Search Results - "Ghafari, Mahan"

Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR by Wikramaratna, Paul S, Paton, Robert S, Ghafari, Mahan, Lourenço, José

“…BackgroundReverse-transcription PCR (RT-PCR) assays are used to test for infection with the SARS-CoV-2 virus. RT-PCR tests are highly specific and the…”
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Estimates of anti-SARS-CoV-2 antibody seroprevalence in Iran by Ghafari, Mahan, Kadivar, Alireza, Katzourakis, Aris

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A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses by Ghafari, Mahan, Simmonds, Peter, Pybus, Oliver G., Katzourakis, Aris

“…Estimating viral timescales is fundamental in understanding the evolutionary biology of viruses. Molecular clocks are widely used to reveal the recent…”
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Excess deaths associated with the Iranian COVID-19 epidemic: A province-level analysis by Ghafari, Mahan, Kadivar, Alireza, Katzourakis, Aris

“…•This is the first province-level study to examine COVID-19-related deaths in Iran.•There were nearly 59 000 extra deaths during the epidemic until September…”
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A framework for reconstructing SARS-CoV-2 transmission dynamics using excess mortality data by Ghafari, Mahan, Watson, Oliver J., Karlinsky, Ariel, Ferretti, Luca, Katzourakis, Aris

“…The transmission dynamics and burden of SARS-CoV-2 in many regions of the world is still largely unknown due to the scarcity of epidemiological analyses and…”
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A quantitative evaluation of the impact of vaccine roll-out rate and coverage on reducing deaths: insights from the first 2 years of COVID-19 epidemic in Iran by Ghafari, Mahan, Hosseinpour, Sepanta, Rezaee-Zavareh, Mohammad Saeid, Dascalu, Stefan, Rostamian, Somayeh, Aramesh, Kiarash, Madani, Kaveh, Kordasti, Shahram

“…Vaccination has played a pivotal role in reducing the burden of COVID-19. Despite numerous studies highlighting its benefits in reducing the risk of severe…”
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Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses by Ghafari, Mahan, Sõmera, Merike, Sarmiento, Cecilia, Niehl, Annette, Hébrard, Eugénie, Tsoleridis, Theocharis, Ball, Jonathan, Moury, Benoît, Lemey, Philippe, Katzourakis, Aris, Fargette, Denis

“…The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating…”
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Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern by Ghafari, Mahan, Liu, Qihan, Dhillon, Arushi, Katzourakis, Aris, Weissman, Daniel B.

“…The emergence of Variants of Concern (VOCs) of SARS-CoV-2 with increased transmissibility, immune evasion properties, and virulence poses a great challenge to…”
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Lessons for preparedness and reasons for concern from the early COVID-19 epidemic in Iran by Ghafari, Mahan, Hejazi, Bardia, Karshenas, Arman, Dascalu, Stefan, Kadvidar, Alireza, Khosravi, Mohammad A., Abbasalipour, Maryam, Heydari, Majid, Zeinali, Sirous, Ferretti, Luca, Ledda, Alice, Katzourakis, Aris

“…•Our phylogenetic analysis reveals the Iranian epidemic started nearly two months before when the first cases were reported.•By analysing 46 genomic samples of…”
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Engaging Religious Institutions and Faith-Based Communities in Public Health Initiatives: A Case Study of the Romanian Orthodox Church During the COVID-19 Pandemic by Dascalu, Stefan, Flammer, Patrik G, Ghafari, Mahan, Henson, Shaun C, Nascimento, Roger, Bonsall, Michael B

“…The success of public health interventions is highly dependent on the compliance of the general population. State authorities often implement policies without…”
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Corrigendum: Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern by Ghafari, Mahan, Liu, Qihan, Dhillon, Arushi, Katzourakis, Aris, Weissman, Daniel B.

