PROVIDED PAPER Forni D, Cagliani R, Clerici M, Sironi M. 2017. .pdf

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PROVIDED PAPER: Forni D, Cagliani R, Clerici M, Sironi M. 2017. Molecular evolution of human coronavirus genomes. Trends in Microbiology 25:36-48. 1) How does your maximun likelihood tree compare to the genome-based tree from the paper? What gene is your tree baed upon? What are the potential functions of the protein made from this coronavirus gene? Are there genetic mechanisms more prevalent in virus genomes that make evolutionary inferences from one gene or a whole genome more complicated than other kinds of organisms? 2) How many different host species were associated with the samples in your dataset? What inferences can be made about the origin of COVID19 prior to infecting humans? Have you heard about any other organisms related to COVID19 that are not represented in your dataset or the provided paper? QHO62376.1:1-7096 orflab polyprotein Severe scute respiratory syndrome coronavins 2 QH2a75a1.11-7096 orfiab polyprotein Severe acule respiratory syndrome coronavirus 2 QHU79171.1:1-7096 ortiab polyprotein Severe acule respiratory syndrome coronavirus 2 QH287591.1:1-7088 ortlab polyproteln Severe acule resplratory syndrome coronavirus 2 QHz00398.1:1-7096 orftab polyprotein Severe acute respiratory syndrome coronavirus 2 QHR63299.1:1-7095 ort1ab polyprotein Bat coronavirus RaTG13 AVP76041.1:1-7070 nen- structural polyprotein 1ab Bat SARS-ike coronavins AVP78030.1:1-7092 non-structural polyprotein 1ab Bat SARS-like coronavirus [ AD16715.1:1-7063 orflab polyprotein Bet SARS- lave coronevirus AM04663.11-7073 replicase p1AB 8ARS coronavinus clvot020 ATO96143.1:1-7073 non-struchural polyprotein 1ab Bat SARS-ike coronavirus A244803.1:1- 7073 ort ob polyprotein Bat coronavirus ARU4798.1:1-7073 oiflab polyprotein Bat coronavinU QDF43629.1:1-7073 ORF 1ab Coronavins BtRs-BetaCoVINN2018C ATOO8155.1:1-7073 non- structural polyprotein 1 ab Bat SARS-like coronavlrus AXNT3357.1 ORF1ab Middle East respiratory syndrome-related coronavirus aFQs6585.1 ORF1ab Middo East rosplratory syndrome-rolatod coronavirus AXN73424.1 ORF 1ab Midde East respiratory syndrome-related coronavirus YP 009555238,1 Or1ab Human coronavirus OC43 AMN88684.1 ortiab polypretein Human coronawirus HKU1 AOG747a2.1 ORF1AB Human coronavinus 229E - AWr59972.1 ORF 1ab Human coronavirus NL63 QHO62876.1:1-7096 orf1 ab polyprotein Severe acute respiratory syndrome coronminus 2 QHz87581.1:1-7096 ortlab polyprotein Severe acute respiratory syndrome coronavinus 2 QHU79171.1:1-7096 orf1ab polyprotein Severe acute respiratory syndrome coronavinus 2 OHz87591.1:-7088 ort1ab polyprotein Severe acute respiratory syndrome coronavins 2 QHz.00398.1:1-7096 orf1ab polyprotein Severe acute respiratory syndrome coronavirus 2 QHA63209,1:1-7005 ort1ab polyprotein Bat coronavirus RaTG13 AVP78041.1:1-7070 non- structural polyprotein 1ab Bat SAPS-like coronavinus AVP7B030.1:1-7092 non-tructural polyprotein 1ab Bat SAPS-Ake coronavinus AID16715.1:1-7063 ort1 ab polyprolein Bat SAPS- like coronavirus AAUO4663.1:1-7073 .

