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Rxivist combines biology preprints from bioRxiv and medRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 144,695 papers from 613,250 authors.

Most tweeted biology preprints, last 24 hours

*There are gaps in historical Twitter data, most notably in spring 2020. This may result in some preprints appearing with less tweets than they should.

106 results found. For more information, click each entry to expand.

1: The BNT162b2 mRNA vaccine against SARS-CoV-2 reprograms both adaptive and innate immune responses
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Posted 06 May 2021

The BNT162b2 mRNA vaccine against SARS-CoV-2 reprograms both adaptive and innate immune responses
157 tweets medRxiv infectious diseases

F. Konstantin Föhse, Büsranur Geckin, Gijs J. Overheul, Josephine van de Maat, Gizem Kilic, Ozlem Bulut, Helga Dijkstra, Heidi Lemmers, S. Andrei Sarlea, Maartje Reijnders, Jacobien Hoogerwerf, Jaap ten Oever, Elles Simonetti, Frank L van de Veerdonk, Leo A.B. Joosten, Bart L. Haagmans, Reinout van Crevel, Yang Li, Ronald P. van Rij, Corine GeurtsvanKessel, Marien I. de Jonge, Jorge Domínguez-Andrés, Mihai G. Netea

The mRNA-based BNT162b2 vaccine from Pfizer/BioNTech was the first registered COVID-19 vaccine and has been shown to be up to 95% effective in preventing SARS-CoV-2 infections. Little is known about the broad effects of the new class of mRNA vaccines, especially whether they have combined effects on innate and adaptive immune responses. Here we confirmed that BNT162b2 vaccination of healthy individuals induced effective humoral and cellular immunity against several SARS-CoV-2 variants. Interestingly, however, the BNT162b2 vaccine also modulated the production of inflammatory cytokines by innate immune cells upon stimulation with both specific (SARS-CoV-2) and non-specific (viral, fungal and bacterial) stimuli. The response of innate immune cells to TLR4 and TLR7/8 ligands was lower after BNT162b2 vaccination, while fungi-induced cytokine responses were stronger. In conclusion, the mRNA BNT162b2 vaccine induces complex functional reprogramming of innate immune responses, which should be considered in the development and use of this new class of vaccines.

2: Necessity of COVID-19 Vaccination in Previously Infected Individuals: A Retrospective Cohort Study
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Posted 04 Jun 2021

Necessity of COVID-19 Vaccination in Previously Infected Individuals: A Retrospective Cohort Study
31 tweets medRxiv infectious diseases

Nabin K. Shrestha, Patrick C. Burke, Amy S. Nowacki, Paul Terpeluk, Steven M. Gordon

Background: There are good reasons to expect natural infection to provide protection against future infection with SARS-CoV-2. The purpose of this study was to evaluate the necessity of COVID-19 vaccination in persons previously infected with SARS-CoV-2. Methods: Employees of the Cleveland Clinic Health System working in Ohio on Dec 16, 2020, the day COVID-19 vaccination was started, were included. Any subject who tested positive for SARS-CoV-2 at least 42 days earlier was considered previously infected. One was considered vaccinated 14 days after receipt of the second dose of a SARS-CoV-2 mRNA vaccine. The cumulative incidence of SARS-CoV-2 infection over the next four months, among previously infected subjects who received the vaccine, was compared with those of previously infected subjects who remained unvaccinated, previously uninfected subjects who received the vaccine, and previously uninfected subjects who remained unvaccinated. Results: Among the 52238 included employees, 1220 (47%) of 2579 previously infected subjects received the vaccine, compared with 29461 (59%) of 49659 not previously infected. The cumulative incidence of SARS-CoV-2 infection did not differ among previously infected unvaccinated subjects, previously infected subjects who were vaccinated, and previously uninfected subjects who were vaccinated, and was much lower than that of previously uninfected subjects who remained unvaccinated. Not one of the 1359 previously infected subjects who remained unvaccinated had a SARS-CoV-2 infection over the duration of the study. Conclusion: Individuals who have had SARS-CoV-2 infection are unlikely to benefit from COVID-19 vaccination, and vaccines can be safely prioritized to those who have not been infected before.

