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Article ; Online: Pareto-based evaluation of national responses to COVID-19 pandemic shows that saving lives and protecting economy are non-trade-off objectives.

Kochańczyk, Marek / Lipniacki, Tomasz

2021 Volume 11, Issue 1, Page(s) 2425

Abstract: Countries worldwide have adopted various strategies to minimize the socio-economic impact of the ongoing COVID-19 pandemic. Stringency of imposed measures universally reflects the standpoint from which protecting public health and avoiding damage to ... ...

Abstract	Countries worldwide have adopted various strategies to minimize the socio-economic impact of the ongoing COVID-19 pandemic. Stringency of imposed measures universally reflects the standpoint from which protecting public health and avoiding damage to economy are seen as contradictory objectives. Based on epidemic trajectories of 25 highly developed countries and 10 US states in the (mobility reduction)-(reproduction number) plane we showed that delay in imposition of nation-wide quarantine elevates the number of infections and deaths, surge of which inevitably has to be suppressed by stringent and sustained lockdown. As a consequence, cumulative mobility reduction and population-normalized cumulative number of COVID-19-associated deaths are significantly correlated and this correlation increases with time. Overall, we demonstrated that, as long as epidemic suppression is the aim, the trade-off between the death toll and economic loss is illusory: high death toll correlates with deep and long-lasting lockdown causing a severe economic downturn.
MeSH term(s)	COVID-19/economics ; COVID-19/epidemiology ; Communicable Disease Control/methods ; Developed Countries/statistics & numerical data ; Humans ; Pandemics/economics ; Pandemics/prevention & control ; Public Health ; Quarantine/economics ; Quarantine/statistics & numerical data ; SARS-CoV-2/isolation & purification ; United States/epidemiology
Language	English
Publishing date	2021-01-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-81869-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0-3.3 Days Can Be Explained by Immune Evasion.

Grabowski, Frederic / Kochańczyk, Marek / Lipniacki, Tomasz

Viruses

2022 Volume 14, Issue 2

Abstract: Omicron, the novel highly mutated SARS-CoV-2 Variant of Concern (VOC, Pango lineage B.1.1.529) was first collected in early November 2021 in South Africa. By the end of November 2021, it had spread and approached fixation in South Africa, and had been ... ...

Abstract	Omicron, the novel highly mutated SARS-CoV-2 Variant of Concern (VOC, Pango lineage B.1.1.529) was first collected in early November 2021 in South Africa. By the end of November 2021, it had spread and approached fixation in South Africa, and had been detected on all continents. We analyzed the exponential growth of Omicron over four-week periods in the two most populated of South Africa's provinces, Gauteng and KwaZulu-Natal, arriving at the doubling time estimates of, respectively, 3.3 days (95% CI: 3.2-3.4 days) and 2.7 days (95% CI: 2.3-3.3 days). Similar or even shorter doubling times were observed in other locations: Australia (3.0 days), New York State (2.5 days), UK (2.4 days), and Denmark (2.0 days). Log-linear regression suggests that the spread began in Gauteng around 11 October 2021; however, due to presumable stochasticity in the initial spread, this estimate can be inaccurate. Phylogenetics-based analysis indicates that the Omicron strain started to diverge between 6 October and 29 October 2021. We estimated that the weekly growth of the ratio of Omicron to Delta is in the range of 7.2-10.2, considerably higher than the growth of the ratio of Delta to Alpha (estimated to be in in the range of 2.5-4.2), and Alpha to pre-existing strains (estimated to be in the range of 1.8-2.7). High relative growth does not necessarily imply higher Omicron infectivity. A two-strain SEIR model suggests that the growth advantage of Omicron may stem from immune evasion, which permits this VOC to infect both recovered and fully vaccinated individuals. As we demonstrated within the model, immune evasion is more concerning than increased transmissibility, because it can facilitate larger epidemic outbreaks.
MeSH term(s)	Australia/epidemiology ; COVID-19/epidemiology ; COVID-19/transmission ; Genome, Viral ; Humans ; Immune Evasion ; New York/epidemiology ; Phylogeny ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; SARS-CoV-2/physiology ; Sequence Analysis, DNA/statistics & numerical data ; South Africa/epidemiology ; Time Factors ; Virus Replication/immunology
Language	English
Publishing date	2022-01-30
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14020294
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Pareto-based evaluation of national responses to COVID-19 pandemic shows that saving lives and protecting economy are non-trade-off objectives

Marek Kochańczyk / Tomasz Lipniacki

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 9

Abstract: Abstract Countries worldwide have adopted various strategies to minimize the socio-economic impact of the ongoing COVID-19 pandemic. Stringency of imposed measures universally reflects the standpoint from which protecting public health and avoiding ... ...