Education

coronavirus YP 009555238,1 Or1ab Human coronavirus OC43 AMN88684.1 ortiab polypretein
Human coronawirus HKU1 AOG747a2.1 ORF1AB Human coronavinus 229E - AWr59972.1
ORF 1ab Human coronavirus NL63
QHO62876.1:1-7096 orf1 ab polyprotein Severe acute respiratory syndrome coronminus 2
QHz87581.1:1-7096 ortlab polyprotein Severe acute respiratory syndrome coronavinus 2
QHU79171.1:1-7096 orf1ab polyprotein Severe acute respiratory syndrome coronavinus 2
OHz87591.1:-7088 ort1ab polyprotein Severe acute respiratory syndrome coronavins 2
QHz.00398.1:1-7096 orf1ab polyprotein Severe acute respiratory syndrome coronavirus 2
QHA63209,1:1-7005 ort1ab polyprotein Bat coronavirus RaTG13 AVP78041.1:1-7070 non-
structural polyprotein 1ab Bat SAPS-like coronavinus AVP7B030.1:1-7092 non-tructural
polyprotein 1ab Bat SAPS-Ake coronavinus AID16715.1:1-7063 ort1 ab polyprolein Bat SAPS-
like coronavirus AAUO4663.1:1-7073 replicase p1AB SAPS coronavirus civet0e0
ATOS8143.1:1-7073 non-structural polyprotein 1ab Bat SAAS-Ske coronavirus A.144803.1:1-
7073 orliab polyprotein Bal coronavirus ARi44798.1:1-7073 ortlab polyprotein Bat coronavirus
OOF43829.1:1-7073 OAFlab Coronavirus B1s-BotaCoVIN2018C ATO98155,1:1-7073 non-
structural polyprotein 1ab Bat SAPS-tke coronavirus AXN73357, OAF1ab Midde East
iespiatory syndrome-related coronavirus QFQ50S8.1 OAF 1ab Midde East respiratory
syndrome-tated coronaviru AXON73424, 1 OAF1ab Midie East respiratory syndrome-related
coronavirus YP Do9s55236.1 Or1ab Human coronavirus OC43 AMNB8664.1 ortlab polyprotein
Human coronavinus HKU! AOG74782.1 OAF1AB Human coronavirus 229E - AWKs9972.1
OAF1ab Human coronavirus NL63

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Human Coronaviruses (HCoV) exhibit positive single stranded RNA genome with enveloped nucleocapsid. Coronavirus belongs to the family Coronaviridae, originated from avian and mammalian species causes upper respiratory tract infection in humans by novel HCoVs viruses named as HCoV-HKU1, HCoV-NL63 but predominant species is Middle East respiratory syndrome (MERS-CoV) across the world. HCoV-HKU1 sp. is associated with chronic pulmonary disease, while HCoV-NL63 causes upper and lower respiratory tract disease in both children and adults, but most recent one was MERS-CoV, which caused acute pneumonia and occasional renal failure. The novel coronavirus SARS-CoV-2 is a new strain that causes the Coronavirus Disease 2019 (COVID-19) as named by the World Health Organization. According to the recent world statistics report about the COVID-19 cases approx. 101,500 confirmed cases and 3,500 death cases appeared. And mostly, a case of infection with CoV was identified in Wuhan, China. Structurally viral genome constitutes of 2/3rd of replicase gene encoding ORFs regions and rest of the 1/3rd region of genome form the structural proteins. The aim of the study was to understand the viral genetic systems in order to facilitate the genetic manipulation of the viral genome and to know the fundamental mechanism during the viral replication, facilitating the development of antidotes against the virus.

