Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ORF1ab (99)

ProteinN (27)

ProteinS (25)

ORF3a (11)

ComplexRdRp (10)


SARS-CoV-2 Proteins
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    Rational Selection of PCR Primer/Probe Design Sites for SARS-CoV-2

    Authors: Divya RSJB Rana

    doi:10.1101/2021.04.04.438420 Date: 2021-04-05 Source: bioRxiv

    Various reports of decreased analytical sensitivities of real-time PCR-based detection of Coronavirus Disease 2019 MESHD ( COVID-19 MESHD) have been associated with occurrence of mutations in the target area of primer/probe binding. Knowledge about propensities of different genes to undergo mutation can inform researchers to select optimal genes to target for the qPCR design. We analyzed supplementary data from over 45 thousand SARS-CoV-2 genomes provided by Mercatelli et al to calculate the unique and prevalent mutations in different genes of SARS-CoV-2. We found that non-structural proteins in the ORF1ab PROTEIN region were more conserved compared to structural genes. Further factors which need to be relied upon for proper selection of genes for qPCR design are discussed.

    Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 lineage (20H/501Y.V2) in Brazil

    Authors: Svetoslav N Slavov PhD; Jose Patane PhD; Rafael S Bezerra BSc; Marta Giovanetti PhD; Vagner Fonseca MSc; Antonio J Martins PhD; Vincent L Viala PhD; Evandra S Rodrigues PhD; Elaine V Santos PhD; Claudia R.S Barros PhD; Elaine C Marqueze PhD; Bibiana Santos MSc; Flavia Aburjaile PhD; Raul M Neto PhD; Debora B Moretti PhD; Ricardo Haddad MSc; Rodrigo T Calado PhD; Joao Paulo Kitajima PhD; Erika Freitas PhD; David Schlesinger PhD; Luiz C.J Alcantara PhD; M. Carolina Elias PhD; Sandra C.S Vessoni PhD; Simone Kashima PhD; Dimas T Covas Md-PhD

    doi:10.1101/2021.03.30.21254591 Date: 2021-04-04 Source: medRxiv

    Sao Paulo State, the most populous area in Brazil, currently experiences a second wave of the COVID-19 pandemic MESHD which overwhelmed the healthcare system. Recently, due to the paucity of SARS-CoV-2 MESHD complete genome sequences, we established a Network for Pandemic Alert of Emerging SARS-CoV-2 Variants to rapidly understand the spread of SARS-CoV-2 and monitor in nearly real-time the circulating SARS-CoV-2 variants into the state. Through full genome analysis of 217 SARS-CoV-2 complete genome sequences obtained from the largest regional health departments we were able to identify the co-circulation of multiple SARS-CoV-2 lineages such as i) B.1.1 (0.92%), ii) B.1.1.1 (0.46%), iii) B.1.1.28 (25.34%), iv) B.1.1.7 (5.99%), v) B.1.566 (1.84%), vi) P.1 (64.05%), and P.2 (0.92%). Further our analysis allowed the detection, for the first time in Brazil of the South African variant of concern (VOC), the B.1.351 (501Y.V2) (0.46%). The identified lineage was characterized by the presence of the following mutations: ORF1ab PROTEIN: T265I, R724K, S1612L, K1655N, K3353R, SGF 3675_F3677del, P4715L, E5585D; Spike: D80A, D215G, L242_L244del, A262D, K417N, E484K, N501Y, D614G, A701V, C1247F; ORF3a PROTEIN: Q57H, S171L, E: P71L; ORF7b PROTEIN: Y10F, N: T205I; ORF14: L52F. Origin of the most recent common ancestor of this genomic variant was inferred to be between middle October to late December 2020. Analysis of generated sequences demonstrated the predominance of the P.1 lineage and allowed the early detection of the South African strain for the first time in Brazil. Our findings highlight the importance to increase active monitoring to ensure the rapid detection of new SARS-CoV-2 variants with a potential impact in pandemic control and vaccination strategies.