3: Heterologous ChAdOx1 nCoV-19 and BNT162b2 prime-boost vaccination elicits potent neutralizing antibody responses and T cell reactivity
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Posted 01 Jun 2021

Heterologous ChAdOx1 nCoV-19 and BNT162b2 prime-boost vaccination elicits potent neutralizing antibody responses and T cell reactivity
18 tweets medRxiv infectious diseases

Ruediger Gross, Michelle Zanoni, Alina Seidel, Carina Conzelmann, Andrea Gilg, Daniela Krnavek, Suemeyye Erdemci-evin, Benjamin Mayer, Markus Hoffmann, Stefan Poehlmann, Alexandra Beil, Joris Kroschel, Bernd Jahrsdoerfer, Hubert Schrezenmeier, Frank Kirchhoff, Jan Muench, Janis A Mueller

Background Heterologous prime-boost schedules with vector- and mRNA-based COVID-19 vaccines are already administered, but immunological responses and elicited protection have not been reported. Methods We here analyzed a cohort of 26 individuals aged 25-46 (median 30.5) years that received a ChAdOx1 nCoV-2019 prime followed by a BNT162b2 boost after an 8-week interval for reactogenicity, antibody responses and T cell reactivity. Results Self-reported solicited symptoms after ChAdOx1 nCoV-2019 prime were in line with previous reports and less severe after the BNT162b2 boost. Antibody titers increased significantly over time resulting in strong neutralization titers 2 weeks after the BNT162b2 boost. Neutralizing activity against the prevalent strain B.1.1.7 was 3.9-fold higher than in individuals receiving homologous BNT162b2 vaccination, only 2-fold reduced for variant of concern B.1.351, and similar for variant B.1.617. In addition, CD4+ and CD8+ T cells reacted to SARS-CoV-2 spike peptide stimulus 2 weeks after the full vaccination. Conclusions The heterologous ChAdOx1 nCoV-2019 / BNT162b2 prime-boost vaccination regimen is not associated with serious adverse events and results in a potent humoral immune response and elicits T cell reactivity. Variants of concern B.1.1.7, B.1.351 and B.1.617 are potently neutralized by sera of all participants. These results suggest that this heterologous vaccination regimen is at least as immunogenic and protective as homologous vaccinations.

4: Pre-pandemic SARS-CoV-2 potential natural immunity among population of the Democratic Republic of Congo
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Posted 01 May 2021

Pre-pandemic SARS-CoV-2 potential natural immunity among population of the Democratic Republic of Congo
16 tweets medRxiv infectious diseases

Marc SOURIS, Léon TSHILOLO, Daniel PARZY, Rachel KAMGAING, Destin MBONGI, Balthazar PHOBA, Marie-Anasthasie TSHILOLO, René MBUNGU, Pierre MORAND, Jean-Paul GONZALEZ

More than a year after the emergence of COVID-19, significant regional differences in terms of morbidity persist, showing lower incidence rates in sub-Saharan Africa, Southeast Asia, and Oceania. Like SARS-CoV-1 and MERS viruses, SARS-CoV-2 is monophyletically positioned with parental species of chiropteran coronavirus. Furthermore, we observe that the spatial distribution of several targeted bat species (i.e., Coronavirus species hosts) overlaps the distribution of countries with low COVID-19 incidence. The work presented here aims to test the presence of natural immunity among population with a low COVD-19 prevalence, potentially due to a previous exposure to coronavirus antigens of a virus close related to SARS-CoV-2. To identify such pre-existing immunity, an ELISA serological test was used to detect IgG antibodies targeting main SARS-CoV-2 proteins including: the N-protein, the Spike 1 (S1) protein, the receptor binding domain (RBD) of the S1 protein, the N-terminal domain (NTD) of the S1 protein, and the S2 protein. A total of 574 sera samples collected before 2019 in the population of the Democratic Republic of Congo (DRC) were tested). 189 control sera from blood donors in France were used as control samples. The results showed a statistically significant difference between the DRC samples and control samples for all antigens (N, S1, S2, NTD) except for RBD. The percentage of positive samples presenting reactive antibodies for S1 antigen was respectively of 19.2% for RDC versus 2.11% for the control, and of 9.3% versus 1.6% for the S2 antigen. In conclusion, our data showed that the study population has been potentially exposed to a SARS-CoV-2-like virus antigen before the pandemic in the Central African sub-region. Therefore, it is quite legitimate to think that this prior immunity may be protective and responsible for the observed low prevalence of COVID-19. Moreover, we can assume that this not yet identified SARS-CoV-2-like could be associated to a chiropteran species in close contact with the studied population. In order to confirm the presence of SARS-CoV-2-like virus antibodies and ultimately identify the neutralizing potential for the detected antibodies, our study is underway in other African and Asian countries, where the COVID-19 prevalence is limited.

5: Reconstructing the COVID-19 epidemic in Delhi, India: infection attack rate and reporting of deaths
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Posted 26 Mar 2021

Reconstructing the COVID-19 epidemic in Delhi, India: infection attack rate and reporting of deaths
13 tweets medRxiv infectious diseases

Margarita Pons-Salort, Jacob John, Oliver John Watson, Nicholas F Brazeau, Robert Verity, Gagandeep Kang, Nicholas C. Grassly

India reported over 10 million COVID-19 cases and 149,000 deaths in 2020. To estimate exposure and the potential for further spread, we used a SARS-CoV-2 transmission model fit to seroprevalence data from three serosurveys in Delhi and the time-series of reported deaths to reconstruct the epidemic. The cumulative proportion of the population estimated infected was 48.7% (95% CrI 22.1% - 76.8%) by end-September 2020. Using an age-adjusted overall infection fatality ratio (IFR) based on age-specific estimates from mostly high-income countries (HICs), we estimate that 15.0% (95% CrI 9.3% - 34.0%) of COVID-19 deaths were reported. This indicates either under-reporting of COVID-19 deaths and/or a lower age-specific IFR in India compared with HICs. Despite the high attack rate of SARS-CoV-2, a third wave occurred in late 2020, suggesting that herd immunity was not yet reached. Future dynamics will strongly depend on the duration of immunity and protection against new variants.

