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SARS-CoV-2 proteins

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    SARS -CoV-2 T-cell immunity to variants of concern following vaccination

    Authors: Kathleen M.E. Gallagher; Mark B. Leick; Rebecca C. Larson; Trisha R. Berger; Katelin Katsis; Jennifer Y. Yam; Gabrielle Brini; Korneel Grauwet; - MGH COVID-19 Collection & Processing Team; Marcela V. Maus

    doi:10.1101/2021.05.03.442455 Date: 2021-05-03 Source: bioRxiv

    Recently, two mRNA vaccines to severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) have become available, but there is also an emergence of SARS-CoV-2 variants with increased transmissibility and virulence. A major concern is whether the available vaccines will be equally effective against these variants. The vaccines are designed to induce an immune response against the SARS-CoV-2 spike PROTEIN protein, which is required for viral entry to host cells. Immunity to SARS-CoV-2 is often evaluated by antibody production, while less is known about the T-cell response. Here we developed, characterized, and implemented two standardized, functional assays to measure T-cell immunity to SARS-CoV-2 in uninfected, convalescent, and vaccinated individuals. We found that vaccinated individuals had robust T-cell responses to the wild type spike and nucleocapsid proteins PROTEIN, even more so than convalescent patients. We also found detectable but diminished T-cell responses to spike variants (B.1.1.7, B.1.351, and B.1.1.248) among vaccinated but otherwise healthy donors. Since decreases in antibody neutralization have also been observed with some variants, investigation into the T-cell response to these variants as an alternative means of viral control is imperative. Standardized measurements of T-cell responses to SARS-CoV-2 are feasible and can be easily adjusted to determine changes in response to variants.

    Multiplex Antibody Analysis of IgM, IgA HGNC and IgG to SARS-CoV-2 in Saliva and Serum from Infected Children and their Close Contacts

    Authors: Carlota Dobano; Selena Alonso; Marta Vidal; Alfons Jimenez; Rocio Rubio; Rebeca Santano; Diana Barrios; Gemma Pons Tomas; Maria Mele Casas; Maria Hernandez Garcia; Monica Girona-Alarcon; Laura Puyol; Natalia Rodrigo Melero; Carlo Carolis; Aleix Garcia-Miquel; Elisenda Bonet-Carne; Joana Claverol; Marta Cubells; Claudia Fortuny; Victoria Fumado; Anna Codina; Quique Bassat; Carmen Munoz-Almagro; Mariona Fernandez de Sevilla; Eduard Gratacos; Luis Izquierdo; Juan Jose Garcia-Garcia; Ruth Aguilar; Iolanda Jordan; Gemma Moncunill

    doi:10.1101/2021.03.22.21254120 Date: 2021-03-26 Source: medRxiv

    COVID-19 MESHD affects children to a lesser extent than adults but they can still get infected and transmit SARS-CoV-2 to their contacts. Field deployable non-invasive sensitive diagnostic techniques are needed to evaluate the infectivity dynamics of the coronavirus in pediatric populations and guide public health interventions. We evaluated the utility of high-throughput Luminex-based assays applied to saliva samples to quantify IgM, IgA HGNC and IgG antibodies against five SARS-CoV-2 spike MESHD SARS-CoV-2 spike PROTEIN (S) and nucleocapsid (N PROTEIN) antigens in the context of a contacts and infectivity longitudinal MESHD study. We compared the antibody levels obtained in saliva versus serum/plasma samples from a group of children and adults tested weekly by RT-PCR over 35 days and diagnosed as positive (n=58), and a group of children and adults who consistently tested negative over the follow up period (n=61), in the Summer of 2020 in Barcelona, Spain. Antibody levels in saliva samples from individuals with confirmed RT-PCR diagnosis of SARS-CoV-2 infection MESHD were significantly higher than in negative individuals and correlated with those measured in sera/plasmas. Higher levels of anti-S IgG were found in asymptomatic individuals that could indicate protection against disease in infected MESHD individuals. Higher anti-S IgG and IgM levels in serum/plasma and saliva, respectively, in infected children compared to infected adults could also be related to stronger clinical immunity in them. Among infected children, males had higher levels of saliva IgG to N and RBD than females. Despite overall correlation, individual clustering analysis suggested that responses that may not be detected in blood could be patent in saliva, and vice versa, and therefore that both measurements are complementary. In addition to serum/plasma, measurement of SARS-CoV-2-specific saliva antibodies should be considered as a complementary non-invasive assay to better estimate the percentage of individuals who have experienced coronavirus infection MESHD. Saliva antibody detection could allow determining COVID-19 MESHD prevalence in pediatric populations, alternative to bleeding MESHD or nasal swab, and serological diagnosis following vaccination.