    Cluster Analysis of SARS-CoV-2 Gene using Deep Learning Autoencoder: Gene Profiling for Mutations and Transitions

    Authors: Jun Miyake; Takaaki Sato; Shunsuke Baba; Hayato Nakamura; Hirohiko Niioka; Yoshihisa Nakazawa

    doi:10.1101/2021.03.16.435601 Date: 2021-03-16 Source: bioRxiv

    We report on a method for analyzing the variant of coronavirus genes using autoencoder. Since coronaviruses have mutated rapidly and generated a large number of genotypes, an appropriate method for understanding the entire population is required. The method using autoencoder meets this requirement and is suitable for understanding how and when the variants emarge and disappear. For the over 30,000 SARS-CoV-2 ORF1ab PROTEIN gene sequences sampled globally from December 2019 to February 2021, we were able to represent a summary of their characteristics in a 3D plot and show the expansion, decline, and transformation of the virus types over time and by region. Based on ORF1ab PROTEIN genes, the SARS-CoV-2 viruses were classified into five major types (A, B, C, D, and E in the order of appearance): the virus type that originated in China at the end of 2019 (type A) practically disappeared in June 2020; two virus types (types B and C) have emerged in the United States and Europe since February 2020, and type B has become a global phenomenon. Type C is only prevalent in the U.S. and is suspected to be associated with high mortality, but this type also disappeared at the end of June. Type D is only found in Australia. Currently, the epidemic is dominated by types B and E.

    Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses

    Authors: Hong Zhou; Jingkai Ji; Xing Chen; Yuhai Bi; Juan Li; Tao Hu; Hao Song; Yanhua Chen; Mingxue Cui; Yanyan Zhang; Alice C. Hughes; Edward C. Holmes; Weifeng Shi

    doi:10.1101/2021.03.08.434390 Date: 2021-03-08 Source: bioRxiv

    Although a variety of SARS-CoV-2 related coronaviruses have been identified, the evolutionary origins of this virus remain elusive. We describe a meta-transcriptomic study of 411 samples collected from 23 bat species in a small (~1100 hectare) region in Yunnan province, China, from May 2019 to November 2020. We identified coronavirus contigs in 40 of 100 sequencing libraries, including seven representing SARS-CoV-2-like contigs. From these data we obtained 24 full-length coronavirus genomes, including four novel SARS-CoV-2 related and three SARS-CoV MESHD related genomes. Of these viruses, RpYN06 exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome and was the closest relative of SARS-CoV-2 in the ORF1ab PROTEIN, ORF7a PROTEIN, ORF8 PROTEIN, N, and ORF10 PROTEIN genes. The other three SARS-CoV-2 related coronaviruses were nearly identical in sequence and clustered closely with a virus previously identified in pangolins from Guangxi, China, although with a genetically distinct spike gene sequence. We also identified 17 alphacoronavirus genomes, including those closely related to swine acute diarrhea syndrome MESHD virus and porcine epidemic diarrhea virus MESHD. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species in Southeast Asia and southern China, with the largest contiguous hotspots extending from South Lao HGNC and Vietnam to southern China. Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China. These data will help guide surveillance efforts to determine the origins of SARS-CoV-2 and other pathogenic coronaviruses.

    Introductions and evolutions of SARS-CoV-2 strains in Japan

    Authors: Reitaro Tokumasu; Dilhan Weeraratne; Jane Snowdon; Laxmi Parida; Michiharu Kudo; Takahiko Koyama