6: A panel of KSHV mutants in the polycistronic kaposin locus for precise analysis of individual protein products
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Posted 11 Jun 2021

A panel of KSHV mutants in the polycistronic kaposin locus for precise analysis of individual protein products
10 tweets bioRxiv microbiology

Mariel Kleer, Grant MacNeil, Eric S. Pringle, Jennifer A. Corcoran

Kaposi's sarcoma-associated herpesvirus (KSHV) is the infectious cause of several human cancers including the endothelial cell (EC) malignancy, Kaposi's sarcoma. Unique KSHV genes absent from other human herpesvirus genomes, known as K-genes, are typically important for KSHV replication and pathogenesis. Among the K-genes, the kaposin mRNA is highly expressed in both latent and lytic phases of infection, but its polycistronic nature has hindered methodical analysis of the role of kaposin translation products in viral replication. At least three proteins are produced from the kaposin transcript, Kaposin A (KapA), B (KapB), and C (KapC). We have previously shown that KapB overexpression is sufficient to recapitulate two KS phenotypes, EC spindling and elevated proinflammatory cytokine transcripts, the latter which proceeds via the disassembly of RNA decay granules called processing bodies (PBs). To pinpoint the relative contributions of kaposin proteins at different stages of KSHV infection, we constructed four recombinant viruses by deleting or recoding the kaposin locus. Latent infection of iSLK cells with kaposin-deficient viruses resulted in reduced viral genome copy number and small LANA nuclear bodies; despite this, all iSLK cells were capable of progeny virion production. De novo infection of ECs revealed that KapB was dispensable for EC spindling but required for PB disassembly during KSHV latency, suggesting other viral proteins contribute to spindling. These findings demonstrate that our panel of viruses enables precise analysis of respective contributions of individual kaposin proteins to KSHV replication. This approach serves as a guide for the functional analysis of complex multicistronic viral loci.

7: Neutralization of variant under investigation B.1.617 with sera of BBV152 vaccinees
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Posted 23 Apr 2021

Neutralization of variant under investigation B.1.617 with sera of BBV152 vaccinees
6 tweets bioRxiv immunology

Pragya Yadav, Gajanan N Sapkal, Priya Abraham, Raches Ella, Gururaj Deshpande, Deepak Y Patil, Dimpal Nyayanit, Nivedita Gupta, Rima R Sahay, Anita M Shete, Samiran Panda, Balram Bhargava, V Krishna Mohan

The drastic rise in the number of cases in Maharashtra, India has created a matter of concern for public health experts. Twelve isolates of VUI lineage B.1.617 were propagated in VeroCCL81 cells and characterized. Convalescent sera of the COVID-19 cases and recipients of BBV152 (Covaxin) were able to neutralize VUI B.1.617.

8: BNT162b2 vaccination induces SARS-CoV-2 specific antibody secretion into human milk with minimal transfer of vaccine mRNA
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Posted 29 Apr 2021

BNT162b2 vaccination induces SARS-CoV-2 specific antibody secretion into human milk with minimal transfer of vaccine mRNA
6 tweets medRxiv pediatrics

Jia Ming Low, Yue Gu, Melissa Shu Feng Ng, Amin Zubair, Le Ye Lee, Yvonne Peng Mei Ng, Bhuvaneshwari D/O Shunmuganathan, Yuxi Niu, Rashi Gupta, Paul Tambyah, Paul A Macary, Liang Wei Wang, Youjia Zhong

