Applications of time series analysis in epidemiology: Literature review and our experience during COVID-19 pandemic

Time series analysis is a valuable tool in epidemiology that complements the classical epidemiological models in two different ways:Prediction and forecast.Prediction is related to explaining past and current data based on various internal and external influences that may or may not have a causative role.Forecasting is an exploration of the possible future values based on the predictive ability of the model and hypothesized future values of the external and/or internal influences.The time series analysis approach has the advantage of being easier to use(in the cases of more straightforward and linear models such as Auto-Regressive Integrated Moving Average).Still,it is limited in forecasting time,unlike the classical models such as Susceptible-Exposed-Infectious-Removed.Its applicability in forecasting comes from its better accuracy for short-term prediction.In its basic form,it does not assume much theoretical knowledge of the mechanisms of spreading and mutating pathogens or the reaction of people and regulatory structures(governments,companies,etc.).Instead,it estimates from the data directly.Its predictive ability allows testing hypotheses for different factors that positively or negatively contribute to the pandemic spread;be it school closures,emerging variants,etc.It can be used in mortality or hospital risk estimation from new cases,seroprevalence studies,assessing properties of emerging variants,and estimating excess mortality and its relationship with a pandemic.

Epidemiology and Mutational Analysis of Global Strains of Crimean-Congo Haemorrhagic Fever Virus

Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high fatality.Cases are reported in several countries in Africa,Europe,the Middle East,and Asia.Phylogenetic analyses based on the virus S (nucleocapsid),M (glycoprotein),and L (polymerase) genome segments sequences indicate distinct geographic lineages exist but their specific genetic characteristics require elucidation.In this work we collected all full length S segment sequences and generated a phylogenetic tree based on the alignment of these 62 samples.We then analyzed the alignment using entries from AAIndex,the Amino Acid Index database,to identify amino acid mutations that performed significant changes in charge,pka,hydropathy and side chain volume.Finally,we mapped these changes back to the tree and alignment to identify correlated mutations or sites that characterized a specific lineage.Based on this analysis we are able to propose a number of sites that appear to be important for virus function and which would be good candidates for experimental mutational analysis studies.

Depression weights in patients with gastric cancer:Bibliometric analysis as a weapon to chart the future of research

Bibliometric analyses are increasing in the field of gastric cancer.This letter discusses a recently published analysis that focused on the bidirectional relationship between depression and gastric cancer and evaluated the types of papers published in this field and the changes in the direction of research.There is an increasing need for new,clinically relevant studies of this association.

Characterization of Avian Influenza A(H7N9) Virus Prevalence in Humans and Poultry in Huai′an,China：Molecular Epidemiology,Phylogenetic,and Dynamics Analyses

Objective To trace the source of human H7N9 cases in Huai＇an and elucidate the genetic characterization of Huai＇an strains associated with both humans and birds in live poultry market.Methods An enhanced surveillance was implemented when the first human H7N9 case was confirmed in Huai＇an.Clinical specimens,cloacal swabs,and fecal samples were collected and screened by real-time reverse transcription-polymerase chain reaction（RT-PCR） for H7N9 virus.The positive samples were subjected to further RT-PCR and genome sequencing.The phylodynamic patterns of H7N9 virus within and separated from Huai＇an and evolutionary dynamics of the virus were analyzed.Results Six patients with H7N9 infection were previously exposed to live poultry market and presented symptoms such as fever（〉38.0 °C） and headaches.Results of this study support the hypothesis that live poultry markets were the source of human H7N9 exposure.Phylogenetic analysis revealed that all novel H7N9 viruses,including Huai＇an strains,could be classified into two distinct clades,A and B.Additionally,the diversified H7N9 virus circulated in live poultry markets in Huai＇an.Interestingly,the common ancestors of the Huai＇an H7N9 virus existed in January 2012.The mean nucleotide substitution rates for each gene segment of the H7N9 virus were（3.09-7.26）×10-3 substitutions/site per year（95% HPD：1.72×10-3 to 1.16×10-2）.Conclusion Overall,the source of exposure of human H7N9 cases in Huai＇an was live poultry market,and our study highlights the presence of divergent genetic lineage of H7N9 virus in both humans and poultry specimens in Huai＇an.

