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Article: How human ecology landscapes shape the circulation of H5N1 avian influenza: A case study in Indonesia.

Tang, Zhuo / Carrel, Margaret / Koylu, Caglar / Kitchen, Andrew

2023 Volume 16, Page(s) 100537

Abstract: Background: Highly pathogenic avian influenza H5N1 virus consistently threatens global public health. A better understanding of the virus' circulation mechanism is needed for future epidemic prevention. Previous studies have focused on the correlations ... ...

Abstract	Background: Highly pathogenic avian influenza H5N1 virus consistently threatens global public health. A better understanding of the virus' circulation mechanism is needed for future epidemic prevention. Previous studies have focused on the correlations between the presence of H5N1 virus and wild bird populations, domestic poultry production, and sociodemographic factors. However, human cultural landscapes and their impact on H5N1 spread have not been adequately explored. Methods: Using 196 HA gene sequences of H5N1 influenza viruses from Indonesia with district-level geographic information, we performed Monmonier barrier and Louvain community detection analyses to explore how human ecological factors impact the circulation of virus and identify barriers to or corridors of dispersal. Results: Spatial discontinuity in the genetic characteristics identified by the Monmonier algorithm were found to mirror the differences in key landscape factors. Our Louvain community detection analysis also found the co-existence of different geographic circulation patterns. The community detection analysis suggests that direct human-related interactions such as poultry transportations between remote areas may result in similar viruses spreading in two distant regions whilst dense localities supported genetically heterogeneous viruses in geographically adjacent areas. Conclusion: Human ecological landscapes shape the circulation mechanism of H5N1 virus in multiple ways contingent upon local context. Physical and cultural barriers may impede its movement between adjacent areas, while natural or human-induced corridors such as wild bird flyways and poultry production networks facilitate its spread between geographically distant areas. Further focus on the importance of cultural landscapes has great potential for increasing our understanding of the circulation of pathogenic H5N1 avian influenza virus in Southeast Asia.
Language	English
Publishing date	2023-04-05
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2834831-X
ISSN	2352-7714
ISSN	2352-7714
DOI	10.1016/j.onehlt.2023.100537
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Article ; Online: Spatial genetic structure of 2009 H1N1 pandemic influenza established as a result of interaction with human populations in mainland China.

Kim, Seungwon / Carrel, Margaret / Kitchen, Andrew

PloS one

2023 Volume 18, Issue 5, Page(s) e0284716

Abstract: Identifying the spatial patterns of genetic structure of influenza A viruses is a key factor for understanding their spread and evolutionary dynamics. In this study, we used phylogenetic and Bayesian clustering analyses of genetic sequences of the A/ ... ...

Abstract	Identifying the spatial patterns of genetic structure of influenza A viruses is a key factor for understanding their spread and evolutionary dynamics. In this study, we used phylogenetic and Bayesian clustering analyses of genetic sequences of the A/H1N1pdm09 virus with district-level locations in mainland China to investigate the spatial genetic structure of the A/H1N1pdm09 virus across human population landscapes. Positive correlation between geographic and genetic distances indicates high degrees of genetic similarity among viruses within small geographic regions but broad-scale genetic differentiation, implying that local viral circulation was a more important driver in the formation of the spatial genetic structure of the A/H1N1pdm09 virus than even, countrywide viral mixing and gene flow. Geographic heterogeneity in the distribution of genetic subpopulations of A/H1N1pdm09 virus in mainland China indicates both local to local transmission as well as broad-range viral migration. This combination of both local and global structure suggests that both small-scale and large-scale population circulation in China is responsible for viral genetic structure. Our study provides implications for understanding the evolution and spread of A/H1N1pdm09 virus across the population landscape of mainland China, which can inform disease control strategies for future pandemics.
MeSH term(s)	Humans ; Influenza, Human/epidemiology ; Influenza, Human/genetics ; Influenza A Virus, H1N1 Subtype/genetics ; Phylogeny ; Bayes Theorem ; China/epidemiology
Language	English
Publishing date	2023-05-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0284716
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Article ; Online: Euglycemic Diabetic Ketoacidosis in Type 1 Diabetes on Insulin Pump, with Acute Appendicitis: A Case Report.

