Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

Mueller, Nicola Felix; Wagner, Cassia; Frazar, Chris; Roychoudhury, Pavitra; Lee, Jover; Moncla, Louise H.; Pelle, Benjamin; Richardson, M; Ryke, Erica; Xie, Hong; Shrestha, Lasata; Addetia, Amin; Rachleff, Victoria M; Lieberman, Nicole A P; Huang, Meei‐Li; Gautom, Romesh; Melly, Geoff; Hiatt, Brian; Dykema, Philip; Adler, Amanda; Brandstetter, Elisabeth; Han, Peter D.; Fay, Kairsten; Ilcisin, Misja; Lacombe, Kirsten; Sibley, Thomas H.; Truong, Melissa; Wolf, Caitlin R; Boeckh, Michael; Englund, Janet A.; Lutz, Barry; Rieder, Mark J.; Thompson, Matthew; Duchin, Jeffrey S.; Chu, Helen Y.; Shendure, Jay; Jerome, Keith R.; Lindquist, Scott; Greninger, Alexander L.; Nickerson, Deborah A.; Bedford, Trevor

doi:10.1101/2020.09.30.20204230

Cited by 21 publications

(26 citation statements)

References 40 publications

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“…Recently detected novel variants of SARS-CoV-2 show mutations at the spike protein leading to higher infectivity of the virus [ 39 ]. Independent authors have determined that there is an increased viral load triggered by the D614G mutation [ 40 , 41 ]. Currently, several mutations are identified, and the risk of a further exacerbation of the pandemic due to the increased infectivity is possible.…”

Section: Viral Structure Of Sars-cov-2mentioning

confidence: 99%

The Transmission of SARS-CoV-2 Infection on the Ocular Surface and Prevention Strategies

Kitazawa

Deinhardt‐Emmer

Inomata

et al. 2021

Cells

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global health problem. Although the respiratory system is the main impaired organ, conjunctivitis is one of its common findings. However, it is not yet understood if SARS-CoV-2 can infect the eye and if the ocular surface can be a potential route of SARS-CoV-2 transmissions. Our review focuses on the viral entry mechanisms to give a better understanding of the interaction between SARS-CoV-2 and the eye. We highlighted findings that give evidence for multiple potential receptors of SARS-CoV-2 on the ocular surface. Additionally, we focused on data concerning the detection of viral RNA and its spike protein in the various ocular tissues from patients. However, the expression level seemed to be relatively low compared to the respiratory tissues as a result of a unique environment surrounding the ocular surface and the innate immune response of SARS-CoV-2. Nevertheless, our review suggests the ocular surface as a potential route for SARS-CoV-2 transmission, and as a result of this study we strongly recommend the protection of the eyes for ophthalmologists and patients at risk.

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Section: Viral Structure Of Sars-cov-2mentioning

confidence: 99%

The Transmission of SARS-CoV-2 Infection on the Ocular Surface and Prevention Strategies

Kitazawa

Deinhardt‐Emmer

Inomata

et al. 2021

Cells

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“…This approach allows us to directly compare (via this proxy estimate) our results to those of Müller et al, in which phylodynamic simulation methods estimated that between 1% and 10% of WA cases were imported. 17 For each of our estimates, we report the median and range aggregated across the 5000 replicate analyses.…”

Section: Sequence Analysesmentioning

confidence: 99%

Phylogenetic estimates of SARS-CoV-2 introductions into Washington State

Tordoff

Greninger

Roychoudhury

et al. 2021

Preprint

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Background: The first confirmed case of SARS-CoV-2 in North America was identified in Washington state on January 21, 2020. We aimed to quantify the number and temporal trends of out-of-state introductions of SARS-CoV-2 into Washington. Methods: We conducted a phylogenetic analysis of 11,422 publicly available whole genome SARS-CoV-2 sequences from GISAID sampled between December 2019 and September 2020. We used maximum parsimony ancestral state reconstruction methods on time-calibrated phylogenies to enumerate introductions/exports, their likely geographic source (e.g. US, non-US, and between eastern and western Washington), and estimated date of introduction. To incorporate phylogenetic uncertainty into our estimates, we conducted 5,000 replicate analyses by generating 25 random time-stratified samples of non-Washington reference sequences, 20 random polytomy resolutions, and 10 random resolutions of the reconstructed ancestral state. Results: We estimated a minimum 287 separate introductions (median, range 244-320) into Washington and 204 exported lineages (range 188-227) of SARS-CoV-2 out of Washington. Introductions began in mid-January and peaked on March 29, 2020. Lineages with the Spike D614G variant accounted for the majority (88%) of introductions. Overall, 61% (range 55-65%) of introductions into Washington likely originated from a source elsewhere within the US, while the remaining 39% (range 35-45%) likely originated from outside of the US. Intra-state transmission accounted for 65% and 28% of introductions into eastern and western Washington, respectively. Conclusions: There is phylogenetic evidence that the SARS-CoV-2 epidemic in Washington is continually seeded by a large number of introductions, and that there was significant inter- and intra-state transmission. Due to incomplete sampling our data underestimate the true number of introductions.

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“…This result suggests a potential transmission advantage of G614 virus over D614 virus, although we cannot exclude the contribution of non-stochastic sampling of virus sequences and random founder effects to its current predominance. At least two groups independently noted that D614G mutation correlated with increased viral loads in COVID-19 patients 22,31 , but because this change is also associated with three or four other mutations in other viral proteins including nsp3 and RdRp, the role of the S protein in these observations remained undefined.…”

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confidence: 99%

SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity

et al. 2020

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SARS-CoV-2 variants with spike (S)-protein D614G mutations now predominate globally. We therefore compare the properties of the mutated S protein (SG614) with the original (SD614). We report here pseudoviruses carrying SG614 enter ACE2-expressing cells more efficiently than those with SD614. This increased entry correlates with less S1-domain shedding and higher S-protein incorporation into the virion. Similar results are obtained with virus-like particles produced with SARS-CoV-2 M, N, E, and S proteins. However, D614G does not alter S-protein binding to ACE2 or neutralization sensitivity of pseudoviruses. Thus, D614G may increase infectivity by assembling more functional S protein into the virion.

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Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

Cited by 21 publications

References 40 publications

The Transmission of SARS-CoV-2 Infection on the Ocular Surface and Prevention Strategies

The Transmission of SARS-CoV-2 Infection on the Ocular Surface and Prevention Strategies

Phylogenetic estimates of SARS-CoV-2 introductions into Washington State

SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity

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