Time Series and Spatial Epidemiological Analysis of the Prevalence of Iodine Deficiency Disorders in China

Objective To recognize the spatial and temporal characteristics of iodine deficiency disorders(IDD),China national IDD surveillance data for the years of 1995–2018 were analyzed.Methods Time series analysis was used to describe and predict the IDD related indicators,and spatial analysis was used to analyze the spatial distribution of salt iodine levels.Results In China,the median urinary iodine concentration increased in 1995–1997,then decreased to adequate levels,and are expected to remain appropriate in 2019–2022.The goiter rate continually decreased and is expected to be maintained at a low level.Since 2002,the coverage rates of iodized salt and the consumption rates of qualified iodized salt(the percentage of qualified iodized salt in all tested salt) increased and began to decline in 2012;they are expected to continue to decrease.Spatial epidemiological analysis indicated a positive spatial correlation in 2016–2018 and revealed feature regarding the spatial distribution of salt related indicators in coastal areas and areas near iodine-excess areas.Conclusions Iodine nutrition in China showed gradual improvements.However,a recent decline has been observed in some areas following changes in the iodized salt supply in China.In the future,more regulations regarding salt management should be issued to strengthen IDD control and prevention measures,and avoid the recurrence of IDD.

Molecular Epidemiology and Vaccine Compatibility Analysis of Seasonal Influenza Viruses in Wuhan, 2016–2019

Influenza viruses(FLUV)cause high morbidity and mortality annually in the world and pose a serious threat to the public health.Wuhan,as an important transportation hub in China,has a dense population and suitable climate,which also lays a major hidden danger for the outbreak of influenza.To survey and characterize the seasonal FLUV in Wuhan during 2016–2019,we collected 44,738 throat swabs,among which 15.5%were influenza A(FLUAV)positive,6.1%influenza B(FLUBV)and 0.3%co-infection.By monitoring FLUV in each month from June 2016 to May 2019,different with the previously seasonality pattern,only a single influenza peak was appeared in winter of 2017–2018 and 2018–2019,respectively.These data indicated that the complex circulation pattern of seasonal influenza in Wuhan.In addition,we found the age group was skewed towards 5–14 years group whose activity were mostly school based,which suggested school may be an important place for influenza outbreaks.Meanwhile,phylogenic analysis revealed that two subtypes(subclade 3C.2 a2 and 3C.2 a1b)of A(H3N2)were circulating in Wuhan and there was an obvious transition in 2018 because the two subclades were detected simultaneously.Furthermore,by estimating the vaccine effectiveness,we found that the vaccine strain of FLUAV didn’t seem to match very well the current epidemic strain,especially A(H3N2).Hence,more accurate prediction of seasonal outbreak is essential for vaccine design.Taken together,our results provided the current information about seasonal FLUV in Wuhan which form the basis for vaccine updating.

A Spatial Epidemiology Case Study of Coronavirus (COVID-19) Disease and Geospatial Technologies

Spatiotemporal pattern analysis provides a new dimension for data interpretation due to new trends in computer vision and big data analysis. The main aim of this study was to explore the recent advances in geospatial technologies to examine the spatiotemporal pattern of COVID-19 at the Public Health Unit (PHU) level in Ontario, Canada. The spatial autocorrelation results showed that the incidence rate (no. of confirmed cases per 100,000 population–IR/100K) was clustered at the PHU level and found a tendency of clustering high values. Some PHUs in Southern Ontario were identified as hot spots, while Northern PHUs were cold spots. The space-time cube showed an overall trend with a 99% confidence level. Considerable spatial variability in incidence intensity at different times suggested that risk factors were unevenly distributed in space and time. The study also created a regression model that explains the correlation between IR/100K values and potential socioeconomic factors.