    Evaluation of anti-SARS-CoV-2 antibody testing in asymptomatic or mild COVID-19 MESHD patients in outbreak on a cruise ship

    Authors: Norihito Kaku; Fumitaka Nishimura; Yui Shigeishi; Rina Tachiki; Hironori Sakai; Daisuke Sasaki; Kenji Ota; Kei Sakamoto; Kosuke Kosai; Hiroo Hasegawa; Koichi Izumikawa; Koya Ariyoshi; Hiroshi Mukae; Jiro Yasuda; Kouichi Morita; Shigeru Konno; Katsunori Yanagihara

    doi:10.1101/2021.03.10.21253064 Date: 2021-03-12 Source: medRxiv

    Background A few studies on antibody testing have focused on asymptomatic or mild coronavirus disease 2019 MESHD ( COVID-19 MESHD) patients with low initial anti-severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) antibody responses. Anti-SARS-CoV-2 antibody-testing performance was evaluated using blood samples from asymptomatic or mild COVID-19 MESHD patients. Methods Blood samples were collected from 143 COVID-19 MESHD patients during an outbreak on a cruise ship 3 weeks after diagnosis. Simultaneously, a second SARS-CoV-2 genetic test was performed. Samples stored before the COVID-19 pandemic MESHD were also used to evaluate the lateral flow immunochromatographic assay (LFA) and electrochemiluminescence immunoassay (ECLIA). Titers of anti-SARS-CoV-2 IgM and IgG antibodies against the nucleocapsid and spike proteins PROTEIN were measured using the enzyme-linked immunosorbent assay to compare false-negative- with positive-result samples. Results Sensitivity, specificity, positive-predictive, and negative-predictive values of LFA-detected IgM antibodies were 0.231, 1.000, 1.000, and 0.613, respectively; those of LFA-detected IgG antibodies were 0.483, 0.989, 0.972, and 0.601, respectively; and those of ECLIA-detected total antibodies were 0.783, 1.000, 1.000, and 0.848, respectively. IgM-, IgG-, and total-antibody positivity rates in the patients with negative results from the second genetic testing were 22.9%, 47.6%, and 72.4%, respectively. All antibody titers, especially those of the IgG antibody against nucleocapsid protein PROTEIN, were significantly lower in blood samples with false-negative results than in those with positive results. Conclusions These findings suggest that anti-SARS-CoV-2 antibody testing has lower performance in asymptomatic or mild COVID-19 MESHD patients than required in the guidelines, and situations in which it is useful are limited.

    Serological reconstruction of COVID-19 MESHD epidemics through analysis of antibody kinetics to SARS-CoV-2 proteins MESHD

    Authors: Stephane Pelleau; Tom Woudenberg; Jason Rosado; Francoise Donnadieu; Laura Garcia; Thomas Obadia; Soazic Gardais; Yasmine Elgharbawy; Aurelie Velay; Maria Gonzalez; Jacques-Yves Nizou; Nizar Khelil; Konstantinos Zannis; Charlotte Cockram; Sarah Merkling; Annalisa Meola; Solen Kerneis; Benjamin Terrier; Jerome de Seze; Delphine Planas; Olivier Schwartz; Francois Dejardin; Stephane Petres; Cassandre von Platen; Laurence Arowas; Louise Perrin de Facci; Darragh Duffy; Cliona Ni Cheallaigh; Niall Conlon; Liam Townsend; Heidi Auerswald; Marija Backovic; Bruno Hoen; Arnaud Fontanet; Ivo Mueller; Samira Fafi-Kremer; Timothee Bruel; Michael T White

