Phylogenomics Analysis of SARS-CoV2 Genomes Reveals Distinct Selection Pressure on Different Viral Strains

<div>Identification of SARS-CoV2 genomes under purifying selection bias (a) and positive selection bias (b) by using the codon-based test aided by the Nei-Gojobori method is shown. The probability of rejecting the null hypothesis of strict-neutrality (<span class="nowrap"><svg height="9.5404pt" id="M12" style="vertical-align:-0.2324991pt" version="1.1" viewbox="-0.0498162 -9.3079 44.6828 9.5404" width="44.6828pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.013,0,0,-0.013,0,0)"><path d="M517 51L485 54C448 58 441 63 441 115V712C404 700 337 684 285 678V653C357 648 362 645 362 580V437C339 446 309 449 295 449C159 449 38 340 38 201C38 61 143 -12 223 -12C234 -12 261 -6 301 17L362 53V-12C420 9 495 22 517 26V51ZM362 85C338 67 301 51 266 51C201 51 128 109 128 228C128 373 212 411 259 411C296 411 338 395 362 360V85Z"></path></g><g transform="matrix(.013,0,0,-0.013,6.864,0)"><path d="M719 650H483V622C553 619 576 606 581 560C585 532 588 487 588 394V148H585L167 650H20V622C67 618 88 610 109 585C127 562 129 557 129 484V264C129 173 126 124 123 93C118 44 92 31 35 28V0H272V28C204 32 181 44 176 95C173 124 170 172 170 264V515H172L598 -9H629V394C629 487 631 532 635 563C639 606 663 619 719 622V650Z"></path></g><g transform="matrix(.013,0,0,-0.013,20.217,0)"><path d="M535 323V373H52V323H535ZM535 138V188H52V138H535Z"></path></g><g transform="matrix(.013,0,0,-0.013,31.48,0)"><path d="M517 51L485 54C448 58 441 63 441 115V712C404 700 337 684 285 678V653C357 648 362 645 362 580V437C339 446 309 449 295 449C159 449 38 340 38 201C38 61 143 -12 223 -12C234 -12 261 -6 301 17L362 53V-12C420 9 495 22 517 26V51ZM362 85C338 67 301 51 266 51C201 51 128 109 128 228C128 373 212 411 259 411C296 411 338 395 362 360V85Z"></path></g><g transform="matrix(.013,0,0,-0.013,38.344,0)"><path d="M409 504C401 567 396 607 392 642C354 654 312 665 266 665C137 665 60 583 60 487C60 374 161 325 225 290C300 250 355 215 355 141C355 68 311 21 235 21C131 21 86 122 71 183L41 176C48 128 61 42 68 21C78 16 93 8 118 0C142 -7 175 -15 216 -15C349 -15 438 69 438 174C438 287 344 333 265 374C186 414 138 449 138 522C138 576 172 631 249 631C336 631 363 562 380 499L409 504Z"></path></g></svg>)</span> in favour of the alternative hypothesis (<svg height="9.9449pt" id="M13" style="vertical-align:-0.6369991pt" version="1.1" viewbox="-0.0498162 -9.3079 44.6828 9.9449" width="44.6828pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.013,0,0,-0.013,0,0)"><path d="M517 51L485 54C448 58 441 63 441 115V712C404 700 337 684 285 678V653C357 648 362 645 362 580V437C339 446 309 449 295 449C159 449 38 340 38 201C38 61 143 -12 223 -12C234 -12 261 -6 301 17L362 53V-12C420 9 495 22 517 26V51ZM362 85C338 67 301 51 266 51C201 51 128 109 128 228C128 373 212 411 259 411C296 411 338 395 362 360V85Z"></path></g><g transform="matrix(.013,0,0,-0.013,6.864,0)"><path d="M719 650H483V622C553 619 576 606 581 560C585 532 588 487 588 394V148H585L167 650H20V622C67 618 88 610 109 585C127 562 129 557 129 484V264C129 173 126 124 123 93C118 44 92 31 35 28V0H272V28C204 32 181 44 176 95C173 124 170 172 170 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631 363 562 380 499L409 504Z"></path></g></svg> for purifying selection and <svg height="9.9449pt" id="M14" style="vertical-align:-0.6369991pt" version="1.1" viewbox="-0.0498162 -9.3079 44.6828 9.9449" width="44.6828pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.013,0,0,-0.013,0,0)"><path d="M517 51L485 54C448 58 441 63 441 115V712C404 700 337 684 285 678V653C357 648 362 645 362 580V437C339 446 309 449 295 449C159 449 38 340 38 201C38 61 143 -12 223 -12C234 -12 261 -6 301 17L362 53V-12C420 9 495 22 517 26V51ZM362 85C338 67 301 51 266 51C201 51 128 109 128 228C128 373 212 411 259 411C296 411 338 395 362 360V85Z"></path></g><g transform="matrix(.013,0,0,-0.013,6.864,0)"><path d="M719 650H483V622C553 619 576 606 581 560C585 532 588 487 588 394V148H585L167 650H20V622C67 618 88 610 109 585C127 562 129 557 129 484V264C129 173 126 124 123 93C118 44 92 31 35 28V0H272V28C204 32 181 44 176 95C173 124 170 172 170 264V515H172L598 -9H629V394C629 487 631 532 635 563C639 606 663 619 719 622V650Z"></path></g><g transform="matrix(.013,0,0,-0.013,20.217,0)"><path d="M512 230V281L75 514V456L453 256V254L75 55V-3L512 230Z"></path></g><g transform="matrix(.013,0,0,-0.013,31.48,0)"><path d="M517 51L485 54C448 58 441 63 441 115V712C404 700 337 684 285 678V653C357 648 362 645 362 580V437C339 446 309 449 295 449C159 449 38 340 38 201C38 61 143 -12 223 -12C234 -12 261 -6 301 17L362 53V-12C420 9 495 22 517 26V51ZM362 85C338 67 301 51 266 51C201 51 128 109 128 228C128 373 212 411 259 411C296 411 338 395 362 360V85Z"></path></g><g transform="matrix(.013,0,0,-0.013,38.344,0)"><path d="M409 504C401 567 396 607 392 642C354 654 312 665 266 665C137 665 60 583 60 487C60 374 161 325 225 290C300 250 355 215 355 141C355 68 311 21 235 21C131 21 86 122 71 183L41 176C48 128 61 42 68 21C78 16 93 8 118 0C142 -7 175 -15 216 -15C349 -15 438 69 438 174C438 287 344 333 265 374C186 414 138 449 138 522C138 576 172 631 249 631C336 631 363 562 380 499L409 504Z"></path></g></svg> for positive selection) is represented as shown in different colours.</div>

BioMed Research International

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Figure 4

Figure 4: Phylogenomics Analysis of SARS-CoV2 Genomes Reveals Distinct Selection Pressure on Different Viral Strains 