Molecular Epidemiology of Nontuberculous Mycobacteria in a German CF Center and Clinical Course of NTM Positive Patients

Goal of this study was to analyse the clinical course of cystic fibrosis (CF) patients with nontuberculous mycobacteria (NTM) in their respiratory secretions and to investigate the molecular epidemiology of the most prevalent NTM species by multilocus sequence analysis (MLSA). The respiratory specimen and the clinical parameters forced expiratory volume in one second (FEV1), body-mass-index (BMI), erythrocyte sedimentation rate (ESR) 1 h and immunoglobulin G (IgG) of 357 CF patients, 0 - 52.4 years, mean FEV1 2009 81.5% pred were analysed between 1998 and 2010. In 13 patients NTM were detected. 12 of 13 patients carried M. abscessus, for one patient the NTM species was not characterized. 4 patients carried a second NTM species (M. avium, M. chelonae (2x), M. intracellulare). 6 patients exhibited a significant decline in FEV1, however changes in BMI, IgG and ESR were discordant. Molecular genotyping of M. abscessus isolates revealed a unique MLSA pattern in 6 patients. 2 patients harboured identical strains, and one patient a closely related strain. Whether the presence of identical strains is attributed to the acquisition of NTM clones from common environmental sources or to patient-to-patient transmission cannot be definitely clarified. Although cross-in- fection of the three patients with identical/closely related strains in the present cohort is highly unlikely, we recommend strict hygiene measures for all CF patients harbouring NTM.

Semen analysis from an epidemiologic perspective

The fifth edition of the World Health Organization （WHO） manual for semen analysis includes for the first time reference values for human semen characteristics. This paper considers whether such values will help to resolve the intensely debated data indicating temporal and geographical shifts in sperm counts and hypotheses that anthropogenic activities that result in the release of chemicals into the environment are detrimental to male reproductive health. The reasons that these reference values will not fulfil these purposes are also explained. Although established reference values for semen characteristics are of limited value in analytical epidemiologic research, the WHO guidelines are of utmost importance for supporting the development of appropriate research protocols. Moreover, in spite of its limitations, semen analysis is still a useful research tool in epidemiological research, and no superior alternatives are on the horizon.

Epidemiological Investigation and Genome Analysis of Duck Circovirus in Southern China

Duck circovirus （DuCV）, a potential immunosuppressive virus, was investigated in Southern China from March 2006 to December 2009 by using a polymerase chain reaction （PCR） based method. In this study, a total of 138 sick or dead duck samples from 18 different farms were examined with an average DuCV infection rate of-35%. It was found that ducks between the ages of 40~60 days were more susceptible to DuCV. There was no evidence showing that the DuCV virus was capable of vertical transmission. Farms with positive PCR results exhibited no regularly apparent clinical abnormalities such as feathering disorders, growth retardation or lower-than-average weight. The complete genomes of 91 strains from Fujian Province and 1 from Zhejiang Province were sequenced and analyzed. The 10 DuCV genomes, comlbared with others genomes downloaded from GenBank, ranged in size from 1988 to 1996 base pairs, with sequence identities ranging from 83.2% to 99.8%. Phylogenetic analysis based on genome sequences demonstrated that DuCVs can be divided into two distinct genetic genotypes, Group I （the Euro-USA lineage） and Group II（the Taiwan lineage）, with approximately 10.0% genetic difference between the two types. Molecular epidemiological data suggest there is no obvious difference among DuCV strains isolated from different geographic locations or different species, including Duck, Muscovy duck, Mule duck, Cheery duck, Mulard duck and Pekin duck.

Top 100 cited articles in ophthalmic epidemiology between 2006 and 2016

AIM: To identify the most-cited articles in ophthalmic epidemiology over the last decade.METHODS: We performed a cited reference search on articles that were included in the ISI Web of Science database using the terms "Epidemi*" AND "ophthalm*" AND "population*" during year 2006 to 2016. TOP 100 most cited articles(T100) in ophthalmic epidemiology were short listed and analysed using bibliometrics.RESULTS: These top 100 articles in ophthalmic epidemiology were cited between 61 to 333 times. Of these T100 articles, 36% originated from United States, and 34% were published in the Ophthalmology journal. The three major topics identified were age-related macular degeneration(AMD, n=23), glaucoma(n=16) and visual impairment(n=12). The top-cited article was a study on outdoor activities and its association with the prevalence of myopia in school-aged children, published in 2008. CONCLUSION: This bibliometric analysis provides useful insights into the current development in ophthalmicepidemiology in the past decade and can help recognizing the quality of the researches, discoveries, and trends steering ophthalmic epidemiology.