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1. PROVIDED PAPER: Forni D, Cagliani R, Clerici M, Sironi M. 2017. Molecular evolution of human coronavirus genomes. Trends in Microbiology 25:36-48. 1) How does your maximun likelihood tree compare to the genome-based tree from the paper? What gene is your tree baed upon? What are the potential functions of the protein made from this coronavirus gene? Are there genetic mechanisms more prevalent in virus genomes that make evolutionary inferences from one gene or a whole genome more complicated than other kinds of organisms? 2) How many different host species were associated with the samples in your dataset? What inferences can be made about the origin of COVID19 prior to infecting humans? Have you heard about any other organisms related to COVID19 that are not represented in your dataset or the provided paper? QHO62376.1:1-7096 orflab polyprotein Severe scute respiratory syndrome coronavins 2 QH2a75a1.11-7096 orfiab polyprotein Severe acule respiratory syndrome coronavirus 2 QHU79171.1:1-7096 ortiab polyprotein Severe acule respiratory syndrome coronavirus 2 QH287591.1:1-7088 ortlab polyproteln Severe acule resplratory syndrome coronavirus 2 QHz00398.1:1-7096 orftab polyprotein Severe acute respiratory syndrome coronavirus 2 QHR63299.1:1-7095 ort1ab polyprotein Bat coronavirus RaTG13 AVP76041.1:1-7070 nen- structural polyprotein 1ab Bat SARS-ike coronavins AVP78030.1:1-7092 non-structural polyprotein 1ab Bat SARS-like coronavirus [ AD16715.1:1-7063 orflab polyprotein Bet SARS- lave coronevirus AM04663.11-7073 replicase p1AB 8ARS coronavinus clvot020 ATO96143.1:1-7073 non-struchural polyprotein 1ab Bat SARS-ike coronavirus A244803.1:1- 7073 ort ob polyprotein Bat coronavirus ARU4798.1:1-7073 oiflab polyprotein Bat coronavinU QDF43629.1:1-7073 ORF 1ab Coronavins BtRs-BetaCoVINN2018C ATOO8155.1:1-7073 non- structural polyprotein 1 ab Bat SARS-like coronavlrus AXNT3357.1 ORF1ab Middle East respiratory syndrome-related coronavirus aFQs6585.1 ORF1ab Middo East rosplratory syndrome-rolatod coronavirus AXN73424.1 ORF 1ab Midde East respiratory syndrome-related

2. coronavirus YP 009555238,1 Or1ab Human coronavirus OC43 AMN88684.1 ortiab polypretein Human coronawirus HKU1 AOG747a2.1 ORF1AB Human coronavinus 229E - AWr59972.1 ORF 1ab Human coronavirus NL63 QHO62876.1:1-7096 orf1 ab polyprotein Severe acute respiratory syndrome coronminus 2 QHz87581.1:1-7096 ortlab polyprotein Severe acute respiratory syndrome coronavinus 2 QHU79171.1:1-7096 orf1ab polyprotein Severe acute respiratory syndrome coronavinus 2 OHz87591.1:-7088 ort1ab polyprotein Severe acute respiratory syndrome coronavins 2 QHz.00398.1:1-7096 orf1ab polyprotein Severe acute respiratory syndrome coronavirus 2 QHA63209,1:1-7005 ort1ab polyprotein Bat coronavirus RaTG13 AVP78041.1:1-7070 non- structural polyprotein 1ab Bat SAPS-like coronavinus AVP7B030.1:1-7092 non-tructural polyprotein 1ab Bat SAPS-Ake coronavinus AID16715.1:1-7063 ort1 ab polyprolein Bat SAPS- like coronavirus AAUO4663.1:1-7073 replicase p1AB SAPS coronavirus civet0e0 ATOS8143.1:1-7073 non-structural polyprotein 1ab Bat SAAS-Ske coronavirus A.144803.1:1- 7073 orliab polyprotein Bal coronavirus ARi44798.1:1-7073 ortlab polyprotein Bat coronavirus OOF43829.1:1-7073 OAFlab Coronavirus B1s-BotaCoVIN2018C ATO98155,1:1-7073 non- structural polyprotein 1ab Bat SAPS-tke coronavirus AXN73357, OAF1ab Midde East iespiatory syndrome-related coronavirus QFQ50S8.1 OAF 1ab Midde East respiratory syndrome-tated coronaviru AXON73424, 1 OAF1ab Midie East respiratory syndrome-related coronavirus YP Do9s55236.1 Or1ab Human coronavirus OC43 AMNB8664.1 ortlab polyprotein Human coronavinus HKU! AOG74782.1 OAF1AB Human coronavirus 229E - AWKs9972.1 OAF1ab Human coronavirus NL63

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PROVIDED PAPER Forni D, Cagliani R, Clerici M, Sironi M. 2017. .pdf