SARS-CoV-2 within-host diversity and transmission
Patterns and bottlenecks
Structured Abstract
INTRODUCTION
RATIONALE
RESULTS
CONCLUSION
Abstract
Detection of variants is influenced by viral load
Within-host variant frequencies are reproducible
Within-host variants vary during infection
The transmission bottleneck size within households is small
Within-host variants are present in most SARS-CoV-2 samples
Distribution of iSNVs across the genome
Gene | Length | iSNVs | Mean iSNVs per 100 sites |
dN/dS (95% CI) |
|||
---|---|---|---|---|---|---|---|
Total | NS | S | |||||
5′UTR | 265 | 82 | - | - | 0.0223 | - | |
ORF1a | 13218 | 572 | 369 | 203 | 0.0031 | 0.51 (0.43, 0.61) | |
nsp1 | 540 | 54 | 39 | 15 | 0.0072 | 0.79 (0.44, 1.47) | |
nsp2 | 1914 | 105 | 65 | 40 | 0.0039 | 0.46 (0.31, 0.69) | |
nsp3 | 5835 | 175 | 108 | 67 | 0.0022 | 0.45 (0.33, 0.61) | |
nsp4 | 1500 | 101 | 61 | 40 | 0.0048 | 0.44 (0.3, 0.66) | |
nsp5A | 918 | 25 | 22 | 3 | 0.002 | 2.08 (0.72, 8.77) | |
nsp6 | 870 | 62 | 42 | 20 | 0.0051 | 0.58 (0.35, 1.01) | |
nsp7 | 249 | 6 | 2 | 4 | 0.0017 | 0.14 (0.02, 0.73) | |
nsp8 | 594 | 13 | 7 | 6 | 0.0016 | 0.32 (0.11, 0.98) | |
nsp9 | 339 | 15 | 9 | 6 | 0.0032 | 0.46 (0.17, 1.37) | |
nsp10 | 417 | 16 | 14 | 2 | 0.0028 | 1.99 (0.56, 12.67) | |
nsp12* | 2795 | 122 | 69 | 53 | 0.0031 | 0.34 (0.24, 0.49) | |
ORF1b | 8088 | 349 | 212 | 137 | 0.0031 | 0.42 (0.34, 0.52) | |
nsp13 | 1803 | 59 | 33 | 26 | 0.0024 | 0.37 (0.22, 0.63) | |
nsp14 | 1581 | 92 | 59 | 33 | 0.0042 | 0.48 (0.31, 0.74) | |
nsp15 | 1038 | 31 | 21 | 10 | 0.0021 | 0.57 (0.27, 1.26) | |
nsp16 | 894 | 45 | 30 | 15 | 0.0036 | 0.54 (0.29, 1.03) | |
S | 3822 | 190 | 129 | 61 | 0.0036 | 0.6 (0.45, 0.82) | |
ORF3a | 828 | 108 | 96 | 12 | 0.0094 | 2.29 (1.31, 4.4) | |
E | 228 | 13 | 4 | 9 | 0.0041 | 0.15 (0.04, 0.47) | |
M | 669 | 32 | 20 | 12 | 0.0034 | 0.51 (0.25, 1.08) | |
ORF6 | 186 | 10 | 8 | 2 | 0.0039 | 0.97 (0.24, 6.43) | |
ORF7a | 366 | 41 | 34 | 7 | 0.0081 | 1.43 (0.67, 3.52) | |
ORF7b | 132 | 8 | 8 | 0 | 0.0044 | ∞ (0.93, ∞) | |
ORF8 | 366 | 49 | 19 | 30 | 0.0096 | 0.17 (0.09, 0.3) | |
N | 1260 | 145 | 106 | 39 | 0.0083 | 0.81 (0.56, 1.18) | |
ORF10 | 117 | 11 | 6 | 5 | 0.0068 | 0.32 (0.09, 1.09) | |
3′UTR | 229 | 74 | - | - | 0.0232 | - | |
All coding regions† | 29260 | 1526 | 1009 | 517 | 0.0038 | 0.55 (0.49, 0.61) | |
Full genome | 22903 | 1708 | - | - | 0.0041 | - |
All genome positions are relative to the Wuhan-Hu-1 reference sequence. iSNVs at the 18 “highly shared” sites and those identified from the synthetic controls are excluded, as are those in the poly-A tail (positions 29865 to 29903). The “mean iSNVs per 100 sites” column is the mean number in each gene over all 1390 sequenced genomes. Note that because of gene overlap and noncoding intergenic regions, the total number of iSNVs (1708) cannot be obtained as the sum of any column in this table, even if the rows for nonstructural proteins in ORF1ab are excluded.
*nsp12 overlaps the boundary between ORF1a and ORF1b.
†Intergenic regions are excluded from this row.
Within-host variant sites are phylogenetically associated
Concluding remarks
Materials and methods
RNA extraction
Targeted metagenomic sequencing
Quantification controls
In-run controls
Minimizing risk of index misassignment
Bioinformatics processing
Alignment
Demonstration of the effect of read down-sampling
Transmission bottleneck analysis
Calculation of dN/dS
Phylogenetics
Phylogenetic association of iSNVs and SNPs
Phylogenetic association of iSNVs at consensus invariant positions
Acknowledgments
Supplementary Material
Summary
Resources
References and Notes
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16 April 2021
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- Katrina A. Lythgoe et al.
