Cambridge University Press

Epidemiology and Infection

Published by Cambridge University Press

Online ISSN: 1469-4409

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Print ISSN: 0950-2688

Disciplines: Infectious diseases

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Proportion of HPAI cases (H5N1 and H5N8) in Alappuzha and Kottayam districts. Inset: Kerala state in India and two districts.
Wetland areas in Alappuzha and Kottayam districts. Majority of proportion of class coastal wetland (including Mangroove, Estuary, Delta, and Lagoon) is in Alappuzha and Kottayam districts.
Network graph of socio-economic variables and proportion of HPAI cases. Proportion of HPAI cases do not have any parent node, but have child nodes to lake irrigation, total irrigation, other irrigation, and river irrigation indicating indirect relationship between them. Variable expansion: LAKE_IRR: lake irrigation; TOT_IRR: total irrigation; TANK_IRR: tank irrigation; OTH_IRR: other irrigation; RIVER_IRR: river irrigation; W_FALL: water fall; CULT_WASTE: cultivable waste; No HH: number of household; TOT_P: total population; P_ILL: population illiterate; P_LIT: population literate; Other COM: other commodities (other than rice, rubber, and coir); AREA_NA_CU: area not available for cultivation; UN_IRR: unirrigated; TOT_EXP: total expenditure; TOT_INC: total income.
Semi-variogram analysis of proportion of H5N1 cases in duck population of Alappuzha and Kottayam districts. It shows that there is spatial dependency in the outbreaks upto 60 km.
Predictor variables used in the Bayesian spatial SPDE model. (A): Lake irrigation; (B): river irrigation; (C): tank irrigation; (D): total irrigation; (E): other irrigated; (F): unirrigated. River and lake irrigation is mostly in the Alappuzha district.

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Unique duck rearing practice in irrigated rice paddy fields driving recurrent H5N1 avian influenza outbreaks in two districts of Kerala, India

January 2025

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47 Reads

Mohammed Mudassar Chanda

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Adhiraj Mishra

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Chakradhar Tosh
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Aims and scope


Epidemiology and Infection is a fully open access journal publishing original reports and reviews on all aspects of infection in humans and animals. Particular emphasis is given to the epidemiology, prevention and control of infectious diseases. The field covered is broad and includes the zoonoses, tropical infections, food hygiene, vaccine studies, statistics and the clinical, social and public-health aspects of infectious disease. Papers covering microbiology and immunology which have an epidemiological relevance are part of this broad field. Papers come from medical and veterinary scientists worldwide. It has become the key periodical in which to find the latest reports on recently discovered infections and new technology. For those concerned with policy and planning for the control of infections, the papers on mathematical modelling of epidemics caused by historical, current and emergent infections, will be of particular value.

Recent articles


Figure 7 shows the percentage of sample pairs with a 1.5-, 2-, 3-or 4-fold increase in N-antibody 213 level by determinants for sample pairs with and without a reported infection between samples. 214 Among sample pairs with a reported infection in the sampling interval 82% showed a 1.5-fold 215 increase, 77% a 2-fold increase, 71% a 3-fold increase and 65% a 4-fold increase. A fold increase was 216 more likely among vaccinated participants, following local and systemic infections, following 217 infections after the first quarter of 2022 and less likely with increasing antibody concentrations of 218
Using SARS-CoV-2 nucleoprotein antibodies to detect (re)infection
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February 2025

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1 Read





Figure 2 Daily SARS-CoV-2 exceedance report published 5 January 2021 for one LTLA 463
Adapting the Flexible Farrington Algorithm for daily situational awareness and alert system to support public health decision making during the SARS-CoV-2 epidemic, England

