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Article ; Online: Predicting COVID-19 Cases in South Korea Using Stringency and Niño Sea Surface Temperature Indices.

Necesito, Imee V / Velasco, John Mark S / Jung, Jaewon / Bae, Young Hye / Yoo, Younghoon / Kim, Soojun / Kim, Hung Soo

2022 Volume 10, Page(s) 871354

Abstract: Most coronavirus disease 2019 (COVID-19) models use a combination of agent-based and equation-based models with only a few incorporating environmental factors in their prediction models. Many studies have shown that human and environmental factors play ... ...

Abstract	Most coronavirus disease 2019 (COVID-19) models use a combination of agent-based and equation-based models with only a few incorporating environmental factors in their prediction models. Many studies have shown that human and environmental factors play huge roles in disease transmission and spread, but few have combined the use of both factors, especially for SARS-CoV-2. In this study, both man-made policies (Stringency Index) and environment variables (Niño SST Index) were combined to predict the number of COVID-19 cases in South Korea. The performance indicators showed satisfactory results in modeling COVID-19 cases using the Non-linear Autoregressive Exogenous Model (NARX) as the modeling method, and Stringency Index (SI) and Niño Sea Surface Temperature (SST) as model variables. In this study, we showed that the accuracy of SARS-CoV-2 transmission forecasts may be further improved by incorporating both the Niño SST and SI variables and combining these variables with NARX may outperform other models. Future forecasting work by modelers should consider including climate or environmental variables (i.e., Niño SST) to enhance the prediction of transmission and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
MeSH term(s)	COVID-19/epidemiology ; Climate ; Forecasting ; Humans ; SARS-CoV-2 ; Temperature
Language	English
Publishing date	2022-06-03
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2022.871354
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Article ; Online: Understanding chaos in COVID-19 and its relationship to stringency index: Applications to large-scale and granular level prediction models.

Necesito, Imee V / Velasco, John Mark S / Jung, Jaewon / Bae, Young Hye / Lee, Jun Hyeong / Kim, Soo Jun / Kim, Hung Soo

PloS one

2022 Volume 17, Issue 6, Page(s) e0268023

Abstract: Understanding the underlying and unpredictable dynamics of the COVID-19 pandemic is important. We supplemented the findings of Jones and Strigul (2020) and described the chaotic behavior of COVID-19 using state space plots which depicted the changes in ... ...

Abstract	Understanding the underlying and unpredictable dynamics of the COVID-19 pandemic is important. We supplemented the findings of Jones and Strigul (2020) and described the chaotic behavior of COVID-19 using state space plots which depicted the changes in asymptotic behavior and trajectory brought about by the increase or decrease in the number of cases which resulted from the easing or tightening of restrictions and other non-pharmaceutical interventions instituted by governments as represented by the country's stringency index (SI). We used COVID-19 country-wide case count data and analyzed it using convergent cross-mapping (CCM) and found that the SI influence on COVID-19 case counts is high in almost all the countries considered. When we utilized finer granular geographical data ('barangay' or village level COVID-19 case counts in the Philippines), the effects of SI were reduced as the population density increased. The authors believe that the knowledge of the chaotic behavior of COVID-19 and the effects of population density as applied to finer granular geographical data has the potential to generate more accurate COVID-19 non-linear prediction models. This could be used at the local government level to guide strategic and highly targeted COVID-19 policies which are favorable to public health systems but with limited impact to the economy.
MeSH term(s)	COVID-19/epidemiology ; Government ; Humans ; Pandemics ; Philippines ; Population Density
Language	English
Publishing date	2022-06-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0268023
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Article ; Online: Four new species of Splendid Ghost Moths (Lepidoptera: Hepialidae: Aenetus) from Australia and Papua New Guinea.

Beaver, Ethan P / Moore, Michael D / Grehan, John R / Velasco-CastrillÓn, Alejandro / Stevens, Mark I

Zootaxa

2020 Volume 4809, Issue 3, Page(s) zootaxa.4809.3.2

Abstract: Four new Aenetus Herrich-Schäffer species are described from northern Australasia; Aenetus simonseni sp. nov. from the top-end of the Northern Territory, Australia, A. maiasinus sp. nov. from the Kimberley region of Western Australia, A. trigonogrammus ... ...