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RE: Can we prevent mutation of SARS-CoV-2?
Congratulations Lythgoe et al (1) for your article that asserts, "...mutations originated within individuals with long durations of infection where the virus was subjected to prolonged immune pressure and high virion load which is expected to stay for longer duration." On the other hand, adaptive evolution is necessary for the SARS-CoV-2 through mutation to survive as fittest!
Why some people produce high virion load of SARS-CoV-2 in nasal and pharyngeal mucosal surface?
Humpy bumpy nasal mucosal surface area is 200+25 square cm (2) and it is not possible to infect nook and crannies of mucous surface at one go. Nevertheless, that is not impossible either in household or in similar contacts by repeat spray of droplets. Evidences support the idea that transmission is facilitated by close proximity, confined environment, and high frequency of contacts (3). Understandably, intensity of virion load is proportional to the involvement of nasal mucosal surface might be through repeat spray of droplets.
Next query is: why SARS-CoV-2 infection stays for longer duration in some people?
Children and younger population have got young, active, vibrant, moist mucociliary conveyer to sweep away mucus contaminated with SARS-CoV-2 (MCS) towards oropharynx and MCS ultimately get through to intestine and stool. On the other hand elderly has got less active, less moist mucociliary conveyer and aged mucous-secreting glands due to decreased nasal blood flow along with decreased body water (4, 5). That might be the basis of longer extent of infection.
Now the problem is; how to prevent high virion load as well as long duration of infection to curtail mutation?
SARS-CoV-2 is a "surface virus" not as systemic virus like Ebola, HIV, Dengue etc (6). It is found that SARS-CoV-2 does not invade alveoli by haematogenous spread. It rather invades lung through the respiratory surface as microaspiration of MCS from nasopharynx (7). Understandably, higher virion load of SARS-CoV-2 is supposed to stay longer in nasal and pharyngeal mucosal surface. That is why nasopharyngeal MCS with higher virion load is a known factor for mutation. So it is logical to wash off MCS with normal saline nasal spray and gargle (NSNSG) from nasal and pharyngeal mucosal surface to prevent spread of mutated virion. One case-control study (6) reveals that the NSNSG significantly (p=0.01) washes off high virion load (cycle threshold value 25 or less) of SARS-CoV-2. Along with, NSNSG keep mucosa moist and revive mucociliary conveyer. So it seems possible to mitigate mutated virion of SARS-CoV-2 with NSNSG.
References:
1. K. A. Lythgoe et al., Science 10.1126/science.abg0821 (2021).
2. D. Zwicker. Physical and geometric constraints shape the labyrinth-like nasal cavity PNAS 115, 2936–41 (2018). www.pnas.org/cgi/doi/10.1073/pnas.1714795115
3. K. Sun et al. Transmission heterogeneities, kinetics, and controllability of SARS-CoV-2. Science 371, 254 (2021). https://doi.org/10.1126/science.abe2424
4. J.M. Pinto, S. Jeswani. Rhinitis in the geriatric population. Allergy, Asthma & Clinical Immunology 6, 1-12 (2010) doi: 10.1186/1710-1492-6-10.
5. R.G. Slavin. Treating rhinitis in the older population: special considerations. Allergy, Asthma & Clinical Immunology 5, 9 (2009) doi:10.1186/1710-1492-5-9
6. U. Chatterjee, A. Chakraborty, S. Naskar, B. Saha, B. Bandyopadhyay, S. Shee. Efficacy of normal saline nasal spray and gargle on SARS-CoV-2 for prevention of COVID-19 pneumonia. Research Square (2021) http://www.researchsquare.com/article/rs-153598/v1).
7. Y.J. Hou, K. Okuda, C.E. Edwards, et al. SARS-CoV-2 Reverse genetics reveals a variable infection gradient in the respiratory tract. Cell 182, 429–46 (2020). https://doi.org/10.1016/j.cell.2020.05.042).
RE: Within-host Diversity and Transmission of COVID-19
The ability to monitor the transmission of COVID-19, and to predict and identify new strains, variants, and lineages of the original wild-type coronavirus (COVID-19) that have emerged in several countries, including the virulent UK lineage, are among the most important issues facing the global community in terms of medical research, healthcare public policy, economic, financial, and social issues.
The important research results reported by a team of medical experts concerns the viral within-host diversity at the population level and transmission of the UK variant.
The main research findings are that escaped mutants are likely to arise infrequently, but could spread rapidly if they are highly transmissible, infectious, and contagious, as seems to be the case of the UK variant.
The unknown effects of combinations of known and unknown variants, as well as the safety, efficacy, and temporal durability of combinations of one- and two-shot vaccines, awaits the outcomes of clinical trials.
As escaped mutants may prevent herd immunity through natural infection and recovery, or through extensive vaccination programs, complacency must be avoided at all costs.
Estimation of thresholds, including within-host diversity, is fraught with difficulties in terms of the assumptions underlying the estimated linear (without threshold) and nonlinear (with threshold) models, as well as the estimation and statistical testing methods that are used.
The apparent absence of diagnostic checks makes it difficult to determine the robustness of the otherwise impressive and informative empirical results.