February 2025

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6 Reads

The Flexible Farrington Algorithm (FFA) is widely used to detect infectious disease outbreaks at national/regional levels on a weekly basis. The rapid spread of SARS-CoV-2 alongside the speed at which diagnostic and public health interventions were introduced made the FFA of limited use. We describe how the methodology was adapted to provide a daily alert system to support local health protection teams (HPT) working in the 316 English lower tier local authorities. To minimize the impact of a rapidly changing epidemiological situation the FFA was altered to use eight weeks of data. The adapted algorithm was based on reported positive counts using total tests as an offset. Performance was assessed using the root mean square error (RMSE) over a period. Graphical reports were sent to local teams enabling targeted public health action. From 1 July 2020 results were routinely reported. Adaptions accommodated the impact on reporting because of changes in diagnostic strategy (introduction of lateral flow devices). RMSE values were relatively small compared to observed counts, increased during periods of increased reporting, and was relatively higher in the northern and western areas of the country. The exceedance reports were well received. This presentation should be considered as a successful proof-of-concept.





Comparisons among observed versus predicted probabilities among count models.
Abbreviations: PRM – Poisson Regression Model. NBRM – Negative Binomial Regression Model. ZIP – Zero-inflated Poisson.
Flowchart of screening and yield from tuberculosis contact investigation in the State of São Paulo, Brazil, 2010–2020.
Caterpillar plot showing the effect of municipalities on tuberculosis prevalence among contacts and their respective 95% confidence intervals (n = 639). São Paulo, Brazil, 2010–2020.
Characteristics of tuberculosis index cases, yield of tuberculosis contact investigations, number needed to screen, and number needed to treat in São Paulo, Brazil, 2010–2020
Prevalences and multilevel Poisson regression analysis adjusted for characteristics of tuberculosis index cases associated with the presence of tuberculosis diagnosis among their contacts. São Paulo, Brazil, 2010–2020
The yield of tuberculosis contact investigation in São Paulo, Brazil: a community-based cross-sectional study

January 2025

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8 Reads

The strategy of tuberculosis (TB) contact investigation is essential for enhancing disease detection. We conducted a cross-sectional study to evaluate the yield of contact investigation for new TB cases, estimate the prevalence of TB, and identify characteristics of index cases associated with infection among contacts of new cases notified between 2010 and 2020 in São Paulo, Brazil. Out of 186466 index TB cases, 131055 (70.3%) underwent contact investigation. A total of 652286 contacts were screened, of which 451704 (69.2%) were examined. Of these, 12243 were diagnosed with active TB (yield of 1.9%), resulting in a number needed to screen of 53 and a number needed to test of 37 to identify one new TB case. The weighted prevalence for the total contacts screened was 2.8% (95% confidence interval [CI]: 2.7%–2.9%), suggesting underreporting of 6021 (95% CI: 5269–6673) cases. The likelihood of TB diagnosis was higher among contacts of cases identified through active case-finding, abnormal chest X-ray, pulmonary TB, or drug resistance, as well as among children, adults, women, individuals in socially vulnerable situations, and those with underlying clinical conditions. The study highlights significant TB underreporting among contacts, recommending strengthened contact investigation to promptly identify and treat new cases.





An outbreak of Shiga toxin-producing Escherichia coli serotype O103:H2 associated with unpasteurized soft cheese, England and Wales, 2022

January 2025

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28 Reads

In July 2022, a genetically linked and geographically dispersed cluster of 12 cases of Shiga toxin-producing Escherichia coli (STEC) O103:H2 was detected by the UK Health Security Agency using whole genome sequencing. Review of food history questionnaires identified cheese (particularly an unpasteurized brie-style cheese) and mixed salad leaves as potential vehicles. A case–control study was conducted to investigate exposure to these products. Case food history information was collected by telephone. Controls were recruited using a market research panel and self-completed an online questionnaire. Univariable and multivariable analyses were undertaken using Firth Logistic Regression. Eleven cases and 24 controls were included in the analysis. Consumption of the brie-style cheese of interest was associated with illness (OR 57.5, 95% confidence interval: 3.10–1,060). Concurrently, the production of the brie-style cheese was investigated. Microbiological sample results for the cheese products and implicated dairy herd did not identify the outbreak strain, but did identify the presence of stx genes and STEC, respectively. Together, epidemiological, microbiological, and environmental investigations provided evidence that the brie-style cheese was the vehicle for this outbreak. Production of unpasteurized dairy products was suspended by the business operator, and a review of practices was performed.