Thompson, Brian D / Kitchen, Anthony

Clinical practice and cases in emergency medicine

2021 Volume 5, Issue 3, Page(s) 136–138

Abstract: Introduction: Recently, euglycemic diabetic ketoacidosis has been an increasing topic of discussion within emergency medicine literature. Euglycemic diabetic ketoacidosis can easily be missed, as a normal point-of-care glucose often mistakenly precludes ...

Abstract	Introduction: Recently, euglycemic diabetic ketoacidosis has been an increasing topic of discussion within emergency medicine literature. Euglycemic diabetic ketoacidosis can easily be missed, as a normal point-of-care glucose often mistakenly precludes the work-up of diabetic ketoacidosis. Case report: A 16-year-old female with a past medical history of type 1 diabetes presented to the emergency department with altered mental status, vomiting, and abdominal pain. She was diagnosed with euglycemic diabetic ketoacidosis. Conclusion: Reported cases of euglycemic diabetic ketoacidosis are most frequently attributed to sodium glucose cotransporter-2 inhibitors, but other potential causes have been discussed in the literature. In this patient, a starvation state with continued insulin use in the setting of acute appendicitis led to her condition.
Language	English
Publishing date	2021-08-26
Publishing country	United States
Document type	Journal Article
ISSN	2474-252X
ISSN (online)	2474-252X
DOI	10.5811/cpcem.2021.1.48905
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Article ; Online: Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population.

Ciubotariu, Ilinca I / Wilkes, Rebecca P / Kattoor, Jobin J / Christian, Erin N / Carpi, Giovanna / Kitchen, Andrew

Microbial genomics

2024 Volume 10, Issue 2

Abstract: Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the coronavirus disease 2019 (COVID-19) pandemic extends into its fourth year. Understanding SARS-CoV-2 circulation in university populations is vital ... ...

Abstract	Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the coronavirus disease 2019 (COVID-19) pandemic extends into its fourth year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in higher education settings and will inform public health policy during pandemics. In this study, we generated 793 whole-genome sequences collected over an entire academic year in a university population in Indiana, USA. We clearly captured the rapidity with which Delta variant was wholly replaced by Omicron variant across the West Lafayette campus over the length of two academic semesters in a community with high vaccination rates. This mirrored the emergence of Omicron throughout the state of Indiana and the USA. Further, phylogenetic analyses demonstrated that there was a more diverse set of potential geographic origins for Omicron viruses introduction into campus when compared to Delta. Lastly, statistics indicated that there was a more significant role for international and out-of-state migration in the establishment of Omicron variants at Purdue. This surveillance workflow, coupled with viral genomic sequencing and phylogeographic analyses, provided critical insights into SARS-CoV-2 transmission dynamics and variant arrival.
MeSH term(s)	Humans ; COVID-19/epidemiology ; SARS-CoV-2/genetics ; Phylogeny ; Universities ; Genomics
Language	English
Publishing date	2024-02-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.001194
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Article ; Online: Applications of Bayesian Skyline Plots and Approximate Bayesian Computation for Human Demography.

Villanea, Fernando A / Kitchen, Andrew / Kemp, Brian M

Human biology

2020 Volume 91, Issue 4, Page(s) 279–296

Abstract: Bayesian methods have been adopted by anthropologists for their utility in resolving complex questions about human history based on genetic data. The main advantages of Bayesian methods include simple model comparison, presenting results as a summary of ... ...

Abstract	Bayesian methods have been adopted by anthropologists for their utility in resolving complex questions about human history based on genetic data. The main advantages of Bayesian methods include simple model comparison, presenting results as a summary of probability distributions, and the explicit inclusion of prior information into analyses. In the field of anthropological genetics, for example, implementing Bayesian skyline plots and approximate Bayesian computation is becoming ubiquitous as means to analyze genetic data for the purpose of demographic or historic inference. Correspondingly, there is a critical need for better understanding of the underlying assumptions, proper applications, and limitations of these two methods by the larger anthropological community. Here we review Bayesian skyline plots and approximate Bayesian computation as applied to human demography and provide examples of the application of these methods to anthropological research questions. We also review the two core components of Bayesian demographic analysis: the coalescent and Bayesian inference. Our goal is to describe their basic mechanics in an attempt to demystify them.
MeSH term(s)	Anthropology/methods ; Bayes Theorem ; Computer Simulation ; Demography/history ; Demography/statistics & numerical data ; Genetics, Population/instrumentation ; History, Ancient ; Humans ; Pedigree ; Phylogeny ; Population Dynamics/history ; Probability
Keywords	covid19
Language	English
Publishing date	2020-08-04
Publishing country	United States
Document type	Historical Article ; Journal Article
ZDB-ID	1116-2
ISSN	1534-6617 ; 0018-7143
ISSN (online)	1534-6617
ISSN	0018-7143
DOI	10.13110/humanbiology.91.4.04
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Article: Cautionary note.

