Co.’s warning about the ways of the new guard and their molecular toys:

Identification of Arboviruses and Certain Rodent-Borne Viruses: Reevaluation of the Paradigm

Diagnostic and epidemiologic virology laboratories have in large part traded conventional techniques of virus detection and identification for more rapid, novel, and sensitive molecular methods. By doing so, useful phenotypic characteristics are not being determined. We feel that the impact of this shift in emphasis has impaired studies of the biology of viruses. This position paper is a plea to the scientific and administrative communities to reconsider the importance of such information. We also suggest a revised paradigm for virus isolation and characterization and provide a rationale for accumulating biologic (phenotypic) information.

Historical Background

Until about 10 years ago, arthropod-borne viruses (arboviruses) were isolated and then identified by methods now referred to as “classical.” That is, clinical or field-collected samples were processed by methods originally established by yellow fever researchers at the Rockefeller Foundation (1-3). As these procedures were shared and adopted by essentially all laboratories conducting arbovirus surveillance and research, they became the standard for arbovirus laboratories worldwide. These techniques were developed to facilitate specific identification of viruses isolated from hematophagous arthropods, vertebrate animals, and human clinical samples. The general scheme included a) isolation of the virus; b) production of a virus seed or stock; c) production of a sucrose-acetone extracted antigen (often inactivated so that it could be used safely for serodiagnostic procedures); d) preparation of an antibody (usually hyperimmune mouse ascitic fluids); e) registration of the virus; and f) deposition of the virus as a voucher specimen in a reference collection (3,4). The accumulation of such reagents by arbovirus laboratories allowed the establishment of reference centers that, with the support and encouragement of the World Health Organization (5,6) and various national governments, distribute useful reagents to regional and local laboratories. Local laboratories, in turn, were then able to conduct serodiagnostic tests for antibody to newly recognized arboviruses, using standardized reagents for virus identification procedures. As an intentional by-product, a network of collaborating centers was established and an international spirit of cooperation and camaraderie evolved, as exemplified by the American Committee on Arthropod-Borne Viruses (ACAV) and its various subcommittees that take responsibility for collating a catalog of the recognized arthropod-borne and rodent-associated viruses (7), evaluating their safety, storing voucher specimens, and determining their antigenic relationships. The resulting catalog, entitled The International Catalogue of Arboviruses and Certain Other Viruses of Vertebrates, has long been the “bible” of arbovirologists. However, with the availability of newer molecular techniques and the current emphasis on genomics, many viruses now are detected by molecular means only. Consequently, few newly discovered viruses now being registered in the arbovirus catalog, although hundreds of genomic sequences of arboviruses, hantaviruses, arenaviruses, and filoviruses are entered annually in GenBank or other sequence databases. The latter data provide little or no phenotypic information, and, although the ACAV is attempting to provide accessible online biological information regarding arboviruses and other viruses, progress has been slow, in part because of lack of funding and perception of needs. The ultimate goal is to merge genotypic information, such as that deposited in sequence databases, with phenotypic and epidemiologic information, such as that published in the arbovirus catalog, and thereby provide a more accurate and complete picture of the biological characteristics of each virus.

In the heyday of arbovirology (ca. 1960-1975), arbovirus laboratories were fully functional in many parts of the world and both government and institutional support was high. The levels of training, reagent availability, virus discovery, epidemiologic assessments, and research activities were likewise high. As new techniques were developed, the name of the group studying arboviral antigenic relationships was changed from the Subcommittee on Immunological Relationships Among Catalogued Arboviruses to the Subcommittee on InterRelationships Among Catalogued Arboviruses (SIRACA), to reflect the introduction of molecular techniques as adjunct tools for virus identification and characterization. Few could have predicted the rapid advances to be made or the detail to which the arboviruses would be characterized.