Mid-point rooted, neighbour-joining tree showing phylogenetic relationships among K. pneumoniae mastitis isolates from Scotland. Tree constructed using pairwise SNP distances across 1972 K. pneumoniae core genes and produced by Pathogenwatch [25]. Multiple isolates came from Farms B (7 isolates) and V (5 isolates), and these are highlighted in green and yellow, respectively. ST107 isolates are highlighted in a black box. The presence of yersiniabactin is denoted by red star and antimicrobial resistance genes are shown by squares as being either present (filled black square) or absent (empty square).
Mid-point rooted, neighbour-joining tree showing phylogenetic relationships among international isolates K. pneumoniae ST107. Tree constructed using pairwise SNP distances across 1972 K. pneumoniae core genes and produced by Pathogenwatch [25]. Geographical location of origin and host are indicated by a coloured key. Labels of study isolates are shaded grey, and UK is differentiated from Europe for the purposes of this figure.
Number and percentage of studied isolates which showed sensitive, intermediate, or resistant susceptibility profiles against the listed antimicrobial agents
Antimicrobial resistance profiles and molecular epidemiology of Klebsiella pneumoniae isolates from Scottish bovine mastitis cases

January 2025

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14 Reads

Klebsiella pneumoniae are opportunistic pathogens which can cause mastitis in dairy cattle. K. pneumoniae mastitis often has a poor cure rate and can lead to the development of chronic infection, which has an impact on both health and production. However, there are few studies which aim to fully characterize K. pneumoniae by whole-genome sequencing from bovine mastitis cases. Here, K. pneumoniae isolates associated with mastitis in dairy cattle were identified using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and whole-genome sequencing. Furthermore, whole-genome sequence data were used for phylogenetic analyses and both virulence and antimicrobial resistance (AMR) prediction, in parallel with phenotypic AMR testing. Forty-two isolates identified as K. pneumoniae were subject to whole-genome sequencing, with 31 multi-locus sequence types being observed, suggesting the source of these isolates was likely environmental. Isolates were examined for key virulence determinants encoding acquired siderophores, colibactin, and hypermucoidy. The majority of these were absent, except for ybST (encoding yersiniabactin) which was present in six isolates. Across the dataset, there were notable levels of phenotypic AMR against streptomycin (26.2%) and tetracycline (19%), and intermediate susceptibility to cephalexin (26.2%) and neomycin (21.4%). Of importance was the detection of two ESBL-producing isolates, which demonstrated multi-drug resistance to amoxicillin-clavulanic acid, streptomycin, tetracycline, cefotaxime, cephalexin, and cefquinome.



Knowledge, attitudes, and practices towards vector-borne diseases in changing climate in Finland

January 2025

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33 Reads

With climate change, the geographic distribution of some VBDs has expanded, highlighting the need for adaptation, and managing the risks associated with emergence in new areas. We conducted a questionnaire survey on the knowledge, attitudes, and practices (KAP) about vector-borne diseases (VBDs) among sample of Finnish residents. The questions were scored and the level of KAP was determined based on scoring as poor, fair, good, or excellent. Binary logistic regression analysis was used to evaluate the associations of different KAP levels with sex, age, education, and possible previous VPD infection. We received 491/1995 (25%) responses across the country and detected generally good knowledge, but only fair practices towards VBDs. Sex and age of the respondents were most often significantly associated with the level of KAP (P > 0.05). Despite the generally good knowledge, we detected major gaps, especially regarding the distinction of tick-borne encephalitis and Lyme borreliosis (LB), risk of disease, and protective measures. Additionally, many respondents thought the vaccination protects against LB or tick bites. This calls for awareness raising on disease risk and prevention measures. With increasing cases and the effects of climate change, surveillance of VBDs communication to the general public should be strengthened.


