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10.7554/eLife.66857 http://scihub22266oqcxt.onion/10.7554/eLife.66857 34387545!8363274!34387545     free     free     free Deprecated: Implicit conversion from float 227.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Elife 2021 ; 10 (ä): ä Nephropedia Template TP {{tp|p=34387545|t=2021. Patterns of within-host genetic diversity in SARS-CoV-2 |pdf=|usr=}}{{34387545}} gab.com Text Patterns of within-host genetic diversity in SARS-CoV-2 JO: Elife http://www.kidney.de/pget.php?&tw=1&pmid=34387545 #FOAvip Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses. Twit Text FOAVip Patterns of within-host genetic diversity in SARS-CoV-2 ????Elife http://www.kidney.de/pget.php?&tw=1&pmid=34387545 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=34387545 #FOAvip English Wikipedia <ref>{{Cite pmid|34387545}}</ref> Patterns of within-host genetic diversity in SARS-CoV-2 #MMPMID34387545 Tonkin-Hill G; Martincorena I; Amato R; Lawson ARJ; Gerstung M; Johnston I; Jackson DK; Park N; Lensing SV; Quail MA; Goncalves S; Ariani C; Spencer Chapman M; Hamilton WL; Meredith LW; Hall G; Jahun AS; Chaudhry Y; Hosmillo M; Pinckert ML; Georgana I; Yakovleva A; Caller LG; Caddy SL; Feltwell T; Khokhar FA; Houldcroft CJ; Curran MD; Parmar S; Alderton A; Nelson R; Harrison EM; Sillitoe J; Bentley SD; Barrett JC; Torok ME; Goodfellow IG; Langford C; Kwiatkowski D Elife 2021[Aug]; 10 (ä): ä PMID34387545show ga Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses. |*Genetic Variation[MESH] |*Genome, Viral[MESH] |*Mutation[MESH] |Base Sequence[MESH] |COVID-19/*genetics/*physiopathology[MESH] |Host-Pathogen Interactions/*genetics[MESH] |Humans[MESH] |Pandemics[MESH] |Phylogeny[MESH]Patterns of within-host genetic diversity in SARS-CoV-2 (epmc).pdf DeepDyve Pubget Overpricing