The Apparent Paradigm Shift

As newer techniques (monoclonal antibodies for specific virus identification, immunohistochemistry, RNA fingerprinting, nucleic acid hybridization, and, in particular, polymerase chain reaction and nucleic acid sequencing) were introduced, the earlier techniques were replaced as front-line diagnostic tests, although they remained adequate for most purposes. One reason for this trend was that nucleic acid sequencing and monoclonal antibody mapping of proteins could be used for remarkably rapid and detailed analyses of virus identities and structures by using reagents that had better production consistency and were easier to standardize between laboratories. However, the reliance on genomic sequencing for virus identification has resulted in an apparent quandary: whether to use molecular or other methods for virus identification. Molecular techniques provide information regarding genotypic characteristics. Serologic techniques (hemagglutination inhibition, complement fixation, immunofluorescence using polyclonal or monoclonal antibodies, enzyme-linked immunosorbent assay, neutralization, and vaccination challenge) provide information regarding phenotype. These serologic techniques provide insight into protection and cross-protection against virus infection, information that is of essential epidemiologic and public health significance.

Information Gained, Opportunities Lost

In reality, there is no quandary. Genotypic and phenotypic data are complementary; the phenotype is simply the outward observable characteristic of a virus as determined by its genotype. The genomic sequence provides the foundation for phenotypic expression, but it is not yet possible to deduce completely the phenotype of a virus solely from its genomic sequence. Although some antigenic properties can be determined by using recombinant antigens, most phenotypic characteristics of a virus (its host range, pathogenicity, cell and tissue tropisms, replication characteristics, and elicitation of protective immunity) still must be determined directly. Because of this, SIRACA continues to support the use of phenotypic assays to identify and classify newly discovered viruses. It is not always necessary to derive genome sequence information for appropriate classification. In fact, for some arboviruses, e.g., those of the families Bunyaviridae and Rhabdoviridae, so little genomic sequence information exists that virus identification must rely on serologic techniques.

Reasons To Accumulate Phenotypic Information

To accurately phenotype a newly discovered virus, infectious virus must be available. Only with an actual isolate is it possible to obtain normal antigenic and other biologic information for comparison with the classical virus databases that have been accrued over many decades. Without a virus isolate, direct cross-protective assays cannot be conducted, and therefore the interrelationships by neutralization of newly recognized arboviruses, hantaviruses, arenaviruses, and filoviruses cannot be determined. Cross-neutralization relationships have been the basis by which most of these viruses have been classified and differentiated (8-15).

Recently, sequencing of virus genomes has opened the fields of viral phylogenetics and molecular epidemiology, allowing comparisons not possible by the older, classical methods. It is now possible to determine rapidly and with some certainty the sources of viruses causing dengue fever (16), West Nile fever (17,18), Venezuelan equine encephalitis (19), hantavirus pulmonary syndrome (20), Ebola fever (21), and outbreaks caused by many other viruses (22). Still, procedures appear to have outpaced process in the study of emerging and reemerging virus diseases.

New Technology Creates New Problems

Detection of viral nucleic acid is not equivalent to isolating a virus. Some hantaviruses have been detected, sequenced and placed in a taxon, and the proteins of some have been expressed without the viruses having been isolated (23). Newly recognized hantaviruses have been described solely on the basis of genomic sequencing, without the agent ever being isolated or the appropriate phenotyping reagents being produced (24-26). Without an isolate, the pathogenic potential, association with human infections and illnesses, and cross-protectivity are difficult to assess. One of the reasons for this development is that agencies funding virus research have opted to support mainly molecular and genetic studies. This funding decision has had a direct effect on the type of virus research carried out at universities, as well as direct and indirect effects on faculty recruitment and graduate education. Research involving the new genetic technologies is promoted as “cutting edge” and “mechanistic,” while more classical phenotypic studies are referred to somewhat disparagingly as “descriptive.” In truth, both types of research are largely descriptive; genome sequencing and phylogenetic studies of viruses are the molecular equivalents of classical (phenotypic) studies of antigenic properties and antigenic interrelationships. However, both types of research are essential to our understanding of the mechanisms of viral pathogenesis, disease expression, and protective immunity.