Importance: To examine the impact of SARS-CoV-2 vaccination of lactating mothers on human milk Objective: (1) To quantify SARS-CoV-2-specific immunoglobulin A (IgA) and immunoglobulin G (IgG) in human milk of lactating mothers who received the BNT162b2 vaccine, with reference to a cohort convalescent from antenatal COVID-19, and healthy lactating mothers. (2) To detect and quantify vaccine mRNA in human milk after BNT162b2 vaccination. Design: Gestational Immunity For Transfer 2 (GIFT-2) is a prospective cohort study of lactating mothers who were due to receive two doses of BNT162b2 vaccine, recruited between 5th February 2021 and 9th February 2021. Setting: Lactating healthcare workers living in Singapore Participants: Convenience sample of ten lactating healthcare workers. Human milk samples were collected at four time points: pre-vaccination, 1 to 3 days after dose one, 7 to 10 days after dose one, and 3 to 7 days after dose two of the BNT162b2 vaccine. Exposure: Two doses of the BNT162b2 vaccine 21 days apart. Main Outcome and Measure: (i) SARS-CoV-2-specific IgA and IgG in human milk of lactating mothers who received BNT162b2 vaccine, (ii) Detection and quantification of vaccine mRNA in human milk after BNT162b2 vaccination. Results: Ten lactating healthcare workers aged 32.5 years (range 29 to 42) were recruited, with 40 human milk samples collected and analysed. SARS-CoV-2-specific IgA was predominant in human milk of lactating mothers who received BNT162b2 vaccine. The sharpest rise in antibody production was 3 to 7 days after dose two of the BNT162b2 vaccine, with medians of 1110 picomolar of anti-SARS-CoV-2 spike and 374 picomolar of anti-Receptor Binding Domain IgA. Vaccine mRNA was detected only on rare occasions, at a maximum concentration of 2 ng/mL. Infants had no reported adverse events, up to 28 days after ingestion of post-vaccination human milk. Conclusions and Relevance: In this cohort of ten lactating mothers following BNT162b2 vaccination, nine (90%) produced SARS-CoV-2 IgA, and ten (100%) produced IgG in human milk with minimal amounts of vaccine mRNA. Lactating individuals should continue breastfeeding in an uninterrupted manner after receiving mRNA vaccination for SARS-CoV-2.

9: Effectiveness of COVID-19 vaccines against the B.1.617.2 variant
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Posted 24 May 2021

Effectiveness of COVID-19 vaccines against the B.1.617.2 variant
4 tweets medRxiv epidemiology

Jamie Lopez Bernal, Nick Andrews, Charlotte Gower, Eileen Gallagher, Ruth Simmons, Simon Thelwall, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Colin Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay

Background: The B.1.617.2 COVID-19 variant has contributed to the surge in cases in India and has now been detected across the globe, including a notable increase in cases in the UK. We estimate the effectiveness of the BNT162b2 and ChAdOx1 COVID-19 vaccines against this variant. Methods: A test negative case control design was used to estimate the effectiveness of vaccination against symptomatic disease with both variants over the period that B.1.617.2 began circulating with cases identified based on sequencing and S-gene target status. Data on all symptomatic sequenced cases of COVID-19 in England was used to estimate the proportion of cases with B.1.617.2 compared to the predominant strain (B.1.1.7) by vaccination status. Results: Effectiveness was notably lower after 1 dose of vaccine with B.1.617.2 cases 33.5% (95%CI: 20.6 to 44.3) compared to B.1.1.7 cases 51.1% (95%CI: 47.3 to 54.7) with similar results for both vaccines. With BNT162b2 2 dose effectiveness reduced from 93.4% (95%CI: 90.4 to 95.5) with B.1.1.7 to 87.9% (95%CI: 78.2 to 93.2) with B.1.617.2. With ChAdOx1 2 dose effectiveness reduced from 66.1% (95% CI: 54.0 to 75.0) with B.1.1.7 to 59.8% (95%CI: 28.9 to 77.3) with B.1.617.2. Sequenced cases detected after 1 or 2 doses of vaccination had a higher odds of infection with B.1.617.2 compared to unvaccinated cases (OR 1.40; 95%CI: 1.13-1.75). Conclusions: After 2 doses of either vaccine there were only modest differences in vaccine effectiveness with the B.1.617.2 variant. Absolute differences in vaccine effectiveness were more marked with dose 1. This would support maximising vaccine uptake with two doses among vulnerable groups.

10: Safety, reactogenicity, and immunogenicity of homologous and heterologous prime-boost immunisation with ChAdOx1-nCoV19 and BNT162b2: a prospective cohort study
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Posted 22 May 2021

Safety, reactogenicity, and immunogenicity of homologous and heterologous prime-boost immunisation with ChAdOx1-nCoV19 and BNT162b2: a prospective cohort study
4 tweets medRxiv infectious diseases

David Hillus, Tatjana Schwarz, Pinkus Tober-Lau, Hana Hastor, Charlotte Thibeault, Stefanie Kasper, Elisa T. Helbig, Lena J. Lippert, Patricia Tscheak, Marie Luisa Schmidt, Johanna Riege, Andr Solarek, Christof von Kalle, Chantip Dang-Heine, Piotr Kopankiewicz, Norbert Suttorp, Christian Drosten, Harald Bias, Joachim Seybold, COVIM/EICOV Study Group, Florian Kurth, Victor M Corman, Leif Erik Sander

