Reply to Sánchez-Pacheco et al., Chookajorn, and Mavian et al.: Explaining phylogenetic network analysis of SARS-CoV-2 genomes

Forster, Peter; Forster, Lucy; Renfrew, Colin; Förster, Michael

doi:10.1073/pnas.2007433117

Cited by 19 publications

(13 citation statements)

References 8 publications

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“…5 ). It has been previously reported by other groups ( 28 , 29 ). CEVg3 showed different geographic and temporal profiles than those described above.…”

Section: Resultssupporting

confidence: 80%

Conserved Genomic Terminals of SARS-CoV-2 as Co-evolving Functional Elements and Potential Therapeutic Targets

Chan

Choi

Schork

2020

Preprint

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ABSTRACTTo identify features in the genome of the SARS-CoV-2 pathogen responsible for the COVID-19 pandemic that may contribute to its viral replication, host pathogenicity, and vulnerabilities, we investigated how and to what extent the SARS-CoV-2 genome sequence differs from other well-characterized human and animal coronavirus genomes. Our analyses suggest the presence of unique sequence signatures in the 3’-untranslated region (UTR) of betacoronavirus lineage B, which phylogenetically encompasses SARS-CoV-2, SARS-CoV, as well as multiple groups of bat and animal coronaviruses. In addition, we identified genome-wide patterns of variation across different SARS-CoV-2 strains that likely reflect the effects of selection. Finally, we provide evidence for a possible host microRNA-mediated interaction between the 3’-UTR and human microRNA hsa-miR-1307-3p based on predicted, yet extensive, complementary base-pairings and similar interactions involving the Influenza A H1N1 virus. This interaction also suggests a possible survival mechanism, whereby a mutation in the SARS-CoV-2 3’-UTR leads to a weakened host immune response. The potential roles of host microRNAs in SARS-CoV-2 replication and infection, and the exploitation of conserved features in the 3’-UTR as therapeutic targets warrant further investigation.

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“…5 ). It has been previously reported by other groups ( 28 , 29 ). CEVg3 showed different geographic and temporal profiles than those described above.…”

Section: Resultssupporting

confidence: 80%

Conserved Genomic Terminals of SARS-CoV-2 as Co-evolving Functional Elements and Potential Therapeutic Targets

Chan

Choi

Schork

2020

Preprint

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“…Such information will be of important value for the development of vaccine, transmission monitoring and ultimately the control of the pandemic. However, most of these studies were based on limited numbers of SARS-CoV-2 genomes collected during early pandemic time, which might lead to debating conclusions (Chookajorn, 2020;Forster et al, 2020b;Kupferschmidt, 2020;Mavian et al, 2020;Rambaut et al, 2020;Sanchez-Pacheco et al, 2020). To date, more than 40,000 SARS-CoV-2 whole genome sequences have been uploaded to the online platform The Global Initiative on Sharing Avian Influenza Data (GISAID) database 1 (Elbe and Buckland-Merrett, 2017;Shu and McCauley, 2017).…”

Section: Introductionmentioning

confidence: 99%

Genetic Spectrum and Distinct Evolution Patterns of SARS-CoV-2

et al. 2020

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Four signature groups of frequently occurred single-nucleotide variants (SNVs) were identified in over twenty-eight thousand high-quality and high-coverage SARS-CoV-2 complete genome sequences, representing different viral strains. Some SNVs predominated but were mutually exclusively presented in patients from different countries and areas. These major SNV signatures exhibited distinguishable evolution patterns over time. A few hundred patients were detected with multiple viral strainrepresenting mutations simultaneously, which may stand for possible co-infection or potential homogenous recombination of SARS-CoV-2 in environment or within the viral host. Interestingly nucleotide substitutions among SARS-CoV-2 genomes tended to switch between bat RaTG13 coronavirus sequence and Wuhan-Hu-1 genome, indicating the higher genetic instability or tolerance of mutations on those sites or suggesting that major viral strains might exist between Wuhan-Hu-1 and RaTG13 coronavirus.

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“…This is unlikely to be the original sequence, as argued in [ 29 ]. The same work suggests rooting with respect to sequences found in bats and there is a debate in the literature concerning the most appropriate rooting strategy [ 29 – 31 ]. However, our haplotypes build upon the ones used in [ 27 ], which use this sequence as a reference.…”

Section: Methodsmentioning

confidence: 99%

SARS-CoV-2 transmission routes from genetic data: A Danish case study

et al. 2020

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Background The first cases of COVID-19 caused by the SARS-CoV-2 virus were reported in China in December 2019. The disease has since spread globally. Many countries have instated measures to slow the spread of the virus. Information about the spread of the virus in a country can inform the gradual reopening of a country and help to avoid a second wave of infections. Our study focuses on Denmark, which is opening up when this study is performed (end-May 2020) after a lockdown in mid-March. Methods We perform a phylogenetic analysis of 742 publicly available Danish SARS-CoV-2 genome sequences and put them into context using sequences from other countries. Results Our findings are consistent with several introductions of the virus to Denmark from independent sources. We identify several chains of mutations that occurred in Denmark. In at least one case we find evidence that the virus spread from Denmark to other countries. A number of the mutations found in Denmark are non-synonymous, and in general there is a considerable variety of strains. The proportions of the most common haplotypes remain stable after lockdown. Conclusion Employing phylogenetic methods on Danish genome sequences of SARS-CoV-2, we exemplify how genetic data can be used to trace the introduction of a virus to a country. This provides alternative means for verifying existing assumptions. For example, our analysis supports the hypothesis that the virus was brought to Denmark by skiers returning from Ischgl. On the other hand, we identify transmission routes which suggest that Denmark was part of a network of countries among which the virus was being transmitted. This challenges the common narrative that Denmark only got infected from abroad. Our analysis concerning the ratio of haplotypes does not indicate that the major haplotypes appearing in Denmark have a different degree of virality.

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Reply to Sánchez-Pacheco et al., Chookajorn, and Mavian et al.: Explaining phylogenetic network analysis of SARS-CoV-2 genomes

Cited by 19 publications

References 8 publications

Conserved Genomic Terminals of SARS-CoV-2 as Co-evolving Functional Elements and Potential Therapeutic Targets

Conserved Genomic Terminals of SARS-CoV-2 as Co-evolving Functional Elements and Potential Therapeutic Targets

Genetic Spectrum and Distinct Evolution Patterns of SARS-CoV-2

SARS-CoV-2 transmission routes from genetic data: A Danish case study

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