Another reason for the lack of phenotypic information about most newly discovered viral pathogens is the increased number of restraints and regulations on the importation, use, and exchange of infectious viruses. The result has been to severely restrict their study to a relatively few high-security laboratories. Inactivated RNA or DNA samples of such agents can be obtained without the need for permits, which favors the use of molecular or genetic methods for studying new viruses. The filoviruses are a case in point. These viruses are extremely hazardous and must be handled under strict Biosafety Level 4 containment. Little is known about their antigenic interrelationships, cross-protectivities, and biological characteristics. Because of the hazards posed by working with these viruses, this is likely to remain the case for the foreseeable future. In contrast, nucleotide sequence analyses of filoviruses provide information adequate for epidemiologic and diagnostic purposes, as well as for phylogenetic studies. Such analyses cannot provide antigenic information for group placement (classification) by neutralization tests or tell us much about pathogenesis or protection. However, in view of their hazardous nature, it would seem prudent for most laboratories to continue assaying filoviruses by molecular techniques, rather than to attempt direct virus isolation.

Despite the remarkable advances in sequencing and phylogenetic analysis, there still is little agreement on the standardization of sequencing approaches, which portions of the genomes of these agents are “best” for designing primers for amplification and diagnostic purposes, and which genome regions will provide the most useful sequence information for taxonomic purposes (for example, the gene coding for the expression of an immunodominant epitope). Uniformity is the sine qua non of such comparisons.

Other issues also impact biological characterization of viruses. For example, little funding is available for the study of animal viruses that are not known or suspected to be pathogens of humans, livestock, or wildlife. The current system of research support in the United States does not encourage the study of orphan viruses until they emerge as proven pathogens, a significant departure from the previous longstanding and productive policy. Likewise, funding agencies have little interest in supporting field studies designed to isolate and identify new viruses. Much lip service is given to the need for biological inventories of species diversity (genetic resources), but in the case of viruses, little funding is available for such studies. As noted, restrictions on the shipment and exchange of some infectious agents, because of biosafety and bioterrorism concerns, have inhibited biological studies with many viruses. Further discussions of these issues are beyond the scope of this paper.

A Solution?

SIRACA continues to emphasize the need for new virus isolates for reference and antigenic studies and for reagent production, even when such isolates are difficult to retrieve. We emphasize that the sources of new arboviruses, hantaviruses, arenaviruses, and filoviruses are field materials, not laboratories. Without support for continued field studies and continued virus isolation, including long-term storage of representative virus isolates, our knowledge of viral ecology, evolution, and disease emergence will continue to suffer.

In summary, remarkable advances in molecular genetics have allowed rapid and precise identifications of viruses and of their genomes; however, such characterizations thus far can provide only limited information about the phenotype and disease potential of a virus. In addition to more support for studies of viral ecology, pathogenesis, and disease potential, there is a need for serologic reagents with which classical studies can be done. We suggest that infectious materials, in the form of seed virus, be submitted to reference repositories, such as those at the University of Texas Medical Branch, Galveston, Texas; the Division of Vector-Borne Infectious Diseases, Centers for Disease Control, Fort Collins, Colorado; and the Institut Pasteur, Paris, France. These and other reference centers are supported by home institutions, government agencies, and other funding sources and serve as repositories, rather like museums without the dust.

We suggest that viruses, not simply their genomes, be registered with ACAV, the specialty group on which the International Committee for Taxonomy of Viruses mainly depends for classification of the arboviruses, hantaviruses, arenaviruses, and filoviruses. Financial and enthusiastic and knowledgeable administrative support are needed to continue the task of updating the arbovirus catalog and making it available electronically. As with disease diagnosis, it is the process, not the procedure, that is critical to success.

American Committee on Arthropod-borne Viruses, Subcommittee on InterRelationships Among Catalogued Arboviruses

http://web.archive.org/web/20020223215742/http://www.cdc.gov/ncidod/eid/vol7no4/calisher.html

For PDF version:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631763/

Molecular ViroLIEgy

Why is this warning from the old guard of virology to the new guard and their over reliance on molecular technology important? Without the old ways of “virus isolation” championed by Calisher and Co., the new guard have nothing physical backing up their random A,C,T,G’s in the computer database. If we are being honest, the “virus isolatioing” ways of the old guard also produced no real isolates either but these virologists were at least able to (wrongly) claim that because their cell culture soup produced a cytopathogenic effect, there was a “virus” present in their non-purified, unisolated soup. The new guard will claim a “viral” genome and thus the assumed presence of a “virus” without the use of cell culture. Case in point, the original “SARS-COV-2” genome which came from the unpurified BALF from one patient:

Creating the “SARS-COV-2” Genome

This is summed up brilliantly by Torsten Engelbrecht in the always amazing Off-Guardian article “Covid-19 PCR Tests are Scientifically Meaningless:”

“And that’s why we asked Dr Calisher whether he knows one single paper in which SARS-CoV-2 has been isolated and finally really purified. His answer:

I know of no such a publication. I have kept an eye out for one.”[4]

This actually means that one cannot conclude that the RNA gene sequences, which the scientists took from the tissue samples prepared in the mentioned in vitro trials and for which the PCR tests are finally being “calibrated,” belong to a specific virus— in this case SARS-CoV-2.

https://off-guardian.org/2020/06/27/covid19-pcr-tests-are-scientifically-meaningless/

In Summary:

  • From the Science article, it states some say that in science, infatuation with modern technology has gone too far
  • A group of veteran virologists argues that the genetic techniques that have revolutionized their field can’t answer some of the most urgent and basic questions
  • The message to the younger generation, with its sleek polymerase chain reaction (PCR) robots, DNA sequencers, and high-speed computers: Without bricks-and-mortar virology, it will be much harder to understand and fight the next dangerous class that comes along
  • Virologist Charles Calisher Calisher has been worrying for years about the wholesale takeover by modern lab toys, fearing that the genetic code they spit out sheds much less light on a class’s workings than “classic” methods
  • They have identified and described quite a few new “viruses” without ever isolating them
  • Calisher says a string of DNA letters in a data bank tells little or nothing about how a “virus” multiplies, which animals carry it, how it makes people sick, or whether antibodies to other “viruses” might protect against it
  • Just studying sequences, Calisher says, is “like trying to say whether somebody has bad breath by looking at his fingerprints
  • Techniques such as cloning and PCR are indispensable for studying “viruses” that are impossible to isolate
  • From Calisher’s letter, diagnostic and epidemiologic virology laboratories have in large part traded conventional techniques of “virus” detection and identification for more rapid, novel, and sensitive molecular methods
  • Calisher and Co. feel that the impact of this shift in emphasis has impaired studies of the biology of “viruses”
  • This position paper is a plea to the scientific and administrative communities to reconsider the importance of such information
  • In the past, the general scheme included:
    1. “Isolation” of the “virus;”
    2. Production of a “virus” seed or stock;
    3. Production of a sucrose-acetone extracted antigen (often inactivated so that it could be used safely for serodiagnostic procedures)
    4. Preparation of an antibody (usually hyperimmune mouse ascitic fluids)
    5. Registration of the “virus”
    6. Deposition of the “virus” as a voucher specimen in a reference collection
  • With the availability of newer molecular techniques and the current emphasis on genomics, many “viruses” now are detected by molecular means only
  • Consequently, few newly discovered “viruses” now being registered in the arbovirus catalog, although hundreds of genomic sequences of arboviruses, hantaviruses, arenaviruses, and filoviruses are entered annually in GenBank or other sequence databases
  • The latter data provide little or no phenotypic information
  • The reliance on genomic sequencing for “virus” identification has resulted in an apparent quandary: whether to use molecular or other methods for “virus” identification
  • The genomic sequence provides the foundation for phenotypic expression, but it is not yet possible to deduce completely the phenotype of a “virus” solely from its genomic sequence
  • To accurately phenotype a newly discovered “virus,” infectious “virus” must be available
  • Only with an actual “isolate” is it possible to obtain normal antigenic and other biologic information for comparison with the classical “virus” databases that have been accrued over many decades
  • Without a “virus isolate,” direct cross-protective assays cannot be conducted, and therefore the interrelationships by neutralization of newly recognized arboviruses, hantaviruses, arenaviruses, and filoviruses cannot be determined
  • Procedures appear to have outpaced process in the study of emerging and reemerging “virus” diseases
  • Detection of “viral” nucleic acid is not equivalent to isolating a “virus”
  • Without an isolate, the pathogenic potential, association with human infections and illnesses, and cross-protectivity are difficult to assess
  • Agencies funding “virus” research have opted to support mainly molecular and genetic studies