Objective: to assess reactogenicity and immunogenicity of heterologous prime-boost immunisations of ChAdOx1-nCoV19 (Vaxzevria, ChAdOx) followed by BNT162b2 (Comirnaty, BNT) compared to homologous BNT/BNT immunisation. Design: prospective, observational cohort study. Setting: unicenter study in a cohort of health care workers at a tertiary care center in Berlin, Germany. Participants: 340 health care workers immunised between 27 December 2020 and 21 May 2021 at Charite - Universitaetsmedizin Berlin, Germany Main outcome measures: the main outcomes were reactogenicity assessed on days one, three, five and seven post prime and boost vaccination, and immunogenicity measured by serum SARS-CoV-2 full spike-, spike S1-, and spike RBD-IgG, virus neutralisation capacity, anti-S1-IgG avidity, and T cell reactivity measured by Interferon gamma release assay at 3-4 weeks post prime and boost immunisation. Results: Heterologous ChAdOx/BNT booster vaccination was overall well-tolerated and reactogenicity was largely comparable to homologous BNT/BNT vaccination. Systemic reactions were most frequent after prime immunisation with ChAdOx (86%, 95CI: 79-91), and less frequent after homologous BNT/BNT (65%, 95CI: 56-72), or heterologous ChAdOx/BNT booster vaccination (48%, 95CI: 36-59). Serum antibody responses and T cell reactivity were strongly increased after both homologous and heterologous boost, and immunogenicity was overall robust, and comparable between both regimens in this cohort, with slightly increased S1-IgG avidity and T cell responses following heterologous booster immunisation. Conclusions: Evidence of rare thrombotic events associated with ChAdOx has led to recommendation of a heterologous booster with mRNA vaccines for certain age groups in several European countries, despite a lack of robust safety and immunogenicity data for this vaccine regimen. This interim analysis provides evidence that the currently recommended heterologous ChAdOx/BNT immunisation regimen with 10-12 week vaccine intervals is well tolerated and slightly more immunogenic compared to homologous BNT/BNT vaccination with three week vaccine intervals. Heterologous prime-boost immunisation for COVID-19 may be generally applicable to optimise logistics and improve immunogenicity and to mitigate potential intermittent supply shortages for individual vaccines.

11: SARS-CoV-2 causes brain inflammation and induces Lewy body formation in macaques
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Posted 23 Feb 2021

SARS-CoV-2 causes brain inflammation and induces Lewy body formation in macaques
4 tweets bioRxiv neuroscience

Ingrid H.C.H.M. Philippens, Kinga P. Boszormenyi, Jacqueline A. Wubben, Zahra C Fagrouch, Nikki van Driel, Amber Q. Mayenburg, Diana Lozovagia, Eva Roos, Bernadette Schurink, Marianna Bugiani, Ronald E Bontrop, Jinte Middeldorp, Willy M Bogers, Lioe-Fee de Geus-Oei, Jan A.M. Langermans, Marieke A Stammes, Babs E Verstrepen, Ernst J Verschoor

SARS-CoV-2 may cause acute respiratory disease, but the infection can also initiate neurological symptoms. Here we show that SARS-CoV-2 infection causes brain inflammation in the macaque model. An increased metabolic activity in the pituitary gland of two macaques was observed by longitudinal positron emission tomography-computed tomography (PET-CT). Post-mortem analysis demonstrated infiltration of T-cells and activated microglia in the brain, and viral RNA was detected in brain tissues from one animal. We observed Lewy bodies in brains of all rhesus macaques. These data emphasize the virus' capability to induce neuropathology in this nonhuman primate model for SARS-CoV-2 infection. As in humans, Lewy body formation is an indication for the development of Parkinson's disease, this data represents a warning for potential long-term neurological effects after SARS-CoV-2 infection.

12: Protection of previous SARS-CoV-2 infection is similar to that of BNT162b2 vaccine protection: A three-month nationwide experience from Israel
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Posted 24 Apr 2021

Protection of previous SARS-CoV-2 infection is similar to that of BNT162b2 vaccine protection: A three-month nationwide experience from Israel
3 tweets medRxiv epidemiology

Yair Goldberg, Micha Mandel, Yonatan Woodbridge, Ronen Fluss, Ilya Novikov, Rami Yaari, Arnona Ziv, Laurence Freedman, Amit Huppert

Worldwide shortage of vaccination against SARS-CoV-2 infection while the pandemic is still uncontrolled leads many states to the dilemma whether or not to vaccinate previously infected persons. Understanding the level of protection of previous infection compared to that of vaccination is critical for policy making. We analyze an updated individual-level database of the entire population of Israel to assess the protection efficacy of both prior infection and vaccination in preventing subsequent SARS-CoV-2 infection, hospitalization with COVID-19, severe disease, and death due to COVID-19. Vaccination was highly effective with overall estimated efficacy for documented infection of 92.8% (CI: [92.6, 93.0]); hospitalization 94.2% (CI: [93.6, 94.7]); severe illness 94.4% (CI: [93.6, 95.0]); and death 93.7% (CI: [92.5, 94.7]). Similarly, the overall estimated level of protection from prior SARS-CoV-2 infection for documented infection is 94.8% (CI: [94.4, 95.1]); hospitalization 94.1% (CI: [91.9, 95.7]); and severe illness 96.4% (CI: [92.5, 98.3]). Our results question the need to vaccinate previously-infected individuals.