Sources of antimicrobial consumption information used in each country, health sectors and healthcare levels represented, and coverage percentage over the total national population
Yearly evolution of the total antimicrobial consumption expressed in DID per country
Country average AMC expressed in DID (%), according to the therapeutical group, during the period 2019–2022
Implementing national antimicrobial consumption in Latin America and the Caribbean: opportunities and lessons learned

January 2025

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26 Reads

Surveillance of antimicrobial consumption (AMC) is essential to anticipate and inform policies and public health decisions to prevent and/or contain antimicrobial resistance (AMR). This manuscript shares the experience on AMC data collection in Latin American & Caribbean (LAC). The WHO GLASS-AMC methodology for AMC surveillance was used for data registration during the period 2019–2022. Focal points belonging to each country were contacted and trained for AMC source of information detection, managing registration tools, and data analysis. Thirteen countries were enrolled with significant heterogeneity in the AMC results (range 2.55–36.26 DID-AMC). This experience reflects the heterogeneity of realities in LAC countries; how each one of the nations selected the best sources to collect AMC data, which were the main problems in applying the WHO-AMC collection tool, and the approach that each country gave to the analysis of its data. Finally, some examples are provided on the use of AMC information in making the best decision-making related to AMR control policies at the national level.


Weekly incidence rate of hand, foot and mouth disease (HFMD) per 100,000 population (all ages), England 2017–2022.
Weekly GP consultation rate of hand, foot and mouth disease (HFMD) per 100,000 population by age group in England (2017–2022).
Hand, foot and mouth disease (HFMD) seasonal activity range
Epidemiological characteristics of GP consultations for hand, foot and mouth disease (HFMD) in England, 2017–2022, presented as the annual number of HFMD GP consultations (annual incidence rate per 100,000).
Trends in general practitioner consultations for hand foot and mouth disease in England between 2017 and 2022

January 2025

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6 Reads

Hand, foot and mouth disease (HFMD) is a contagious communicable disease, with a high incidence in children aged under 10 years. It is a mainly self-limiting disease but can also cause serious neurological or cardiopulmonary complications in some cases, which can lead to death. Little is known about the burden of HMFD on primary care health care services in the UK. The aim of this work was to describe trends in general practitioner (GP) consultations for HFMD in England from January 2017 to December 2022 using a syndromic surveillance network of GPs. Daily GP consultations for HFMD in England were extracted from 1 January 2017 to 31 December 2022. Mean weekly consultation rates per 100,000 population and 95% confidence intervals (CI) were calculated. Consultation rates and rate ratios (RR) were calculated by age group and sex. During the study period, the mean weekly consultation rate for HFMD (per 100,000 registered GP patients) was 1.53 (range of 0.27 to 2.47). In England, children aged 1–4 years old accounted for the largest affected population followed by children <1 years old. We observed a seasonal pattern of HFMD incidence during the non-COVID years, with a seasonal peak of mean weekly rates between months of September and December. HFMD is typically diagnosed clinically rather than through laboratory sampling. Therefore, the ability to look at the daily HFMD consultation rates provides an excellent epidemiological overview on disease trends. The use of a novel GP-in-hours surveillance system allowed a unique epidemiological insight into the recent trends of general practitioner consultations for HFMD. We demonstrate a male predominance of cases, the impact of the non-pharmaceutical interventions during the COVID-19 pandemic, and a change in the week in which the peak number of cases happens post-pandemic.