    doi:10.1101/2021.02.26.21252555 Date: 2021-03-02 Source: medRxiv

    COVID-19 MESHD caused by SARS-CoV-2 was first identified in Japan on January 15th, 2020, soon after the pandemic originated in Wuhan, China. Subsequently, Japan experienced three distinct waves of the outbreak in the span of a year and has been attributed to new exogenous strains and evolving existing strains. Japan engaged very early on in tracking different COVID-19 MESHD sub-strains and have sequenced approximately 5% of all confirmed cases. While Japan has enforced stringent airport surveillance on cross-border travelers and returnees, some carriers appear to have advanced through the quarantine stations undetected. In this study, 17112 genomes sampled in Japan were analyzed to understand the strains, heterogeneity and temporal evolution of different SARS-CoV-2 strains. We identified 11 discrete strains with a substantial number of cases with most strains possessing the spike (S) D614G and nucleocapsid (N PROTEIN) 203_204delinsKR mutations. Besides these variants, ORF1ab PROTEIN P3371S, A4815V, S1361P, and N P151L were also detected in nearly half the samples constituting the most common strain in Japan. 115 distinct strains have been introduced into Japan and 12 of them were introduced after strict quarantine policy was implemented. In particular, the B.1.1.7 strain, that emerged in the United Kingdom (UK) in September 2020, has been circulating in Japan since late 2020 after eluding cross-border quarantine stations. Similarly, the B.1.351 strain dubbed the South African variant, P.1 Brazilian strain and R.1 strain with the spike E484K mutation have been detected in Japan. At least four exogenous B.1.1.7 sub-strains have been independently introduced in Japan as of late January 2021, and these strains carry mutations that give selective advantage including N501Y, H69_V70del, and E484K that confer increased transmissibility, reduced efficacy to vaccines and possible increased virulence. It is imperative that the quarantine policy be revised, cross-border surveillance reinforced, and new public health measures implemented to mitigate further transmission of this deadly disease and to identify strains that may engender resistance to vaccines.

    The detection of SARS-CoV-2 in autolysed samples from an exhumed decomposed body: Implications to virus survival, genome stability, and spatial distribution in tissues

    Authors: Mahadeshwara Prasad; Somanna Ajjamada Nachappa; Niveditha Anand; Deepika Udayawara Rudresh; Yashika Singh; Surabhi P. Gangani; Forum K. Bhansali; Basista Rabina Sharma; Deep Nithun Senathipathi; Shashidhar H. Byrappa; Prakash M. Halami; Ravindra P Veeranna

    doi:10.1101/2021.02.16.21251805 Date: 2021-02-19 Source: medRxiv

    Here we report for the first time the SARS-CoV-2 detection in autolysed samples from an exhumed decomposed body post-thirty six days after death. Both naso-oropharyngeal swabs and visceral samples from the lung, intestine, liver, and kidney were collected from the body exhumed post-fifteen days after burial, stored in viral transport medium and in saturated salt solution respectively. Naso-oropharyngeal swabs showed the presence of the SARS-CoV-2 genome as identified by the amplification of viral E, N, RdRP PROTEIN, or ORF1ab PROTEIN genes by RT-PCR. Subsequent examination of tissues reveal the detection of the virus genome in the intestine and liver, while no detection in the kidney and lung. These results signify the genome stability and implicate the virus survival in decomposed swab samples and in tissues and thereafter in storage solution. Further results also indicate spatial distribution of the virus in tissues during the early stage of infection in the subject with no respiratory distress. Considering the presence of cool, humid, and moist location of the exhumation, the presence of virus genome might also indicate that SARS-CoV-2 can persist for more than seven days on the surface of dead bodies similar to the Ebola virus, confirming that transmission from deceased subjects is possible for an extended period after death. These results further reaffirm the robustness of the RT-PCR aiding in the detection of viruses or their genome in decomposed samples when other methods of detection could not be useful.

    SARS-CoV-2 specific T cell responses are lower in children and increase with age and time after infection

    Authors: Carolyn A Cohen; Athena PY Li; Asmaa Hachim; David SC Hui; Mike YW Kwan; Owen TY Tsang; Susan S Chiu; Wai Hung Chan; Yat Sun Yau; Niloufar Kavian; Fionn NL Ma; Eric HY Lau; Samuel MS Cheng; Leo LM Poon; Malik JS Peiris; Sophie A Valkenburg