  • This funding decision has had a direct effect on the type of “virus” research carried out at universities, as well as direct and indirect effects on faculty recruitment and graduate education
  • Another reason for the lack of phenotypic information about most newly discovered “viral” pathogens is the increased number of restraints and regulations on the importation, use, and exchange of infectious “viruses”
  • The result has been to severely restrict their study to a relatively few high-security laboratories
  • Example: “Filoviruses”
    1. Little is known about their antigenic interrelationships, cross-protectivities, and biological characteristics
    2. Because of the hazards posed by working with these “viruses,” this is likely to remain the case for the foreseeable future
    3. In contrast, nucleotide sequence analyses of “filoviruses” provide information adequate for epidemiologic and diagnostic purposes, as well as for phylogenetic studies
    4. Such analyses cannot provide antigenic information for group placement (classification) by neutralization tests or tell us much about pathogenesis or protection
    5. However, in view of their hazardous nature, it would seem prudent for most laboratories to continue assaying “filoviruses” by molecular techniques, rather than to attempt direct “virus” isolation
  • There still is little agreement on the standardization of sequencing approaches, which portions of the genomes of these agents are “best” for designing primers for amplification and diagnostic purposes, and which genome regions will provide the most useful sequence information for taxonomic purposes
  • Uniformity is the sine qua non (an essential condition; a thing that is absolutely necessary) of such comparisons
  • Other issues also impact biological characterization of “viruses” such as:
    1. Little funding is available for the study of animal “viruses” that are not known or suspected to be pathogens of humans, livestock, or wildlife
    2. The current system of research support in the United States does not encourage the study of orphan “viruses” until they emerge as proven pathogens, a significant departure from the previous longstanding and productive policy
    3. Funding agencies have little interest in supporting field studies designed to isolate and identify new “viruses”
    4. Much lip service is given to the need for biological inventories of species diversity (genetic resources), but in the case of “viruses,” little funding is available for such studies
    5. Restrictions on the shipment and exchange of some infectious agents, because of biosafety and bioterrorism concerns, have inhibited biological studies with many “viruses”
  • SIRACA continues to emphasize the need for new “virus isolates” for reference and antigenic studies and for reagent production, even when such isolates are difficult to retrieve
  • Without support for continued field studies and continued “virus isolation,” including long-term storage of representative “virus isolates,” our knowledge of “viral” ecology, evolution, and disease emergence will continue to suffer
  • Molecular advances can provide only limited information about the phenotype and disease potential of a “virus”
  • Calisher and co. ask for more support for studies of “viral” ecology, pathogenesis, and disease potential and state there is a need for serologic reagents with which classical studies can be done
  • They suggest that infectious materials, in the form of seed “virus,” be submitted to reference repositories
  • They also suggest that “viruses,” not simply their genomes, be registered
  • As with disease diagnosis, it is the process, not the procedure, that is critical to success
  • In 2020, Charles Calisher was asked whether he knows one single paper in which “SARS-CoV-2” has been isolated and finally really purified. His answer:
    • I know of no such a publication. I have kept an eye out for one.”
  • Thus there can be no conclusion that the RNA gene sequences, which the scientists took from the tissue samples prepared in the in vitro trials and for which the PCR tests are finally being “calibrated,” belong to a specific “virus”— in this case “SARS-CoV-2”

The old virologists were concerned that the ways of “virus isolation” from the past were being lost on the new generation with their shiny new molecular toys. It was a prescient warning as PCR and genomics have taken over virology in a big way since then and this can easily be seen with the rise of “SARS-COV-2” which was created entirely in silico (in a computer). The cell culture process itself, while an invalid method for the purification/isolation of any “virus,” has become almost an afterthought as virology continues to look for ways to skip this step completely and create “viruses” entirely in the database.

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