13: Live-cell imaging shows uneven segregation of extrachromosomal DNA elements and transcriptionally active extrachromosomal DNA clusters in cancer
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Posted 21 Oct 2020

Live-cell imaging shows uneven segregation of extrachromosomal DNA elements and transcriptionally active extrachromosomal DNA clusters in cancer
3 tweets bioRxiv cancer biology

Eunhee Yi, Amit D Gujar, Molly Guthrie, Hoon Kim, Kevin C. Johnson, Samir B. Amin, Sunit Das, Patricia A Clow, Albert W. Cheng, Roel GW Verhaak

Oncogenic extrachromosomal DNA elements (ecDNAs) promote intratumoral heterogeneity, creating a barrier for successful cancer treatments. The underlying mechanisms are poorly understood and studies are hampered in part by a lack of adequate tools enabling studies of ecDNA behavior. Here, we show that single-cell ecDNA copy numbers follow a Gaussian distribution across tumor cells in vitro and in patient glioblastoma specimens, suggesting uneven ecDNA segregation during mitosis. We established a CRISPR-based approach which leverages unique ecDNA breakpoint sequences to tag ecDNA with fluorescent markers in living cells. Applying this method during mitosis revealed disjointed ecDNA inheritance patterns, providing an explanation for rapid ecDNA accumulation in cancer. Post-mitosis, ecDNAs tended to cluster and clustered ecDNAs colocalized with RNA polymerase II, promoting transcription of cargo oncogenes. Our observations provide direct evidence for uneven segregation of ecDNA and shed new lights of mechanisms through which ecDNAs contribute to oncogenesis. ### Competing Interest Statement R.G.W.V. is a scientific co-founder of and has received research funding from Boundless Bio, Inc.

14: Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities
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Posted 05 Mar 2021

Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities
3 tweets medRxiv infectious diseases

Qing Yang, Tassa Saldi, Erika Lasda, Carolyn J. Decker, Camille L. Paige, Denise Muhlrad, Patrick Gonzalez, Morgan R. Fink, Kimngan L. Tat, Cole R. Hager, Jack C. Davis, Christopher D Ozeroff, Nicholas R. Meyerson, Stephen K. Clark, Will T. Fattor, Alison R. Gilchrist, Arturo Barbachano-Guerrero, Emma R. Worden-Sapper, Sharon S. Wu, Gloria R. Brisson, Matthew B McQueen, Robin D Dowell, Leslie A Leinwand, Roy Parker, Sara L Sawyer

We analyze data from the Fall 2020 pandemic response efforts at the University of Colorado Boulder (USA), where more than 72,500 saliva samples were tested for SARS-CoV-2 using quantitative RT-PCR. All samples were collected from individuals who reported no symptoms associated with COVID-19 on the day of collection. From these, 1,405 positive cases were identified. The distribution of viral loads within these asymptomatic individuals was indistinguishable from what has been previously reported in symptomatic individuals. Regardless of symptomatic status, approximately 50% of individuals who test positive for SARS-CoV-2 seem to be in non-infectious phases of the disease, based on having low viral loads in a range from which live virus has rarely been isolated. We find that, at any given time, just 2% of individuals carry 90% of the virions circulating within communities, serving as viral "super-carriers" and possibly also super-spreaders.

15: The SARS-CoV-2 spike protein disrupts the cooperative function of human cardiac pericytes - endothelial cells through CD147 receptor-mediated signalling: a potential non-infective mechanism of COVID-19 microvascular disease
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Posted 21 Dec 2020

The SARS-CoV-2 spike protein disrupts the cooperative function of human cardiac pericytes - endothelial cells through CD147 receptor-mediated signalling: a potential non-infective mechanism of COVID-19 microvascular disease
3 tweets bioRxiv cell biology

Elisa Avolio, Monica Gamez, Kapil Gupta, Rebecca Foster, Imre Berger, Massimo Caputo, Andrew Davidson, Darryl Hill, Paolo Madeddu