Characteristics of the participants by population group
Factors associated with HEV IgG seroprevalence a
Multivariable negative binomial regression model of factors associated with HEV IgG seropositivity
Hepatitis E virus (HEV) infection among the Arab population in Northern Israel: an insight into the seroepidemiology and associated risk factors

January 2025

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27 Reads

Hepatitis E virus (HEV) is one of the most common causes of viral hepatitis. We examined HEV seroprevalence and associations of sociodemographic and lifestyle characteristics with HEV immunoglobulin G (IgG) seropositivity in the Arab population. A cross-sectional single-centre study was conducted among adults in the Nazareth area during 2022. Blood samples were tested using the Altona Real-Star HEV-RNA and the Wantai IgG assays. Data on sociodemographics, health status, and lifestyle were collected using structured questionnaires. Overall, 490 individuals (55.9% males) aged 18 − 96 (mean = 53.2, SD = 28.0) were enrolled. HEV IgG seropositivity was estimated at 21.4% (95% CI 17.9–25.3). No samples were HEV-RNA positive. The correlates of HEV IgG seropositivity were older age (prevalence ratio (PR) 1.07, 95% CI 1.04–1.09, P < 0.001) and consuming beef frequently (PR 2.81, 95% CI 1.40–5.63, P = 0.003). No associations were found between Arab religious groups (Muslim, Christian or Druze, representing different socioeconomic status and dietary habits) or pork consumption and HEV IgG seropositivity. In conclusion, HEV seropositivity was high in the Arab population, and assessing HEV in Ruminants, particularly cows, is warranted.


Epidemic Curve: day of onset of confirmed and probable cases (n = 10).
Wall-mounted water-heater unit.
Pseudomonas aeruginosa results for swabs and water samples from the ear-piercing and tattoo rooms in the premises used by patients
Outbreak of Pseudomonas aeruginosa perichondritis associated with ear piercings and a contaminated water system

January 2025

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10 Reads

In September 2023, the UK Health Security Agency’s (UKHSA) South West Health Protection Team received notification of patients with Pseudomonas aeruginosa perichondritis. All five cases had attended the same cosmetic piercing studio and a multi-disciplinary outbreak control investigation was subsequently initiated. An additional five cases attending the same studio were found. Seven of the ten cases had isolates available for Variable Number Tandem Repeat (VNTR) typing at the UKHSA national reference laboratory. Clinical and environmental P. aeruginosa isolates from the patients, handwash sink, tap water and throughout the wall-mounted point-of-use water heater (including outlet water) were indistinguishable by VNTR typing (11,6,2,2,1,3,6,3,11). No additional cases were identified after control measures were implemented, which included replacing the sink and point-of-use heater. The lack of specific recommendations to control for P. aeruginosa within Council-adopted ear-piercing byelaws or national guidance means that a cosmetic piercing artist could inadvertently overlook the risks from this bacterial pathogen despite every intention to comply with the law and follow industry best practice advice. Clinicians, Environmental Health Officers and public health professionals should remain alert for single cases of Pseudomonas perichondritis infections associated with piercings and have a low threshold for notification to local health protection teams.


SFG and TG seropositivity in Humans suspected of TBD in Yucatan, Mexico

January 2025

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63 Reads

Since 1996, the incidence of rickettsiosis has been increasing in Yucatán, Mexico, but recent prevalence data are lacking. This study aimed to determine exposure to the Spotted Fever Group (SFG) and Typhus Group (TG) in human serum samples suspected of tick-borne diseases (TBD) between 2015 and 2022. A total of 620 samples were analysed using indirect immunofluorescence assay (IFA) to detect IgG antibodies against SFG (Rickettsia rickettsii) and TG (Rickettsia typhi), considering a titer of ≥64 as positive. Results showed that 103 samples (17%) were positive for R. rickettsii and 145 (24%) for R. typhi, while 256 (41%) and 229 (37%) were negative, respectively. There was a cross-reaction in 244 samples (39%). Individuals with contact with vectors, such as ticks, showed significant exposure to fleas (p = 0.0010). The study suggests a high prevalence of rickettsiosis and recommends prospective studies to assess the disease burden and strengthen surveillance and prevention in Yucatán, considering factors like temperature and ecological changes.