Kitchen, A

Vox sanguinis

2000 Volume 78, Issue 2, Page(s) 132

MeSH term(s)	Antibodies, Viral/blood ; Antibodies, Viral/pharmacology ; Hepatitis A/transmission ; Hepatitis B/transmission ; Hepatitis C/transmission ; Humans ; Parvoviridae Infections/transmission ; Parvovirus ; Plasma/virology ; Transfusion Reaction
Chemical Substances	Antibodies, Viral
Language	English
Publishing date	2000
Publishing country	England
Document type	Letter
ZDB-ID	80313-3
ISSN	1423-0410 ; 0042-9007
ISSN (online)	1423-0410
ISSN	0042-9007
DOI	10.1046/j.1423-0410.2000.78201304.x
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Article ; Online: Blood Supply Testing for Infectious Diseases

Dhingra, N. / Kitchen, A.

Reference Module in Biomedical Sciences

Abstract: Blood transfusion is a lifesaving intervention that has an essential role in patient management within health care systems. It is the responsibility of governments to ensure that safe and sufficient supplies of blood are available and accessible to all ... ...

Abstract	Blood transfusion is a lifesaving intervention that has an essential role in patient management within health care systems. It is the responsibility of governments to ensure that safe and sufficient supplies of blood are available and accessible to all patients requiring transfusion. The provision of safe and efficacious blood for transfusion involves a number of processes, including assessment of the suitability of prospective blood donors to donate blood, blood collection, processing, and testing of blood donations, and the issue of blood and its transfusion to the patients. While blood transfusion can be lifesaving, there are associated risks, particularly the transmission of blood-borne infections including human immunodeficiency virus and hepatitis B and C viruses. Screening for transfusion-transmissible infections (TTIs) to exclude blood donations at risk of transmitting infection from donors to recipients is a critical part of the process of ensuring that transfusion is as safe as possible. Effective screening for evidence of the presence of the most common and dangerous TTIs can reduce the risk of transmission to very low levels. Blood transfusion services should therefore establish efficient systems to ensure that all donated blood is correctly screened for the appropriate TTIs and that only nonreactive blood is issued for transfusion to patients.
Keywords	covid19
Publisher	Elsevier; PMC
Document type	Article ; Online
DOI	10.1016/b978-0-12-801238-3.00163-x
Database	COVID19

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Article ; Online: Dissecting the decline of hepatitis C in first-time donors in England and Wales.

Reynolds, C A / Davison, K L / Andrews, N / Patel, P / Kitchen, A / Brailsford, S R

Vox sanguinis

2018 Volume 113, Issue 4, Page(s) 329–338

Abstract: Background and objectives: The rate of confirmed hepatitis C virus (HCV) cases, in first-time donors, is much lower in 2015 than 20 years ago. We investigate reasons for the decline.: Materials and methods: HCV rates were analysed by gender and birth ...

