SARS-CoV-2 transmission bottleneck is of the order of one to three virions

Prior research by two Emory University researchers to characterize the transmission dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), found that the size of the virus's transmission bottleneck was large, i.e., on the order of 1,000 virions. Now,  a new study, posted to the bioRxiv* preprint server by the same researchers, focussing on the Austrian region, found that SARS-CoV-2 transmission bottlenecks to be much tighter than previously thought.

A new computational analysis using more than 500 deep-sequences was carried out. A combination of genetic and epidemiological data of a wide range of viruses was analyzed to characterize the transmission dynamics of SARS-CoV-2 in Austria between the period February to April 2020. Further, the researchers investigated the patterns of shared low-frequency variants between the transmission pairs where a de novo genetic mutation was present in the recipient.

After a thorough reanalysis, researchers obtained a contradictory result from the earlier paper. They found SARS-CoV-2 transmission bottlenecks are extremely small and tight, i.e., on the order of 1-3 virions. The most significant aspect of this result is that it has shed light on how the virus evolves between hosts. Further, it has also helped understand the process or pattern by which the genetic mutation occurs within the population.

The reason for the reanalysis of the data was the presence of a few doubtful elements. The prior research estimated the bottleneck size (using a 3% variant) to be bimodal, with 14 of the 39 transmission pairs having an inferred size. To better understand the above result, scientists reanalyzed the deep sequencing data (transmission bottleneck sizes at 1% and 3%) and found similarities between the obtained result and previous research. However, on conducting further analyses, they found a drop in the bottleneck size. This drop was estimated during a 1% cutoff to a 3% cutoff for every one of the 13 transmission pairs that had donors with a maximum intrahost single-nucleotide variants (iSNV) frequency of >6%.

The scientists reported that an increase in the variant calling threshold removes the iSNVs from the analysis. Additionally, a consistent decrease in the inferred bottleneck size may occur if low-frequency donor iSNVs depict large bottleneck sizes and high-frequency donor iSNVs depicting small bottleneck sizes. The current investigation has shown the presence of low-frequency iSNVs across donor-recipient transmission pairs, indicating a significant congruence between their frequencies, revealing a wide transmission bottleneck. However, the high-frequency donor iSNVs, which were rarely present for donor-recipient transmission, would suggest a narrow transmission bottleneck.

To understand the conflicting patterns, scientists considered genetic mutations that were present, since the beginning, in the recipient hosts. The genetic variations were present in the "tv plots" as iSNVs were absent from a donor and present in the corresponding recipient.

Scientists explained that in a de novo variant having a constant or fixed factor in a recipient sample, no sharing of iSNVs should be observed between a donor and a recipient. Their presence in the recipient can only be observed at subclonal frequencies where rapid intra-host recombination occurs, or the fixed de novo variant occurs several times in different genetic backgrounds. However, the previous study showed shared subclonal iSNVs at remarkably similar frequencies between the transmission pairs and a fixed de novo variant present in the recipient. This result was reanalyzed as shared low-frequency iSNVs are highly unlikely to constitute transmitted genetic variation. The low-frequency iSNVs shared between donor-recipient pairs occurred either spuriously or independently in the recipient (homoplasies). Scientists further pointed out that these factors should be omitted from any transmission bottleneck analysis that involves a transmission pair.

In the re-estimation study, scientists have used the beta-binomial method at a conservative variant calling threshold of 6%. 13 transmission pairs with one or more donor iSNVs were found at a 6% cutoff, which indicated bottleneck sizes could only be estimated for these pairs. The increase in the variant calling threshold holds no significance in the bottleneck size estimation. The current study revealed that an estimation of a mean bottleneck size of 1.21, such that 99% of transmissions are successful, is expected to result from 3 or fewer virions.

Therefore, this analysis indicates that SARS-CoV-2 has a narrow transmission bottleneck, which is similar in size to influenza A viruses. A small bottleneck size also suggests that infections are commonly initiated at very low viral genetic diversity. Scientists believe that their research would substantially add value to the existing information about SARS-CoV-2 evolution between and within infected individuals.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Dr. Priyom Bose

Written by

Dr. Priyom Bose

Priyom holds a Ph.D. in Plant Biology and Biotechnology from the University of Madras, India. She is an active researcher and an experienced science writer. Priyom has also co-authored several original research articles that have been published in reputed peer-reviewed journals. She is also an avid reader and an amateur photographer.


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