BackgroundSevere coronavirus disease 2019 (COVID-19) manifests as a life-threatening microvascular syndrome. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses primarily the capsid spike (S) protein to engage with its receptors and infect host cells. To date, it is still not known if the S protein alone, without the other viral elements, is able to trigger vascular cell signalling and provoke cell dysfunction. MethodsWe investigated the effects of the recombinant, stabilised S protein on primary human cardiac pericytes (PCs) signalling and function. Endpoints included cell viability, proliferation, migration, cooperation with endothelial cells (ECs) in angiogenesis assays, and release of pro-inflammatory cytokines. Adopting a blocking strategy against the S protein receptors ACE2 and CD147, we explored which receptor mediates the S protein signalling in PCs. FindingsWe show, for the first time, that the recombinant S protein alone elicits functional alterations in cardiac PCs. This was documented as: (1) increased migration, (2) reduced ability to support EC network formation on Matrigel, (3) secretion of pro-inflammatory molecules typically involved in the cytokine storm, and (4) production of pro-apoptotic factors responsible for EC death. Furthermore, the S protein stimulates the phosphorylation/activation of the extracellular signal-regulated kinase 1/2 (ERK1/2) through the CD147 receptor, but not ACE2, in cardiac PCs. Accordingly, the neutralization of CD147, using a blocking antibody, prevented the activation of ERK1/2 and partially rescued the PC function in the presence of the S protein. InterpretationOur findings suggest the new, intriguing hypothesis that the S protein may elicit vascular cell dysfunction, potentially amplifying, or perpetuating, the damage caused by the whole coronavirus. This mechanism may have clinical and therapeutic implication. FundingElizabeth Blackwell Institute (EBI) Rapid Response COVID-19 award. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses primarily the capsid spike (S) protein to engage with its receptors and infect host cells. Co-receptors and host cell proteases may also be involved. Angiotensin-converting enzyme 2 (ACE2) is the well-recognized entry receptor used by the virus in respiratory epithelial cells; it is also abundantly expressed in the human heart. Alongside ACE2, CD147 has recently emerged as a novel receptor for SARS-CoV-2. Yet, it is not clear if SARS-CoV-2 triggers adverse responses in cardiac vascular mural cells. Likewise, no investigation was devoted to verifying if the recombinant S protein alone can mimic the whole virus signalling. Added value of this studyThis study provides the first evidence that the recombinant S protein alone, without the other viral elements, is capable of eliciting cellular signalling in human cardiac pericytes, thereby inducing cell dysfunction. In addition, this study proposes CD147 as the leading receptor mediating S protein signalling in cardiac pericytes. Implications of all the available evidenceThese reports imply that fragments of the S protein might be able to elicit vascular cell dysfunction. Blocking the CD147 receptor may help protect the vasculature not only from infection, but also from the collateral damage caused by the S protein.

16: False positives in reverse transcription PCR testing for SARS-CoV-2
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Posted 01 May 2020

False positives in reverse transcription PCR testing for SARS-CoV-2
3 tweets medRxiv epidemiology

Andrew N Cohen, Bruce Kessel, Michael G Milgroom

Contrary to the practice during previous epidemics, with COVID-19 health authorities have treated a single positive result from a PCR-based test as confirmation of infection, irrespective of signs, symptoms and exposure. This is based on a widespread belief that positive results in these tests are highly reliable. However, evidence from external quality assessments and real-world data indicate enough a high enough false positive rate to make positive results highly unreliable over a broad range of scenarios. This has clinical and case management implications, and affects an array of epidemiological statistics, including the asymptomatic ratio, prevalence, and hospitalization and death rates, as well as epidemiologic models. Steps should be taken to raise awareness of false positives and reduce their frequency. The most important immediate action is to check positive results with additional tests, at least when prevalence is low.

17: Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag
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Posted 31 Jan 2020

Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag
3 tweets bioRxiv evolutionary biology

Prashant Pradhan, Ashutosh Kumar Pandey, Akhilesh Mishra, Parul Gupta, Praveen Kumar Tripathi, Manoj Balakrishnan Menon, James Gomes, Perumal Vivekanandan, Bishwajit Kundu

This paper has been withdrawn by its authors. They intend to revise it in response to comments received from the research community on their technical approach and their interpretation of the results. If you have any questions, please contact the corresponding author.

18: Deep learning-based real-time detection of novel pathogens during sequencing
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Posted 27 Jan 2021

Deep learning-based real-time detection of novel pathogens during sequencing
3 tweets bioRxiv bioinformatics

Jakub M Bartoszewicz, Ulrich Genske, Bernhard Y Renard

Novel pathogens evolve quickly and may emerge rapidly, causing dangerous outbreaks or even global pandemics. Next-generation sequencing is the state-of-the-art in open-view pathogen detection, and one of the few methods available at the earliest stages of an epidemic, even when the biological threat is unknown. Analyzing the samples as the sequencer is running can greatly reduce the turnaround time, but existing tools rely on close matches to lists of known pathogens and perform poorly on novel species. Machine learning approaches can predict if single reads originate from more distant, unknown pathogens, but require relatively long input sequences and processed data from a finished sequencing run. Incomplete sequences contain less information, leading to a trade-off between sequencing time and detection accuracy. Using a workflow for real-time pathogenic potential prediction, we investigate which subsequences already allow accurate inference. We train deep neural networks to classify Illumina and Nanopore reads and integrate the models with HiLive2, a real-time Illumina mapper. This approach outperforms alternatives based on machine learning and sequence alignment on simulated and real data, including SARS-CoV-2 sequencing runs. After just 50 Illumina cycles, we observe an 80-fold sensitivity increase compared to real-time mapping. The first 250bp of Nanopore reads, corresponding to 0.5s of sequencing time, are enough to yield predictions more accurate than mapping the finished long reads. The approach could also be used for screening synthetic sequences against biosecurity threats.