Abstract	Abstract Countries worldwide have adopted various strategies to minimize the socio-economic impact of the ongoing COVID-19 pandemic. Stringency of imposed measures universally reflects the standpoint from which protecting public health and avoiding damage to economy are seen as contradictory objectives. Based on epidemic trajectories of 25 highly developed countries and 10 US states in the (mobility reduction)–(reproduction number) plane we showed that delay in imposition of nation-wide quarantine elevates the number of infections and deaths, surge of which inevitably has to be suppressed by stringent and sustained lockdown. As a consequence, cumulative mobility reduction and population-normalized cumulative number of COVID-19-associated deaths are significantly correlated and this correlation increases with time. Overall, we demonstrated that, as long as epidemic suppression is the aim, the trade-off between the death toll and economic loss is illusory: high death toll correlates with deep and long-lasting lockdown causing a severe economic downturn.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The MAPK/ERK channel capacity exceeds 6 bit/hour.

Nałęcz-Jawecki, Paweł / Gagliardi, Paolo Armando / Kochańczyk, Marek / Dessauges, Coralie / Pertz, Olivier / Lipniacki, Tomasz

PLoS computational biology

2023 Volume 19, Issue 5, Page(s) e1011155

Abstract: Living cells utilize signaling pathways to sense, transduce, and process information. As the extracellular stimulation often has rich temporal characteristics which may govern dynamic cellular responses, it is important to quantify the rate of ... ...

Abstract	Living cells utilize signaling pathways to sense, transduce, and process information. As the extracellular stimulation often has rich temporal characteristics which may govern dynamic cellular responses, it is important to quantify the rate of information flow through the signaling pathways. In this study, we used an epithelial cell line expressing a light-activatable FGF receptor and an ERK activity reporter to assess the ability of the MAPK/ERK pathway to transduce signal encoded in a sequence of pulses. By stimulating the cells with random light pulse trains, we demonstrated that the MAPK/ERK channel capacity is at least 6 bits per hour. The input reconstruction algorithm detects the light pulses with 1-min accuracy 5 min after their occurrence. The high information transmission rate may enable the pathway to coordinate multiple processes including cell movement and respond to rapidly varying stimuli such as chemoattracting gradients created by other cells.
MeSH term(s)	Cell Line ; MAP Kinase Signaling System/physiology ; Signal Transduction ; Epithelial Cells/metabolism ; Extracellular Signal-Regulated MAP Kinases/metabolism
Chemical Substances	Extracellular Signal-Regulated MAP Kinases (EC 2.7.11.24)
Language	English
Publishing date	2023-05-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1011155
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Antagonism between viral infection and innate immunity at the single-cell level.

Grabowski, Frederic / Kochańczyk, Marek / Korwek, Zbigniew / Czerkies, Maciej / Prus, Wiktor / Lipniacki, Tomasz

PLoS pathogens

2023 Volume 19, Issue 9, Page(s) e1011597

Abstract: When infected with a virus, cells may secrete interferons (IFNs) that prompt nearby cells to prepare for upcoming infection. Reciprocally, viral proteins often interfere with IFN synthesis and IFN-induced signaling. We modeled the crosstalk between the ... ...