    doi:10.1101/2021.03.04.21252532 Date: 2021-03-08 Source: medRxiv

    Infection with severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) induces a complex antibody response that varies by orders of magnitude between individuals and over time. Waning antibody levels lead to reduced sensitivity of serological diagnostic tests over time. This undermines the utility of serological surveillance as the SARS-CoV-2 pandemic progresses into its second year. Here we develop a multiplex serological test for measuring antibodies of three isotypes (IgG, IgM, IgA) to five SARS-CoV-2 antigens (Spike (S), receptor binding domain (RBD), Nucleocapsid (N PROTEIN), Spike subunit 2, Membrane-Envelope fusion) and the Spike proteins PROTEIN of four seasonal coronaviruses. We measure antibody responses in several cohorts of French and Irish hospitalized patients and healthcare workers followed for up to eleven months after symptom onset. The data are analysed with a mathematical model of antibody kinetics to quantify the duration of antibody responses accounting for inter-individual variation. One year after symptoms, we estimate that 36% (95% range: 11%, 94%) of anti-S IgG remains, 31% (9%, 89%) anti-RBD IgG remains, and 7% (1%, 31%) anti-N IgG remains. Antibodies of the IgM isotype waned more rapidly, with 9% (2%, 32%) anti-RBD IgM remaining after one year. Antibodies of the IgA isotype also waned rapidly, with 10% (3%, 38%) anti-RBD IgA remaining after one year. Quantitative measurements of antibody responses were used to train machine learning algorithms for classification of previous infection and estimation of time since infection. The resulting diagnostic test classified previous infections with 99% specificity and 98% (95% confidence interval: 94%, 99%) sensitivity, with no evidence for declining sensitivity over the time scale considered. The diagnostic test also provided accurate classification of time since infection into intervals of 0 - 3 months, 3 - 6 months, and 6 - 12 months. Finally, we present a computational method for serological reconstruction of past SARS-CoV-2 transmission using the data from this test when applied to samples from a single cross-sectional sero-prevalence survey.

    Evaluation of vertical transmission of SARS-CoV-2 in utero: nine pregnant women and their newborns

    Authors: Liang Dong; Shiyao Pei; Qin Ren; Shuxiang Fu; Liang Yu; Hui Chen; Xiang Chen; Mingzhu Yin

    doi:10.1101/2020.12.28.20248874 Date: 2021-01-08 Source: medRxiv

    BackgroundSevere acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2), mainly transmitted by droplets and close contact, has caused a pandemic worldwide as of November 2020. According to the current case reports and cohort studies, the symptoms of pregnant women infected with SARS-CoV-2 were similar to normal adults and may cause a series of adverse consequences of pregnancy (placental abruption, fetal distress, epilepsy MESHD during pregnancy, etc.). However, whether SARS-CoV-2 can be transmitted to the fetus through the placental barrier is still a focus of debate. MethodsIn this study, in order to find out whether SARS-CoV-2 infect MESHD fetus through placental barrier, we performed qualitative detection of virus structural protein (spike PROTEIN protein and nucleoprotein PROTEIN) and targeted receptor protein ( ACE2 HGNC, CD147 HGNC and GRP78 HGNC) expression on the placental tissue of seven pregnant women diagnosed with COVID-19 MESHD through immunohistochemistry. Amniotic fluid, neonatal throat, anal swab and breastmilk samples were collected immediately in the operating room for verification after delivery, which were all tested for SARS-CoV-2 by reverse transcriptionpolymerase chain reaction (RT-PCR). Results: The result showed that CD147 HGNC was expressed on the basal side of the chorionic trophoblast cell membrane and ACE2 HGNC was expressed on the maternal side, while GRP78 HGNC was strongly expressed in the cell membrane and cytoplasm. The RT-PCR results of Amniotic fluid, neonatal throat, anal swab and breastmilk samples were all negative. Conclusions: We believed that despite the detection of viral structural proteins in the placenta, SARS-CoV-2 cannot be transmitted to infants due to the presence of the placental barrier.