Abstract	Background and objectives: The rate of confirmed hepatitis C virus (HCV) cases, in first-time donors, is much lower in 2015 than 20 years ago. We investigate reasons for the decline. Materials and methods: HCV rates were analysed by gender and birth cohort for 1996 to 2015 and ethnic group for 2006 to 2015. Variables for confirmed positive cases were compared for two ten-year periods (1996 to 2005 and 2006 to 2015) including genotyping data for 2006 to 2015. Results: There were 2007 confirmed HCV cases identified between 1996 and 2015. The rate per 100 000 donations fell from 78·6 in 1996 to 26·9 by 2015. By birth cohort, HCV rates were highest in donors born in the 1950s and 1960s who contributed a decreasing proportion of first-time donors. Between 2006 and 2015, there was no significant decline in HCV rate. The HCV-positive donor profile has changed in the last 10 years with increased proportions of younger donors, donors born abroad and decreased reported injecting drug use. Genotype 1a remains predominate, but genotype 1b has increased associated with this change in birth cohort and ethnicity. Conclusion: The decline in number and rate of confirmed HCV-positive first-time donors is mainly due to a decrease in first-time donors born before 1970, with the highest rate of HCV. However, the decline has slowed and the profile of HCV-positive first-time donors is changing. A better understanding of behaviour and sources of HCV in younger and ethnic minority donors are needed.
MeSH term(s)	Blood Donors/statistics & numerical data ; England ; Female ; Genotype ; Hepacivirus/genetics ; Hepacivirus/isolation & purification ; Hepatitis C/blood ; Hepatitis C/epidemiology ; Humans ; Male ; Serologic Tests ; Wales
Language	English
Publishing date	2018-02-14
Publishing country	England
Document type	Journal Article
ZDB-ID	80313-3
ISSN	1423-0410 ; 0042-9007
ISSN (online)	1423-0410
ISSN	0042-9007
DOI	10.1111/vox.12638
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Article: Treating immigrant populations--cultural competence in health care.

Kitchen, A

Bioethics forum

1999 Volume 15, Issue 2, Page(s) 11–18

Abstract: Delivering health care to non-English speaking immigrant populations requires knowledge and appreciation of the patient's culture. Acquiring the skills to bridge the two worlds calls for self-awareness by the practitioner and a commitment to cultural ... ...

Abstract	Delivering health care to non-English speaking immigrant populations requires knowledge and appreciation of the patient's culture. Acquiring the skills to bridge the two worlds calls for self-awareness by the practitioner and a commitment to cultural competence by the organization.
MeSH term(s)	Communication Barriers ; Cultural Diversity ; Emigration and Immigration ; Female ; Humans ; Male ; Patient Care ; Professional Competence/standards ; Professional-Patient Relations/ethics ; Quality of Health Care ; Sex Factors ; United States
Language	English
Publishing date	1999
Publishing country	United States
Document type	Journal Article
ISSN	1065-7274
ISSN	1065-7274
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Article: Hepatitis B and blood safety.

Kitchen, A

Vaccine

1998 Volume 16 Suppl, Page(s) S34–7

Abstract: The safety of blood and blood products is a global issue. Blood transfusion is an important part of modern medicine, but it is also an efficient route of transmission for a number of infectious agents. Although many countries screen all blood donations ... ...

Abstract	The safety of blood and blood products is a global issue. Blood transfusion is an important part of modern medicine, but it is also an efficient route of transmission for a number of infectious agents. Although many countries screen all blood donations for a number of infectious agents, a significant proportion of the world's blood supply is either unscreened or poorly screened, with the resultant risk to recipients of transfusion transmitted infections (TTI). Hepatitis B virus (HBV) is of concern because it is transmitted parenterally, many HBV infections are asymptomatic (and infected individuals may thus unwittingly present as blood donors) and the virus is stable in blood and blood products over long periods. The transmission of HBV is minimized by the screening of donors prior to donation, exclusion of high-risk donors, followed by the in-vitro screening of donations for HBsAg (+anti-HBc in some countries) prior to transfusion. However, even in countries with good quality, active screening programmes, there is still a small residual risk of transmission of HBV from undetected donors with early acute infection, resolving infection, silent infection or infection with atypical virus serology. Unfortunately, as with so many infectious agents, the prevalence of HBV is most often higher in those countries with poorly developed healthcare systems and limited resources. In these countries, the safety of the blood supply is compromised frequently, either because of lack of resources with which to purchase screening assays, or because of acute blood shortages and insufficient time to screen blood prior to transfusion. In such situations it is important to encourage and actively support the introduction of appropriate screening programmes which can be based upon simple assay formats, such as agglutination, rather than the favoured but more complex enzyme immunoassays which are more expensive, require specific equipment and support, and take longer to perform. Such approaches will help reduce greatly the transfusion transmission of HBV.
MeSH term(s)	Blood Banks/standards ; Blood-Borne Pathogens ; Hepatitis B/blood ; Hepatitis B/prevention & control ; Hepatitis B/transmission ; Hepatitis B virus ; Humans ; Transfusion Reaction
Language	English
Publishing date	1998-11
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/s0264-410x(98)00290-4
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