Abstract	When infected with a virus, cells may secrete interferons (IFNs) that prompt nearby cells to prepare for upcoming infection. Reciprocally, viral proteins often interfere with IFN synthesis and IFN-induced signaling. We modeled the crosstalk between the propagating virus and the innate immune response using an agent-based stochastic approach. By analyzing immunofluorescence microscopy images we observed that the mutual antagonism between the respiratory syncytial virus (RSV) and infected A549 cells leads to dichotomous responses at the single-cell level and complex spatial patterns of cell signaling states. Our analysis indicates that RSV blocks innate responses at three levels: by inhibition of IRF3 activation, inhibition of IFN synthesis, and inhibition of STAT1/2 activation. In turn, proteins coded by IFN-stimulated (STAT1/2-activated) genes inhibit the synthesis of viral RNA and viral proteins. The striking consequence of these inhibitions is a lack of coincidence of viral proteins and IFN expression within single cells. The model enables investigation of the impact of immunostimulatory defective viral particles and signaling network perturbations that could potentially facilitate containment or clearance of the viral infection.
MeSH term(s)	Humans ; Virus Diseases ; Immunity, Innate ; Interferons ; Respiratory Syncytial Virus, Human ; Viral Proteins
Chemical Substances	Interferons (9008-11-1) ; Viral Proteins
Language	English
Publishing date	2023-09-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1011597
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Respiratory Syncytial Virus Protects Bystander Cells against Influenza A Virus Infection by Triggering Secretion of Type I and Type III Interferons.

Czerkies, Maciej / Kochańczyk, Marek / Korwek, Zbigniew / Prus, Wiktor / Lipniacki, Tomasz

Journal of virology

2022 Volume 96, Issue 22, Page(s) e0134122

Abstract: We observed the interference between two prevalent respiratory viruses, respiratory syncytial virus (RSV) and influenza A virus (IAV) (H1N1), and characterized its molecular underpinnings in alveolar epithelial cells (A549). We found that RSV induces ... ...

Abstract	We observed the interference between two prevalent respiratory viruses, respiratory syncytial virus (RSV) and influenza A virus (IAV) (H1N1), and characterized its molecular underpinnings in alveolar epithelial cells (A549). We found that RSV induces higher levels of interferon beta (IFN-β) production than IAV and that IFN-β priming confers higher-level protection against infection with IAV than with RSV. Consequently, we focused on the sequential infection scheme of RSV and then IAV. Using A549 wild-type (WT), IFNAR1 knockout (KO), IFNLR1 KO, and IFNAR1-IFNLR1 double-KO cell lines, we found that both IFN-β and IFN-λ are necessary for maximum protection against subsequent infection. Immunostaining revealed that preinfection with RSV partitions the cell population into a subpopulation susceptible to subsequent infection with IAV and an IAV-proof subpopulation. Strikingly, the susceptible cells turned out to be those already compromised and efficiently expressing RSV, whereas the bystander, interferon-primed cells are resistant to IAV infection. Thus, virus-virus exclusion at the cell population level is not realized through direct competition for a shared ecological niche (single cell) but rather is achieved with the involvement of specific cytokines induced by the host's innate immune response.
MeSH term(s)	Humans ; Influenza A Virus, H1N1 Subtype ; SARS-CoV-2 ; COVID-19 ; Respiratory Syncytial Virus, Human ; Influenza A virus ; Interferons/metabolism ; Influenza, Human ; Interferon Lambda
Chemical Substances	Interferons (9008-11-1) ; Interferon Lambda
Language	English
Publishing date	2022-11-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.01341-22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Super-spreading events initiated the exponential growth phase of COVID-19 with ℛ

Kochańczyk, Marek / Grabowski, Frederic / Lipniacki, Tomasz

Royal Society open science

2020 Volume 7, Issue 9, Page(s) 200786

Abstract: The basic reproduction ... ...

Abstract	The basic reproduction number
Keywords	covid19
Language	English
Publishing date	2020-09-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2787755-3
ISSN	2054-5703
ISSN	2054-5703
DOI	10.1098/rsos.200786
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The MAPK/ERK channel capacity exceeds 6 bit/hour.