    doi:10.1101/2021.02.02.21250988 Date: 2021-02-05 Source: medRxiv

    SARS-CoV-2 infection MESHD of children leads to a mild illness and the immunological differences with adults remains unclear. We quantified the SARS-CoV-2 specific T cell responses in adults and children (<13 years of age) with RT-PCR confirmed asymptomatic and symptomatic infection for long-term memory, phenotype and polyfunctional cytokines. Acute and memory CD4+ T cell responses to structural SARS-CoV-2 proteins significantly increased with age, whilst CD8+ T cell responses increased with time post infection. Infected children had significantly lower CD4+ and CD8+ T cell responses to SARS-CoV-2 structural and ORF1ab PROTEIN proteins compared to infected adults. SARS-CoV-2-specific CD8+ T cell responses were comparable in magnitude to uninfected negative adult controls. In infected adults CD4+ T cell specificity was skewed towards structural peptides, whilst children had increased contribution of ORF1ab PROTEIN responses. This may reflect differing T cell compartmentalisation for antigen processing during antigen exposure or lower recruitment of memory populations. T cell polyfunctional cytokine production was comparable between children and adults, but children had a lower proportion of SARS-CoV-2 CD4+ T cell effector memory. Compared to adults, children had significantly lower levels of antibodies to {beta}-coronaviruses, indicating differing baseline immunity. Total T follicular helper responses was increased in children during acute infection indicating rapid co-ordination of the T and B cell responses. However total monocyte responses were reduced in children which may be reflective of differing levels of inflammation MESHD between children and adults. Therefore, reduced prior {beta}-coronavirus immunity and reduced activation and recruitment of de novo responses in children may drive milder COVID-19 MESHD pathogenesis.

    Updated SARS-CoV-2 Single Nucleotide Variants and Mortality Association

    Authors: Shuyi Fang; Sheng Liu; Jikui Shen; Alex Z Lu; Yucheng Zhang; Kailing Li; Juli Liu; Lei Yang; Chang-Deng Hu; Jun Wan

    doi:10.1101/2021.01.29.21250757 Date: 2021-02-01 Source: medRxiv

    Since its outbreak in December 2019, COVID-19 MESHD has caused 100,5844,555 cases and 2,167,313 deaths as of Jan 27, 2021. Comparing our previous study of SARS-CoV-2 single nucleotide variants (SNVs) before June 2020, we found out that the SNV clustering had changed considerably since June 2020. Apart from that the group SNVs represented by two non-synonymous mutations A23403G (S: D614G) and C14408T ( ORF1ab PROTEIN: P4715L) became dominant and carried by over 95% genomes, a few emerging groups of SNVs were recognized with sharply increased monthly occurrence ratios up to 70% in November 2020. Further investigation revealed that several SNVs were strongly associated with the mortality, but they presented distinct distribution in specific countries, e.g., Brazil, USA, Saudi Arabia, India, and Italy. SNVs including G25088T, T25A, G29861T and G29864A were adopted in a regularized logistic regression model to predict the mortality status in Brazil with the AUC of 0.84. Protein structure analysis showed that the emerging subgroups of non-synonymous SNVs and those mortality-related ones in Brazil were located on protein surface area. The clashes in protein structure introduced by these mutations might in turn affect virus pathogenesis through conformation changes, leading to the difference in transmission and virulence. Particularly, we found that SNVs tended to occur in intrinsic disordered regions (IDRs) of Spike (S) and ORF1ab PROTEIN, suggesting a critical role of SNVs in protein IDRs to determine protein folding and immune evasion.

    A Rapid and Low-Cost protocol for the detection of B.1.1.7 lineage of SARS-CoV-2 by using SYBR Green-Based RT-qPCR

