Preprint Concept Paper Version 1 Preserved in Portico This version is not peer-reviewed

A Hierarchical Framework for Assessing Transmission Causality of Respiratory Viruses

Version 1 : Received: 22 April 2021 / Approved: 23 April 2021 / Online: 23 April 2021 (11:59:58 CEST)
Version 2 : Received: 28 June 2022 / Approved: 30 June 2022 / Online: 30 June 2022 (03:33:13 CEST)

How to cite: Jefferson, T.; Heneghan, C.; Spencer, E.; Brassey, J.; Pluddeman, A.; Onakpoya, I.; Evans, D.; Conly, J. A Hierarchical Framework for Assessing Transmission Causality of Respiratory Viruses . Preprints 2021, 2021040633. Jefferson, T.; Heneghan, C.; Spencer, E.; Brassey, J.; Pluddeman, A.; Onakpoya, I.; Evans, D.; Conly, J. A Hierarchical Framework for Assessing Transmission Causality of Respiratory Viruses . Preprints 2021, 2021040633.


We propose a hierarchical framework based on our experience of systematically reviewing and synthesizing 378 primary studies for an evidence-based update of the modes of transmission for SARS-CoV-2. These studies revealed significant methodological shortcomings with a lack of standardization in the design, conduct, testing and reporting of SARS-CoV-2 transmission. While this situation is in part excusable at the outset of a pandemic, evidence rules of proof for assessing the transmission of this virus are needed for this and future pandemics of viral respiratory pathogens. We review the history of causality assessment related to microbial etiologies with a focus on respiratory viruses and suggest a hierarchy of evidence to integrate clinical, epidemiologic, molecular and laboratory perspectives on transmission. The hierarchy, if applied to future studies, should narrow the uncertainty over the twin concepts of causality and transmission of human respiratory viruses. We attempt to address the translational gap between the current research evidence and the assessment of causality in the transmission of respiratory viruses with a focus on SARS-CoV-2. Experimentation, consistency and independent replication of research alongside our proposed framework provide a chain of evidence that can reduce the uncertainty over the transmission of respiratory viruses and increase the level of confidence in specific modes of transmission and the measures that should be undertaken to prevent transmission


viral transmission; causation; evidence hierarchy; SARS-CoV-2; respiratory pathogens


Medicine and Pharmacology, Immunology and Allergy

Comments (4)

Comment 1
Received: 27 April 2021
Commenter: Pieter Peach
The commenter has declared there is no conflict of interests.
Comment: “To document how the second person got infected requires evidence they were exposed in their environment (the route) and that the source was sufficiently contaminated (low Ct) with infectious material (cultivatable virus) to transmit an infection to another human.
Availability of all such evidence provides a high standard of proof of transmission in the age of genomics.“

The requirement that the source is sufficiently contaminated with cultivatable virus is unnecessary in the age of genomics. What is required is evidence that the source carried the virus and that the second person now carries a virus with an adequate sequence match, and that the environmental conditions sufficiently rule out specific routes of transmission.

An example of the above are multiple cases of transmission events within hotel quarantine within several Australian states where hotel guests have become infected by SARS-CoV-2 which, on genomic analysis, matches that of guests in adjacent rooms. These are under conditions where the possibility of fomite, direct droplet, or orofaecal transmission have been excluded through close observation, lack of any prior exposure opportunities, and can only be explained by infectious virions traversing indirect paths to the infected individual.

Demonstrating low viral load and non-cultivatable virus in the specific sample taken from the source does not exclude the possibility of transmission from that source as factors such as timing in illness relative to point of transmission, anatomic location of sample, or quality of sample may affect measured viral load and ability to cultivate the virus. Requiring high copy numbers and culturable virus on a specific sample adds no additional certainty above that already provided by genomic analysis.
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Response 1 to Comment 1
Received: 10 May 2021
Commenter: Tom Jefferson
Commenter's Conflict of Interests: I am the first author of the paper. See the text for full disclosure
Comment: Thank you for your insightful comment. The role of viral culture and genome sequencing (GS) is complex and depends on the question being asked and the epidemiological context.

If we are testing integrity of the transmission chain, then GS should be sufficient to narrow uncertainty on person to person transmission.

However, if we are testing for the presence of a contagious agent, then live culture is essential as complete or consensus genomes are not necessarily proof of replicability and their predictive power depends on the methods of assembly. Some of the limitations of sequencing are discussed by Campbell et al. (reference)

Regardless of their role, we need replication of study results.

Campbell F, Strang C, Ferguson N, Cori A, Jombart T (2018) When are pathogen genome sequences informative of transmission events? PLoS Pathog 14(2): e1006885.
Comment 2
Received: 29 April 2021
Commenter: Fergal Daly
The commenter has declared there is no conflict of interests.
Comment: This paper proposes a method of determining the transmission route of a disease. It makes no attempt to evaluate the method as fit for purpose.

I would suggest applying the method to several well-known disease to determine whether it's result agree with what is already known. Does the method incorrectly include or excludes transmission routes of well-known diseases?

I would also suggest applying the method to hypothetical future disease in order to evaluate whether the method is suitable for use under time-pressure, e.g. in a pandemic. Would it take a minimum of months or years for this method to correctly identify all of the transmission routes of a disease? If so then perhaps it is useful for older diseases but not emergent diseases.

How would the methods it proposes to replace fare on these hypothetical disease and how does this improve on them?

Without any critical evaluation of the new method, it's application to SARS-CoV-2 seems premature.
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Response 1 to Comment 2
Received: 12 May 2021
The commenter has declared there is no conflict of interests.
Comment: Thank you for your insightful comment. We agree that the method should be applied in practice and modified, if needed as required.

We are at present doing just that. See: The evidence on transmission dynamics of COVID-19 from pre and asymptomatic cases: protocol for a systematic review. Tom Jefferson, Annette Pluddemann, Elisabeth Spencer, Jon Brassey, Cecilia Rosca, IGHO ONAKPOYA, Carl Heneghan, David Evans, John Conly
medRxiv 2021.05.06.21256615; doi:

We would like to reiterate that at present there is no standard recognised method to test transmission hypothesis for respiratory viruses and would be delighted if the levels of evidence were applied to a variety of agents by other groups.

We encourage comments and feedback from a broad range of readers. See criteria for comments and our Diversity statement.

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