    Structure-function investigation of a new VUI-202012/01 SARS-CoV-2 variant

    Authors: Jasdeep Singh; Nasreen Z Ehtesham; Syed Asad Rahman; Yakob G. Tsegay; Daniel S. Abebe; Mesay G. Edo; Endalkachew H. Maru; Wuletaw C. Zewde; Lydia K. Naylor; Dejen F. Semane; Menayit T. Deresse; Bereket B. Tezera; Lovisa Skoglund; Jamil Yousef; Elisa Pin; Wanda Christ; Mikaela Olausson; My Hedhammar; Hanna Tegel; Sara Mangsbo; Mia Phillipson; Anna Manberg; Sophia Hober; Peter Nilsson; Charlotte Thalin; Samuel Bates; Chevaun Morrison-Smith; Benjamin Nicholson; Edmond Wong; Leena El-Mufti; Michael Kann; Anna Bolling; Brooke Fortin; Hayden Ventresca; Wen Zhou; Santiago Pardo; Megan Kwock; Aditi Hazra; Leo Cheng; Rushdy Ahmad; James A. Toombs; Rebecca Larson; Haley Pleskow; Nell Meosky Luo; Christina Samaha; Unnati M. Pandya; Pushpamali De Silva; Sally Zhou; Zakary Ganhadeiro; Sara Yohannes; Rakiesha Gay; Jacqueline Slavik; Shibani S. Mukerji; Petr Jarolim; David R. Walt; Becky C. Carlyle; Lauren L. Ritterhouse; Sara Suliman

    doi:10.1101/2021.01.01.425028 Date: 2021-01-04 Source: bioRxiv

    The SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus MESHD) has accumulated multiple mutations during its global circulation. Recently, a new strain of SARS-CoV-2 (VUI 202012/01) had been identified leading to sudden spike in COVID-19 MESHD cases in South-East England. The strain has accumulated 23 mutations which have been linked to its immune evasion and higher transmission capabilities. Here, we have highlighted structural-function impact of crucial mutations occurring in spike (S), ORF8 PROTEIN and nucleocapsid (N) protein PROTEIN of SARS-CoV-2. Some of these mutations might confer higher fitness to SARS-CoV-2 MESHD. SummarySince initial outbreak of COVID-19 MESHD in Wuhan city of central China, its causative agent; SARS-CoV-2 virus has claimed more than 1.7 million lives out of 77 million populations and still counting. As a result of global research efforts involving public-private-partnerships, more than 0.2 million complete genome sequences have been made available through Global Initiative on Sharing All Influenza Data (GISAID). Similar to previously characterized coronaviruses (CoVs), the positive-sense single-stranded RNA SARS-CoV-2 genome codes for ORF1ab PROTEIN non-structural proteins (nsp(s)) followed by ten or more structural/nsps [1, 2]. The structural proteins include crucial spike (S), nucleocapsid (N PROTEIN), membrane (M), and envelope (E) proteins PROTEIN. The S protein PROTEIN mediates initial contacts with human hosts while the E and M proteins PROTEIN function in viral assembly and budding. In recent reports on evolution of SARS-CoV-2, three lineage defining non-synonymous mutations; namely D614G in S protein PROTEIN (Clade G), G251V in ORF3a PROTEIN (Clade V) and L84S in ORF 8 (Clade S) were observed [2-4]. The latest pioneering works by Plante et al and Hou et al have shown that compared to ancestral strain, the ubiquitous D614G variant (clade G) of SARS-CoV-2 exhibits efficient replication in upper respiratory tract epithelial cells and transmission, thereby conferring higher fitness MESHD [5, 6]. As per latest WHO reports on COVID-19 MESHD, a new strain referred as SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01) had been identified as a part of virological and epidemiological analysis, due to sudden rise MESHD in COVID-19 MESHD detected cases in South-East England [7]. Preliminary reports from UK suggested higher transmissibility (increase by 40-70%) of this strain, escalating Ro (basic reproduction number) of virus to 1.5-1.7 [7, 8]. This apparent fast spreading variant inculcates 23 mutations; 13 non-synonymous, 6 synonymous and 4 amino acid deletions [7]. In the current scenario, where immunization programs have already commenced in nations highly affected by COVID-19 MESHD, advent of this new strain variant has raised concerns worldwide on its possible role in disease severity and antibody responses. The mutations also could also have significant impact on diagnostic assays owing to S gene target failures.