Paweł Nałęcz-Jawecki / Paolo Armando Gagliardi / Marek Kochańczyk / Coralie Dessauges / Olivier Pertz / Tomasz Lipniacki

PLoS Computational Biology, Vol 19, Iss 5, p e

2023 Volume 1011155

Abstract	Living cells utilize signaling pathways to sense, transduce, and process information. As the extracellular stimulation often has rich temporal characteristics which may govern dynamic cellular responses, it is important to quantify the rate of information flow through the signaling pathways. In this study, we used an epithelial cell line expressing a light-activatable FGF receptor and an ERK activity reporter to assess the ability of the MAPK/ERK pathway to transduce signal encoded in a sequence of pulses. By stimulating the cells with random light pulse trains, we demonstrated that the MAPK/ERK channel capacity is at least 6 bits per hour. The input reconstruction algorithm detects the light pulses with 1-min accuracy 5 min after their occurrence. The high information transmission rate may enable the pathway to coordinate multiple processes including cell movement and respond to rapidly varying stimuli such as chemoattracting gradients created by other cells.
Keywords	Biology (General) ; QH301-705.5
Subject code	003
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Antagonism between viral infection and innate immunity at the single-cell level.

Frederic Grabowski / Marek Kochańczyk / Zbigniew Korwek / Maciej Czerkies / Wiktor Prus / Tomasz Lipniacki

PLoS Pathogens, Vol 19, Iss 9, p e

2023 Volume 1011597

Abstract	When infected with a virus, cells may secrete interferons (IFNs) that prompt nearby cells to prepare for upcoming infection. Reciprocally, viral proteins often interfere with IFN synthesis and IFN-induced signaling. We modeled the crosstalk between the propagating virus and the innate immune response using an agent-based stochastic approach. By analyzing immunofluorescence microscopy images we observed that the mutual antagonism between the respiratory syncytial virus (RSV) and infected A549 cells leads to dichotomous responses at the single-cell level and complex spatial patterns of cell signaling states. Our analysis indicates that RSV blocks innate responses at three levels: by inhibition of IRF3 activation, inhibition of IFN synthesis, and inhibition of STAT1/2 activation. In turn, proteins coded by IFN-stimulated (STAT1/2-activated) genes inhibit the synthesis of viral RNA and viral proteins. The striking consequence of these inhibitions is a lack of coincidence of viral proteins and IFN expression within single cells. The model enables investigation of the impact of immunostimulatory defective viral particles and signaling network perturbations that could potentially facilitate containment or clearance of the viral infection.
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2023-09-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0–3.3 Days Can Be Explained by Immune Evasion

Grabowski, Frederic / Kochańczyk, Marek / Lipniacki, Tomasz

Viruses. 2022 Jan. 30, v. 14, no. 2

2022

Abstract	Omicron, the novel highly mutated SARS-CoV-2 Variant of Concern (VOC, Pango lineage B.1.1.529) was first collected in early November 2021 in South Africa. By the end of November 2021, it had spread and approached fixation in South Africa, and had been detected on all continents. We analyzed the exponential growth of Omicron over four-week periods in the two most populated of South Africa’s provinces, Gauteng and KwaZulu-Natal, arriving at the doubling time estimates of, respectively, 3.3 days (95% CI: 3.2–3.4 days) and 2.7 days (95% CI: 2.3–3.3 days). Similar or even shorter doubling times were observed in other locations: Australia (3.0 days), New York State (2.5 days), UK (2.4 days), and Denmark (2.0 days). Log–linear regression suggests that the spread began in Gauteng around 11 October 2021; however, due to presumable stochasticity in the initial spread, this estimate can be inaccurate. Phylogenetics-based analysis indicates that the Omicron strain started to diverge between 6 October and 29 October 2021. We estimated that the weekly growth of the ratio of Omicron to Delta is in the range of 7.2–10.2, considerably higher than the growth of the ratio of Delta to Alpha (estimated to be in in the range of 2.5–4.2), and Alpha to pre-existing strains (estimated to be in the range of 1.8–2.7). High relative growth does not necessarily imply higher Omicron infectivity. A two-strain SEIR model suggests that the growth advantage of Omicron may stem from immune evasion, which permits this VOC to infect both recovered and fully vaccinated individuals. As we demonstrated within the model, immune evasion is more concerning than increased transmissibility, because it can facilitate larger epidemic outbreaks.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; immune evasion ; models ; pathogenicity ; Australia ; Denmark ; New York ; South Africa
Language	English
Dates of publication	2022-0130
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14020294
Database	NAL-Catalogue (AGRICOLA)

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