Abstract	Four new Aenetus Herrich-Schäffer species are described from northern Australasia; Aenetus simonseni sp. nov. from the top-end of the Northern Territory, Australia, A. maiasinus sp. nov. from the Kimberley region of Western Australia, A. trigonogrammus sp. nov. from south-eastern Queensland, Australia, and A. albadamanteum sp. nov. from eastern Papua New Guinea. Aenetus simonseni sp. nov. and A. maiasinus sp. nov. appear to belong to the tegulatus-group of species (sensu Grehan et al. 2018), A. trigonogrammus sp. nov. is part of the splendens-group of species (sensu Simonsen 2018), while A. albadamanteum sp. nov. shares morphological similarities with A. hampsoni (Joicey Noakes, 1914), A. crameri Viette, 1956, and A. toxopeusi Viette, 1956, from New Guinea, and A. cohici Viette, 1961 from New Caledonia. The four new species are illustrated and compared with superficially similar species in morphology and, for two species, molecular (mtDNA COI gene) sequences.
MeSH term(s)	Animals ; Moths ; Papua New Guinea
Language	English
Publishing date	2020-07-08
Publishing country	New Zealand
Document type	Journal Article
ISSN	1175-5334
ISSN (online)	1175-5334
DOI	10.11646/zootaxa.4809.3.2
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Article ; Online: Predicting COVID-19 Cases in South Korea Using Stringency and Niño Sea Surface Temperature Indices

Imee V. Necesito / John Mark S. Velasco / Jaewon Jung / Young Hye Bae / Younghoon Yoo / Soojun Kim / Hung Soo Kim

Frontiers in Public Health, Vol

2022 Volume 10

Abstract	Most coronavirus disease 2019 (COVID-19) models use a combination of agent-based and equation-based models with only a few incorporating environmental factors in their prediction models. Many studies have shown that human and environmental factors play huge roles in disease transmission and spread, but few have combined the use of both factors, especially for SARS-CoV-2. In this study, both man-made policies (Stringency Index) and environment variables (Niño SST Index) were combined to predict the number of COVID-19 cases in South Korea. The performance indicators showed satisfactory results in modeling COVID-19 cases using the Non-linear Autoregressive Exogenous Model (NARX) as the modeling method, and Stringency Index (SI) and Niño Sea Surface Temperature (SST) as model variables. In this study, we showed that the accuracy of SARS-CoV-2 transmission forecasts may be further improved by incorporating both the Niño SST and SI variables and combining these variables with NARX may outperform other models. Future forecasting work by modelers should consider including climate or environmental variables (i.e., Niño SST) to enhance the prediction of transmission and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
Keywords	COVID-19 ; stringency index ; Niño SST index ; NARX ; South Korea ; Public aspects of medicine ; RA1-1270
Subject code	330
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Clinical characterization of COVID-19 breakthrough infections, Philippines.

Velasco, John Mark / Vila, Vicente / Diones, Paula Corazon / Valderama, Maria Theresa / Mendez, Cecille / Turao-Agoncillo, Ma Melissa Monica / Chinnawirotpisan, Piyawan / Manasatienkij, Wudtichai / Joonlasak, Khajohn / Klungthong, Chonticha / Jones, Anthony / Fernandez, Stefan / Navarro, Fatima Claire

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2022 Volume 150-151, Page(s) 105157

Abstract: We clinically characterized PCR detected breakthrough infections among partially/fully vaccinated cases with majority given an inactivated vaccine, CoronaVac. From 1 March to 15 July 2021, we detected 182 SARS-CoV-2 infections among vaccinated cases with ...

Abstract	We clinically characterized PCR detected breakthrough infections among partially/fully vaccinated cases with majority given an inactivated vaccine, CoronaVac. From 1 March to 15 July 2021, we detected 182 SARS-CoV-2 infections among vaccinated cases with 129 classified as breakthrough infections. Majority were male, 30-39 y.o., and were asymptomatic or mildly symptomatic with few severe cases. Alpha, Beta and Delta VOCs were detected from sequenced breakthrough infections. Healthcare workers had significantly lower Ct values(higher viral loads) versus non-HCWs. Our results underscore the importance of regular PCR screening for HCWs due to the risk of SARS-CoV-2 transmission from asymptomatic breakthrough infections and provide evidence supporting administration of a booster dose especially to HCWs.
MeSH term(s)	Asymptomatic Infections ; COVID-19 ; COVID-19 Vaccines ; Female ; Humans ; Male ; Philippines/epidemiology ; SARS-CoV-2
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2022-04-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2022.105157
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Article ; Online: Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines.

Velasco, John Mark / Chinnawirotpisan, Piyawan / Valderama, Maria Theresa / Joonlasak, Khajohn / Manasatienkij, Wudtichai / Huang, Angkana / Diones, Paula Corazon / Navarro, Fatima Claire / Vila, Vicente / Tabinas, Henry / Chua, Domingo / Fernandez, Stefan / Jones, Anthony / Klungthong, Chonticha

Microbiology resource announcements

2021 Volume 10, Issue 28, Page(s) e0049821

Abstract: Here, we report the complete genome sequences of 11 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants from the Philippines. Lineage analysis showed 3 B.1.1.7 and 8 B.1.351 sequences. One B.1.1.7 sequence contained two additional ... ...