19: Anti-SARS-CoV-2 Antibodies Persist for up to 13 Months and Reduce Risk of Reinfection
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Posted 14 May 2021

Anti-SARS-CoV-2 Antibodies Persist for up to 13 Months and Reduce Risk of Reinfection
3 tweets medRxiv infectious diseases

Floriane Gallais, Pierre Gantner, Timothee Bruel, Aurelie Velay, Delphine Planas, Marie-Josee Wendling, Sophie Bayer, Morgane Solis, Elodie Laugel, Nathalie Reix, Anne Schneider, Ludovic Glady, Baptiste Panaget, Nicolas Collongues, Marialuisa Partisani, Jean-Marc Lessinger, Arnaud Fontanet, David Rey, Yves Hansmann, Laurence Kling-Pillitteri, Olivier Schwartz, Jerome De Seze, Nicolas Meyer, Maria Gonzalez, Catherine Schmidt-Mutter, Samira Fafi-Kremer

Assessment of the kinetics of SARS-CoV-2 antibodies is essential in predicting protection against reinfection and durability of vaccine protection. Here, we longitudinally measured Spike (S) and Nucleocapsid (N)-specific antibodies in 1,309 healthcare workers (HCWs), including 916 COVID-19 negative HCWs and 393 convalescent COVID-19 for up to 422 days post-symptom. From month (M)1 to M7-9 post-infection, SARS-CoV-2 antibodies decreased moderately in convalescent HCWs in a biphasic model, with men showing a slower decay of anti-N (p=0.02), and a faster decay of anti-S (p=0.0008) than women. At M11-13, anti-N dramatically decreased (half-life: 283 days) while anti-S stabilized (half-life: 725 days) at a median of 2.39 log Arbitrary Units (AU)/mL (Interquartile Range (IQR): 2.10 -2.75). Overall, 69 SARS-CoV-2 infections developed in the COVID-19 negative group (incidence of 12.22 per 100 person-years) versus one in the COVID-19 positive group (incidence of 0.40 per 100 person-years), indicating a relative reduction in the incidence of SARS-CoV-2 reinfection of 96.7% (p<0.0001). Correlation with live-virus neutralization assay revealed that variants D614G and B.1.1.7, but not B.1.351, were sensitive to anti-S antibodies at 2.3 log AU/mL, while IgG [&ge;] 3 log AU/mL neutralized all three variants. After SARS-CoV-2 vaccination, anti-S levels were increased by > 3 logs regardless of pre-vaccination IgG levels, type of vaccine, and number of doses. Our study demonstrates a long-term persistence of anti-S IgG antibodies that may protect against reinfection. By significantly increasing cross-neutralizing antibody titers, a single-dose vaccination strengthens protection against escape mutants.

20: FDR control in GWAS with population structure
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Posted 04 Aug 2020

FDR control in GWAS with population structure
2 tweets bioRxiv genomics

Matteo Sesia, Stephen Bates, Emmanuel Candès, Jonathan Marchini, Chiara Sabatti

We present a comprehensive statistical framework to analyze data from genome-wide association studies of polygenic traits, producing distinct and interpretable discoveries while controlling the false discovery rate. This approach leverages sophisticated multivariate models, correcting for linkage disequilibrium, and accounts for population structure and relatedness, adapting to the characteristics of the samples at hand. A key element is the recognition that the observed genotypes can be considered as a random sample from an appropriate model, encapsulating our knowledge of genetic inheritance and human populations. This allows us to generate imperfect copies (knockoffs) of these variables which serve as ideal negative controls; knockoffs are indistinguishable from the original genotypes in distribution, and independent from the phenotype. In sharp contrast with state-of-the-art methods, the validity of our inference in no way depends on assumptions about the unknown relation between genotypes and phenotype. We develop and leverage a model for the genotypes that accounts for arbitrary and unknown population structure, which may be due to diverse ancestries or familial relatedness. We build a pipeline that is robust to the most prominent possible confounders, facilitating the discovery of causal variants. Validity and effectiveness are demonstrated by extensive simulations with real data, as well as by the analysis of several phenotypes in the UK Biobank. Finally, fast software is made available for researchers to apply the proposed methodology to Biobank-scale data sets.

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