Epidemiological Analysis on Reported Hepatitis C Cases in China from 2012 to 2016

Viral hepatitis is an important challenge to public health worldwide.As hepatitis B is well controlled due to vaccination,the disease burden caused by the spread of hepatitis C has become increasingly prominent.Hepatitis C is an infectious disease that is mainly blood-borne.The rate of chronicity ranges from 55% to 85% after people are infected with the hepatitis C virus （HCV）.

Epidemiological Analysis of the Coronavirus Disease Outbreak with Random Effects

Today,coronavirus appears as a serious challenge to the whole world.Epidemiological data of coronavirus is collected through media and web sources for the purpose of analysis.New data on COVID-19 are available daily,yet information about the biological aspects of SARS-CoV-2 and epidemiological characteristics of COVID-19 remains limited,and uncertainty remains around nearly all its parameters’values.This research provides the scientic and public health communities better resources,knowledge,and tools to improve their ability to control the infectious diseases.Using the publicly available data on the ongoing pandemic,the present study investigates the incubation period and other time intervals that govern the epidemiological dynamics of the COVID-19 infections.Formulation of the testing hypotheses for different countries with a 95%level of condence,and descriptive statistics have been calculated to analyze in which region will COVID-19 fall according to the tested hypothesized mean of different countries.The results will be helpful in decision making as well as in further mathematical analysis and control strategy.Statistical tools are used to investigate this pandemic,which will be useful for further research.The testing of the hypothesis is done for the differences in various effects including standard errors.Changes in states’variables are observed over time.The rapid outbreak of coronavirus can be stopped by reducing its transmission.Susceptible should maintain safe distance and follow precautionary measures regarding COVID-19 transmission.

Molecular Epidemiological Analysis of Group A Streptococci Isolated from Children in Chaoyang District of Beijing, 2011:emm Types, Virulence Factor Genes and Erythromycin Resistant Genes

Group A streptococcus （GAS） causes a wide range of diseases in the human population. GAS diseases are more common in children than in adults, with clinical manifestations ranging from pharyngitis and impetigo to invasive infections and post streptococcal sequelae, such as acute rheumatic fever and acute post-streptococcal glomerulonephritis[1]. GAS harbors a host of virulence factors that contribute to its complex pathogenicity and differences in the disease severity and frequency. M protein, one of the major virulence factors, is encoded by the emm gene induces a type of specific host immune response and confers antiphagocytic properties.

Combination Use of PFGE and Drug-resistant Analysis in the Epidemiological Investigation of Listeria Monocytogenes

Listeria monocytogenes is the pathogen of listeriosis and it causes severe infections like septicemia, encephalitis, and meningitis, especially in immunocompromised individuals, newborns, and pregnant women. Its wide distribution in the environment and ability to survive or even grow under adverse conditions has made L. monocytogenes an important public health concern and in food industry.

Epidemiological Analysis of Sexually Transmitted Disease Control and Prevention from 1998 to 2003 in Chongqing

Objectives： To understand trends and epidemiology of STDs in Chongqing from 1998 to 2003 and to provide scientific evidence for developing preventive strategies and distributing government health resources effectively. Methods： STD case-reporting data collected from 43 counties and districts in Chongqing from 1998 to 2003 were analyzed with STD Data Management Software and Excel Software. Results： A total of 133,323 cases of eight different STDs were reported from 1998-2003. The annual incidence of all eight STDs combined was 71.89/10^5.Generally, reported cases and incidence have decreased since 2001. Although gonorrhoea diagnoses made up a significant proportion of the STD burden, this proportion decreased annually. The proportion of the STD burden attributed to Condyloma accuminatum （CA） was always above 30 percent. The proportions of non-gonoccocal urethritis, genital herpes and syphilis within the combinedSTD burden increased gradually from 1998 to 2003.Reported cases of HIV increased rapidly over this time. A total of 214 HIV cases were reported from 1998 to 2003,the majority of which were among men. For HIV, the maleto-female ratio was 1.17, but CA was found among more women than men. Incidence for all STDs was highest among 20-39 year olds, who accounted for 72.2% of reported infections. The majority of STDs were transmitted through extra-marital intercourse,accounting for 55.3%. Conclusion： The STD epidemic in Chongqing changed from 1998-2003. STD incidence declined, as a result of various factors. The epidemiology of STDs has changed.HIV incidence has increased rapidly. This indicates that the AIDS epidemic has reached a critical period. The results of this study suggest a need for readjusting control measures and redistributing health resources.