    Identification of NPC1 as a novel SARS-CoV-2 intracellular target

    Authors: Isabel Garcia-Dorival; Miguel Angel Cuesta-Geijo; Lucia Barrado-Gil; Inmaculada Galindo; Jesus Urquiza; Ana Del Puerto; Carmen Gil; Nuria Campillo; Ana Martinez; Covadonga Alonso

    doi:10.1101/2020.12.19.423584 Date: 2020-12-20 Source: bioRxiv

    Niemann-Pick type C1 (NPC1) receptor is an endosomal membrane protein that regulates intracellular cholesterol trafficking, which is crucial in the Ebola virus (EBOV) cycle. The severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) enters the cell by binding of the viral spike (S) protein PROTEIN to the ACE2 receptor. This requires S-protein PROTEIN processing either by the surface transmembrane serine protease TMPRSS2 for plasma membrane fusion or cathepsin L for endosomal entry. Additional host factors are required for viral fusion at endosomes. Here, we report a novel interaction of the SARS-CoV-2 nucleoprotein (N PROTEIN) with the cholesterol transporter NPC1. Moreover, small molecules interfering with NPC1 that inhibit EBOV entry, also inhibited human coronavirus. Our findings suggest an important role for NPC1 in SARS-CoV-2 infection MESHD, a common strategy shared with EBOV, and a potential therapeutic target to fight against COVID-19 MESHD.

    Detection of SARS-CoV-2-specific antibodies via rapid diagnostic immunoassays in COVID-19 MESHD patients

    Authors: Jira Chansaenroj; Ritthideach Yorsaeng; Nawarat Posuwan; Jiratchaya Puenpa; Natthinee Sudhinaraset; Chintana Chirathaworn; Yong Poovorawan

    doi:10.21203/rs.3.rs-125190/v2 Date: 2020-12-09 Source: ResearchSquare

    Background: Efficient monitoring and control of coronavirus disease 2019 MESHD ( COVID-19 MESHD) require access to diagnostic tests, and serological diagnostic testing is desirable. In the current study, antibodies were investigated in patients recently diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection MESHD.Methods: Cross-sectional data were obtained from 245 patients in whom SARS-CoV-2 infection MESHD had been confirmed via real-time reverse transcriptase-polymerase chain reaction between March and October 2020. Serum samples were acquired between 2 and 60 days following the onset of COVID-19 MESHD symptoms or the first detection of SARS-CoV-2 in asymptomatic patients. All specimens were tested simultaneously using an IgM/IgG rapid diagnostic test (RDT), IgG nucleocapsid protein PROTEIN-based chemiluminescent microparticle immunoassay (CMIA), IgG, and IgA spike protein PROTEIN-based enzyme-linked immunosorbent assays (ELISAs). Blood donor samples obtained in 2018 were used as negative controls. Results: The sensitivity and specificity of the RDT IgG were compared with the IgG immunoassays as standards. The RDT IgG exhibited 97.5% sensitivity and 89.4% specificity compared with a CMIA IgG, 98.4% sensitivity, and 78.8% specificity compared with an ELISA IgG. IgM, IgG, and IgA seropositivity rates were low between 1-2 weeks after COVID-19 MESHD symptom onset or the detection of SARS-CoV-2 RNA. IgM seropositivity rate began decreasing after 4 weeks, whereas IgG and IgA seropositivity rate remained at appreciable levels over the 8-week study period. No cross-reactivity with seasonal coronaviruses was detected.Conclusions: IgM/IgG RDTs alone or combined with molecular diagnostic tests may be useful for identifying recent SARS-CoV-2 infection MESHD.