Abstract	Here, we report the complete genome sequences of 11 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants from the Philippines. Lineage analysis showed 3 B.1.1.7 and 8 B.1.351 sequences. One B.1.1.7 sequence contained two additional mutations, F318N and V320F, with V320F located in the receptor binding domain of the S1 subunit.
Language	English
Publishing date	2021-07-15
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00498-21
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Article ; Online: Understanding chaos in COVID-19 and its relationship to stringency index

Imee V. Necesito / John Mark S. Velasco / Jaewon Jung / Young Hye Bae / Jun Hyeong Lee / Soo Jun Kim / Hung Soo Kim

PLoS ONE, Vol 17, Iss

Applications to large-scale and granular level prediction models

2022 Volume 6

Abstract	Understanding the underlying and unpredictable dynamics of the COVID-19 pandemic is important. We supplemented the findings of Jones and Strigul (2020) and described the chaotic behavior of COVID-19 using state space plots which depicted the changes in asymptotic behavior and trajectory brought about by the increase or decrease in the number of cases which resulted from the easing or tightening of restrictions and other non-pharmaceutical interventions instituted by governments as represented by the country’s stringency index (SI). We used COVID-19 country-wide case count data and analyzed it using convergent cross-mapping (CCM) and found that the SI influence on COVID-19 case counts is high in almost all the countries considered. When we utilized finer granular geographical data (‘barangay’ or village level COVID-19 case counts in the Philippines), the effects of SI were reduced as the population density increased. The authors believe that the knowledge of the chaotic behavior of COVID-19 and the effects of population density as applied to finer granular geographical data has the potential to generate more accurate COVID-19 non-linear prediction models. This could be used at the local government level to guide strategic and highly targeted COVID-19 policies which are favorable to public health systems but with limited impact to the economy.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2022-01-01T00:00:00Z
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: Performance of a Rapid Diagnostic Test for Influenza in a Tertiary Military Hospital, Philippines.

Velasco, John Mark / Valderama, Maria Theresa / Diones, Paula Corazon / Navarro, Fatima Claire / Develos, Maribel / Lopez, Ma Nila / Liao, Cynthia / Chua, Domingo / Macareo, Louis / Fernandez, Stefan

Military medicine

2021 Volume 187, Issue 1-2, Page(s) e197–e200

Abstract: Introduction: It is important to evaluate the performance of existing rapid influenza diagnostic tests (RIDTs) and the factors that can affect performance especially when the circulation dynamics of influenza strains change such as the displacement and ... ...

Abstract	Introduction: It is important to evaluate the performance of existing rapid influenza diagnostic tests (RIDTs) and the factors that can affect performance especially when the circulation dynamics of influenza strains change such as the displacement and replacement of the circulating seasonal influenza strains. Materials and methods: Nasal swabs were collected from patients presenting at V Luna Medical Center, Armed Forces of the Philippines Health Service Command, with influenza-like illness (ILI) with one swab tested using Quickvue (QV) influenza A+B RIDT (Quidel) and the other swab tested using the ABI 7500 (Applied Biosystems) real-time reverse transcriptase-polymerase chain reaction. Sensitivity, specificity, positive predictive value, and negative predictive value were estimated. We identified clinical symptoms predictive of influenza subtype and evaluated the independence of QV sensitivity on (1) Cycle threshold (Ct) value, controlling for timing of collection; (2) timing of collection, controlling for Ct value; and (3) Ct value and timing of collection taken together. Results: Between August 2011 and October 2016, patients presenting with ILI (n = 2333) underwent testing. Quickvue sensitivity across all subtypes was significantly correlated with lower Ct values (higher virus titers) (P <.001) and, except for flu A/H3 (P = .974), was also significantly associated with timing of specimen collection (P <.05). No statistically significant difference was noted in QV sensitivity for Flu A/H3 (P = .130), pandemic H1/N1 (P = .207), Flu A/H3 + pandemic H1/N1 (P = .341), and Flu B (P = .103) across different age groups but sensitivity of QV significantly differed (P <.001) across the different influenza subtypes. Conclusion: Overall specificity of QV was high across all flu subtypes, but overall sensitivity was low (Flu A/pdm H1) to moderate (Flu A/H3 and Flu B). The findings highlight the need to develop more sensitive influenza RDTs to detect circulating influenza strains and the use of the quadrivalent flu vaccine during the annual influenza vaccination.
MeSH term(s)	Diagnostic Tests, Routine ; Hospitals, Military ; Humans ; Influenza Vaccines ; Influenza, Human/diagnosis ; Philippines ; Sensitivity and Specificity ; United States
Chemical Substances	Influenza Vaccines
Language	English
Publishing date	2021-01-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	391061-1
ISSN	1930-613X ; 0026-4075
ISSN (online)	1930-613X
ISSN	0026-4075
DOI	10.1093/milmed/usab006
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Article: A multi-country field validation of the FluChip-8G Insight Assay