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Insights into SARS-CoV-2 in Angola during the COVID-19 peak: Molecular epidemiology and genome surveillance by Francisco, Ngiambudulu M, van Wyk, Stephanie, Moir, Monika, San, James Emmanuel, Sebastião, Cruz S, Tegally, Houriiyah, Xavier, Joicymara, Maharaj, Akhil, Neto, Zoraima, Afonso, Pedro, Jandondo, Domingos, Paixão, Joana, Miranda, Julio, David, Kumbelembe, Inglês, Luzia, Pereira, Amilton, Paulo, Agostinho, Carralero, Raisa Rivas, Freitas, Helga Reis, Mufinda, Franco, Lutucuta, Silvia, Ghafari, Mahan, Giovanetti, Marta, Giandhari, Jennifer, Pillay, Sureshnee, Naidoo, Yeshnee, Singh, Lavanya, Tshiabuila, Derek, Martin, Darren Patrick, Chabuka, Lucious, Choga, Wonderful, Wanjohi, Dorcas, Mwangi, Sarah, Pillay, Yusasha, Kebede, Yenew, Shumba, Edwin, Ondoa, Pascale, Baxter, Cheryl, Wilkinson, Eduan, Tessema, Sofonias Kifle, Katzourakis, Aris, Lessells, Richard, de Oliveira, Tulio, Morais, Joana

“…In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the…”
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The evolution of SARS-CoV-2 by Markov, Peter V., Ghafari, Mahan, Beer, Martin, Lythgoe, Katrina, Simmonds, Peter, Stilianakis, Nikolaos I., Katzourakis, Aris

“…Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to…”
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Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza by Ghafari, Mahan, du Plessis, Louis, Raghwani, Jayna, Bhatt, Samir, Xu, Bo, Pybus, Oliver G, Katzourakis, Aris

“…Abstract High-throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the…”
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Quantitative Analysis of the Mode and Tempo of Virus Molecular Evolution by Ghafari, Mahan

“…Estimating the rate of nucleotide and amino acid substitutions is fundamental to our understanding of how fast species evolve. It also enables us to…”
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Inferring Transmission Bottleneck Size from Viral Sequence Data Using a Novel Haplotype Reconstruction Method by Ghafari, Mahan, Lumby, Casper K, Weissman, Daniel B, Illingworth, Christopher J R

“…The transmission bottleneck is defined as the number of viral particles that transmit from one host to establish an infection in another. Genome sequence data…”
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The expected time to cross extended fitness plateaus by Ghafari, Mahan, Weissman, Daniel B.

“…For a population to acquire a complex adaptation requiring multiple individually neutral mutations, it must cross a plateau in the fitness landscape. We…”
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Prevalence of persistent SARS-CoV-2 in a large community surveillance study by Ghafari, Mahan, Hall, Matthew, Golubchik, Tanya, Ayoubkhani, Daniel, House, Thomas, MacIntyre-Cockett, George, Fryer, Helen R., Thomson, Laura, Nurtay, Anel, Kemp, Steven A., Ferretti, Luca, Buck, David, Green, Angie, Trebes, Amy, Piazza, Paolo, Lonie, Lorne J., Studley, Ruth, Rourke, Emma, Smith, Darren L., Bashton, Matthew, Nelson, Andrew, Crown, Matthew, McCann, Clare, Young, Gregory R., Santos, Rui Andre Nunes dos, Richards, Zack, Tariq, Mohammad Adnan, Cahuantzi, Roberto, Barrett, Jeff, Fraser, Christophe, Bonsall, David, Walker, Ann Sarah, Lythgoe, Katrina

“…Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks 1 – 5 , give rise to highly divergent lineages 6 – 8 and…”
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Luria-Delbruck, revisited: The classic experiment does not rule out Lamarckian evolution by Holmes, Caroline, Ghafari, Mahan, Anzar, Abbas, Saravanan, Varun, Nemenman, Ilya

“…We re-examined data from the classic Luria-Delbruck fluctuation experiment, which is often credited with establishing a Darwinian basis for evolution. We argue…”
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Estimating SARS-CoV-2 variant fitness and the impact of interventions in England using statistical and geo-spatial agent-based models by Hinch, Robert, Panovska-Griffiths, Jasmina, Probert, William J M, Ferretti, Luca, Wymant, Chris, Di Lauro, Francesco, Baya, Nikolas, Ghafari, Mahan, Abeler-Dörner, Lucie, Fraser, Christophe

“…The SARS-CoV-2 epidemic has been extended by the evolution of more transmissible viral variants. In autumn 2020, the B.1.177 lineage became the dominant…”
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