    Comparative analysis of antigen-specific anti-SARS-CoV-2 antibody isotypes in COVID-19 MESHD patients

    Authors: Hidetsugu Fujigaki; Masato Inaba; Michiko Osawa; Saya Moriyama; Yoshimasa Takahashi; Tadaki Suzuki; Kenya Yamase; Yukihiro Yoshida; Yo Yagura; Takayoshi Oyamada; Masao Takemura; Yohei Doi; Kuniaki Saito; Daniel Batlle; Thomas J Hope; Yang Shen; Yuan Luo; Young Chae; Hui Zhang; Suchitra Swaminathan; Glenn C. Randall; Alexis R Demonbreun; Michael G Ison; Deyu Fang; Huiping Liu; Nicholas C. Morano; Gregory J. Krause; Joseph M. Sweeney; Kelsie Cowman; Stephanie Allen; Jayabhargav Annam; Ariella Applebaum; Daniel Barboto; Ahmed Khokhar; Brianna J. Lally; Audrey Lee; Max Lee; Avinash Malaviya; Reise Sample; Xiuyi A. Yang; Yang Li; Rafael Ruiz; Raja Thota; Jason Barnhill; Doctor Y. Goldstein; Joan Uehlinger; Scott J. Garforth; Steven C. Almo; Jonathan R. Lai; Morayma Reyes Gil; Amy S. Fox; Kartik Chandran; Tao Wang; Johanna P. Daily; Liise-anne Pirofski

    doi:10.1101/2020.12.04.407510 Date: 2020-12-04 Source: bioRxiv

    Serological tests for detection of anti-severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) antibodies in blood are expected to identify individuals who have acquired immunity against SARS-CoV-2 and indication of seroprevalence of SARS-CoV-2 infection MESHD. Many serological tests have been developed to detect antibodies against SARS-CoV-2. However, these tests have considerable variations in their specificity and sensitivity, and whether they can predict levels of neutralizing activity is yet to be determined. This study aimed to investigate the kinetics and neutralizing activity of various antigen-specific antibody isotypes against SARS-CoV-2 in serum of coronavirus disease 2019 MESHD ( COVID-19 MESHD) patients confirmed via polymerase chain reaction test. We developed IgG, IgM and IgA measurement assays for each antigen, including receptor-binding domain (RBD) of spike (S) protein PROTEIN, S1 domain, full length S protein PROTEIN, S trimer and nucleocapsid (N PROTEIN) domain, based on enzyme-linked immunosorbent assay. The assays of the S protein PROTEIN for all isotypes showed high specificity, while the assays for all isotypes against N protein PROTEIN showed lower specificity. The sensitivity of all antigen-specific antibody isotypes depended on the timing of the serum collection and all of them, except for IgM against N protein PROTEIN, reached more than 90% at 15-21 days post-symptom onset. The best correlation with virus neutralizing activity was found for IgG against RBD (RBD-IgG), and levels of RBD-IgG in sera from four severe COVID-19 MESHD patients increased concordantly with neutralizing activity. Our results provide valuable information regarding the selection of serological test for seroprevalence and vaccine evaluation studies.

    Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin

    Authors: Vladimir Makarenkov; Bogdan Mazoure; Guillaume Rabusseau; Pierre Legendre; Gustavo Ferrer; Xiaoping Jiang; Ya-Nan Dai; Haiyan Zhao; Lucas Adams; Michael Holtzman; Adam Bailey; James Brett Case; Daved Fremont; Robyn S Klein; Michael Diamond; Adrianus Boon

    doi:10.1101/2020.12.03.410233 Date: 2020-12-03 Source: bioRxiv

    The SARS-CoV-2 pandemic is among the most dangerous infectious diseases that have emerged in recent history. Human CoV strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV MESHD and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus MESHD (CoV) strains for the receptor binding (RB) domain of the spike protein PROTEIN. We provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-Cov-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV MESHD have been identified in region [1215-1425] of gene S and region [534-727] of gene N PROTEIN. Moreover, some significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV MESHD and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab PROTEIN, S, ORF3a PROTEIN, ORF7a PROTEIN, ORF8 PROTEIN and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab PROTEIN, S and N forming the first cluster, gene phylogenies of ORF3a PROTEIN, E, M, ORF6 PROTEIN, ORF7a PROTEIN, ORF7b PROTEIN and ORF8 PROTEIN forming the second cluster, and phylogeny of gene ORF10 PROTEIN forming the third cluster. The results of our horizontal gene transfer and recombination analysis suggest that SARS-Cov-2 could not only be a chimera resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of SARS-CoV-2.

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SARS-CoV-2 Proteins


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