The Application of Epidemiology for Categorising DNS Cyber Risk Factors

This Epidemiology can be applied to cybersecurity as a novel approach for analysing and detecting cyber threats and their risks. It provides a systematic model for the analysis of likelihood, consequence, management, and prevention measures to examine malicious behaviours like disease. There are a few research studies in discrete cybersecurity risk factors;however, there is a significant research gap on the analysis of collective cyber risk factors and measuring their cyber risk impacts. Effective cybersecurity risk management requires the identification and estimation of the probability of infection, based on a comprehensive range of historical and environmental factors, including human behaviour and technology characteristics. This paper explores how an epidemiological principle can be applied to identify cybersecurity risk factors. These risk factors comprise both human and machine behaviours profiled as risk factors. This paper conducts a preliminary analysis of the relationships between these risk factors utilising Domain Name System (DNS) data sources. The experimental results indicated that the epidemiological principle can effectively examine and estimate cyber risk factors. The proposed principle has a great potential in enhancing new machine learning-enabled intrusion detection solutions by utilising this principle as a risk assessment module of the solutions.

Clinical Analysis of 137 Cases of Fungal Keratitis

Objective: To analyze the epidemiology, clinical diagnosis and treatment of fungal keratitis (FK) in hospitalized patients at the First Affiliated Hospital of Yangtze University in recent years. Methods: A retrospective investigation was conducted on the data of 137 cases of FK in our hospital from January 2019 to December 2022. The epidemiological characteristics, identification results of fungal strains, clinical treatment, and prognosis of the patients were analyzed. Results: Among the 137 FK patients, 89 were males and 48 were females, and the ratio of male to female was 1.85:1, The age of onset was the largest number of patients in 50-59 years old and 60-69 years old. The disease occurred most in autumn, winter and summer farming season (from September to December, January, May, June). 72 cases (52.6%) had a clear history of corneal injury, and 43 cases (31.4%) had a history of plant injury. Other risk factors include eye surface diseases, ophthalmic surgery, and wearing corneal contact lenses. The top three pathogens were fusarium (38.7%), aspergillus (23.3%), and alternaria (17.5%). 101 eyes showed improvement or cure after treatment with medication, 9 eyes underwent corneal stromal injection, 11 eyes were covered with conjunctival flap covering or amniotic membrane transplantation, 12 eyes were covered with corneal transplantation, and enucleation of ocular contents was performed in 4 eyes;Visual acuity was improved or maintained in 123 patients (about 89.8%). Conclusions: The incidence of FK in our hospital was mostly middle-aged and elderly men, mostly caused by corneal injury in the process of agricultural labor. The pathogens were mainly fusarium and aspergillus. The preferred treatment was medication, with severe cases requiring combined surgical treatment. Most patients can maintain or improve their vision after treatment.

Molecular epidemiology and phylogeny of Nipah virus infection:A mini review

Nipah virus(Ni V) is a member of the genus Henipavirus of the family Paramyxoviridae,characterized by high pathogenicity and endemic in South Asia.It is classified as a Biosafety Level-4(BSL-4) agent.The case-fatality varies from 40%-70% depending on the severity of the disease and on the availability of adequate healthcare facilities.At present no antiviral drugs are available for Ni V disease and the treatment is just supportive.Phylogenetic and evolutionary analyses can be used to help in understanding the epidemiology and the temporal origin of this virus.This review provides an overview of evolutionary studies performed on Nipah viruses circulating in different countries.Thirty phylogenetic studies have been published from 2000 to 2015 years,searching on pub-med using the key words ‘Nipah virus AND phylogeny' and twenty-eight molecular epidemiological studies from 2006 to 2015 have been performed,typing the key words ‘Nipah virus AND molecular epidemiology'.Overall data from the published study demonstrated as phylogenetic and evolutionary analysis represent promising tools to evidence NiV epidemics,to study their origin and evolution and finally to act with effective preventive measure.