    Authors: Fadi Abdel-Sater; Mahmoud Younes; Hassan Nassar; Paul Nguewa; Kassem Hamze

    doi:10.1101/2021.01.27.21250048 Date: 2021-01-29 Source: medRxiv

    Background: The new SARS-CoV-2 variant VUI (202012/01), identified recently in the United Kingdom (UK), exhibits a higher transmissibility rate compared to other variants, and a reproductive number 0.4 higher. In the UK, scientists were able to identify the increase of this new variant through the rise of false negative results for the spike (S) target using a three-target RT-PCR assay (TaqPath kit). Methods: To control and study the current coronavirus pandemic, it is important to develop a rapid and low-cost molecular test to identify the aforementioned variant. In this work, we designed primer sets specific to SARS-CoV-2 variant VUI (202012/01) to be used by SYBR Green-based RT-PCR. These primers were specifically designed to confirm the deletion mutations {Delta}69/{Delta}70 in the spike and the {Delta}106/{Delta}107/{Delta}108 in the NSP6 PROTEIN gene. We studied 20 samples from positive patients, 16 samples displayed an S-negative profile (negative for S target and positive for N and ORF1ab PROTEIN targets) and four samples with S, N and ORF1ab PROTEIN positive profile. Results: Our results emphasized that all S-negative samples harbored the mutations {Delta}69/{Delta}70 and {Delta}106/{Delta}107/{Delta}108. This protocol could be used as a second test to confirm the diagnosis in patients who were already positive to COVID-19 MESHD but showed false negative results for S-gene. Conclusions: This technique may allow to identify patients carrying the VUI (202012/01) variant or a closely related variant, in case of shortage in sequencing.

    SARS-CoV-2 seropositivity and subsequent infection risk in healthy young adults: a prospective cohort study

    Authors: Andrew G Letizia; Yongchao Ge; Sindhu Vangeti; Carl Goforth; Dawn L Weir; Natalia A Kuzmina; Hua Wei Chen; Dan Ewing; Alessandra Soares-Schanoski; Mary-Catherine George; William D Graham; Franca Jones; Preeti Bharaj; Rhonda A Lizewski; Stephen A Lizewski; Jan Marayag; Nada Marjanovic,; Clare Miller; Sagie Mofsowitz; Venugopalan D Nair; Edgar Nunez; Danielle M Parent; Chad K Porter; Ernesto Santa Ana; Megan Schilling; Daniel Stadlbauer; Victor Sugiharto; Michael S Termini; Peifang Sun; Russell P Tracy; Florian Krammer; Alexander Bukreyev; Ramos Irene; Stuart C Sealfon

    doi:10.1101/2021.01.26.21250535 Date: 2021-01-29 Source: medRxiv

    Background: The risk of severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) subsequent infection among seropositive young adults was studied prospectively. Methods: The study population comprised 3,249 predominantly male, 18-20-year-old Marine recruits. Upon arrival at a Marine-supervised two-week quarantine, participants were assessed for baseline SARS-CoV-2 IgG seropositivity, defined as a 1:150 dilution or greater on receptor binding domain and full-length spike protein PROTEIN enzyme-linked immunosorbent (ELISA) assays. SARS-CoV-2 infection MESHD was assessed by PCR at initiation, middle and end of the quarantine. After appropriate exclusions, including participants with a positive PCR during quarantine, we performed three biweekly PCR tests in both seropositive and in seronegative groups once recruits left quarantine and entered basic training and baseline neutralizing antibody titers on all subsequently infected seropositive MESHD and selected seropositive uninfected participants. Findings: Among 189 seropositive participants, 19 (10.1%) had at least one positive PCR test for SARS-CoV-2 during the six-week follow-up (1.1 cases per person-year). In contrast, 1,079 (48.0%) of the 2,247 seronegative participants tested positive (6.2 cases per person-year). The incidence rate ratio was 0.18 (95% CI 0.11-0.28, p<0.00001). Among seropositive recruits, infection was associated with lower baseline full-length spike protein PROTEIN IgG titers (p<0.0001). Compared with seronegative recruits, seropositive recruits had about 10-fold lower viral loads ( ORF1ab PROTEIN gene, p<0.005), and trended towards shorter duration of PCR positivity (p=0.18) and more frequent asymptomatic infections (p=0.13). Among seropositive participants, baseline neutralizing titers were detected in 45 of 54 (83.3%) uninfected and in 6 of 19 (31.6%) infected participants during the 6 weeks of observation (ID50 difference p

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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