Velasco, John Mark / Shrestha, Sanjaya / Valderama, Maria Theresa / Shrestha, Jasmin / Shrestha, Binob / Diones, Paula Corazon / Leonardia, Susie / Poolpanichupatam, Yongyuth / Hussem, Kittinun / Chua, Domingo / Navarro, Fatima Claire / Develos, Maribel / Macareo, Louis / Ellison, Damon / Fernandez, Stefan / Klungthong, Chonticha

Journal of virological methods. 2021 Mar., v. 289

2021

Abstract: It is critical to rapidly detect novel and non-seasonal influenza strains. Currently available assays have limited sensitivity in detecting novel influenza subtypes. We performed a multi-country field validation of the FluChip-8G Insight, an assay able ... ...

Abstract	It is critical to rapidly detect novel and non-seasonal influenza strains. Currently available assays have limited sensitivity in detecting novel influenza subtypes. We performed a multi-country field validation of the FluChip-8G Insight, an assay able to detect and characterize influenza A/B viruses and non-seasonal influenza viruses.We evaluated the performance of the FluChip-8G Insight on nasal and throat swab clinical samples from Thailand, Philippines and Nepal. Influenza PCR positive and negative samples tested using the US CDC Human Influenza Dx Panel reference standard were selected for testing using the FluChip-8G Influenza Insight.A total of 909 specimens were included in the analysis. The overall sensitivity and specificity of the FluChip-8G Insight to detect combined influenza A+B was 86 % and 100%, respectively. PPV and NPV were estimated at 100 % (95 % CI 99–100) and 73 % (95 % CI 68–78), respectively. Sensitivity across all influenza subtypes was 100% for specimens with <20 and 20–25 Ct values, respectively, but as Ct values increased, sensitivity across all influenza subtypes decreased significantly (p < 0.001) for specimens with Ct values ≥32.The FluChip-8G Insight showed good precision and reproducibility among all 3 sites with robust identification of both influenza A and B targets with Ct values <32 and in the absence of co-infection. Positioning this platform in countries considered as hotspots for the emergence of novel/zoonotic influenza strains can increase the lead time in detecting and containing novel influenza strains with pandemic potential.
Keywords	Philippines ; human influenza ; mixed infection ; nose ; pandemic ; reference standards ; throat ; Nepal ; Thailand
Language	English
Dates of publication	2021-03
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2020.114029
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Failures of nerve regeneration caused by aging or chronic denervation are rescued by restoring Schwann cell c-Jun.

Wagstaff, Laura J / Gomez-Sanchez, Jose A / Fazal, Shaline V / Otto, Georg W / Kilpatrick, Alastair M / Michael, Kirolos / Wong, Liam YN / Ma, Ki H / Turmaine, Mark / Svaren, John / Gordon, Tessa / Arthur-Farraj, Peter / Velasco-Aviles, Sergio / Cabedo, Hugo / Benito, Cristina / Mirsky, Rhona / Jessen, Kristjan R

eLife

2021 Volume 10

Abstract: After nerve injury, myelin and Remak Schwann cells reprogram to repair cells specialized for regeneration. Normally providing strong regenerative support, these cells fail in aging animals, and during chronic denervation that results from slow axon ... ...

Abstract	After nerve injury, myelin and Remak Schwann cells reprogram to repair cells specialized for regeneration. Normally providing strong regenerative support, these cells fail in aging animals, and during chronic denervation that results from slow axon growth. This impairs axonal regeneration and causes significant clinical problems. In mice, we find that repair cells express reduced c-Jun protein as regenerative support provided by these cells declines during aging and chronic denervation. In both cases, genetically restoring Schwann cell c-Jun levels restores regeneration to control levels. We identify potential gene candidates mediating this effect and implicate Shh in the control of Schwann cell c-Jun levels. This establishes that a common mechanism, reduced c-Jun in Schwann cells, regulates success and failure of nerve repair both during aging and chronic denervation. This provides a molecular framework for addressing important clinical problems, suggesting molecular pathways that can be targeted to promote repair in the PNS.
MeSH term(s)	Aging ; Animals ; Female ; Male ; Mice ; Nerve Regeneration ; Proto-Oncogene Proteins c-jun/genetics ; Proto-Oncogene Proteins c-jun/metabolism ; Schwann Cells/metabolism
Chemical Substances	Proto-Oncogene Proteins c-jun
Language	English
Publishing date	2021-01-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.62232
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