Unique duck rearing practice in irrigated rice paddy fields driving recurrent H5N1 avian influenza outbreaks in two districts of Kerala, India

January 2025

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47 Reads

Highly pathogenic avian influenza (HPAI) outbreaks have repeatedly occurred in two districts of Kerala state, India, over the last few years. The outbreaks in the wetland areas coincided with the arrival of migratory birds. At the time, the factors responsible for local transmission in ducks were not known. This study aimed to identify the socio-economic factors responsible for spatial variation in the occurrence of HPAI outbreaks in the two districts using Bayesian network modelling (BNM) and Stochastic Partial Differential Equation (SPDE) model. Further, information was collected on the duck rearing practices in rice paddy fields to identify the risk factors for local – spread of the outbreaks. We found that the SPDE model without covariates explained variation in occurrence of outbreaks. The number of rice paddy fields used by the duck farmers was identified as risk factor. We concluded based on BNM and SPDE that the infected migratory birds were the source of infection for the first few duck farms in the wetland areas and subsequent transmission was driven by shifting of ducks from one rice paddy field to other fields. There is a probability of persistent and recurrent infections in the ducks and possible spill over to humans. Hence, it is important to have surveillance in ducks to prevent recurrent outbreaks in the region.


The total number of dengue cases and deaths reported in each month in 2023 compared to the total number of cases and deaths during the period from 2000 to 2022 in Bangladesh. Log 10 base is used to display the cases and deaths for the convenience of visualization and comparison.
Number of days of hospital stays of 1,705 dengue cases in Bangladesh from 1 January to 31 December 2023. More than 67% (n = 1,015) of people died within one day of hospital admission.
A (Top) Daily number of dengue cases in different divisions of Bangladesh (1 January–31 December 2023). B (Bottom). Monthly relative changes of dengue cases in each division in Bangladesh, 2023 from previous months. Although Dhaka city remains the centre of the outbreak, the percentage of cases has increased outside Dhaka city after July 2023.
A (Left). Distribution of dengue cases in different districts of Bangladesh, 1 January 2023–2031 December 2023. B (Right) The incidence of dengue cases in each district in Bangladesh (1 January–31 December 2023). The horizontal line in the middle of the country divides the southern and northern divisions. The southern divisions (Khulna, Barisal, and Chattogram) have a higher mean incidence (2.30 vs. 0.50) and CFR (0.24 vs. 0.13) of dengue cases than the northern divisions. The southern division also had a higher annual mean temperature (27.46 vs. 26.54 °C) compared to the northern divisions in 2023.
Factors associated with dengue cases in different divisions using a generalized linear mixed model between 1 January 2023 and 31 December 2023
The 2023 fatal dengue outbreak in Bangladesh highlights a paradigm shift of geographical distribution of cases

January 2025

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58 Reads

In 2023, Bangladesh experienced its largest and deadliest outbreak of the Dengue virus (DENV), reporting the highest-ever recorded annual cases and deaths. Historically, most of the cases were recorded in the capital city, Dhaka. We aimed to characterize the geographical transmission of DENV in Bangladesh. From 1 January–31 December 2023, we extracted and analyzed daily data on dengue cases and deaths from the Management Information System of the Ministry of Health and Family Welfare. We performed a generalized linear mixed model to identify the associations between division-wise daily dengue counts and various geographical and meteorological covariates. The number of dengue cases reported in 2023 was 1.3 times higher than the total number recorded in the past 23 years (321,179 vs. 244,246), with twice as many deaths than the total fatalities recorded over the past 23 years (1705 vs. 849). Of the 1,705 deaths in 2023, 67.4% (n = 1,015) died within one day after hospital admission. The divisions southern to Dhaka had a higher dengue incidence/1000 population (2.30 vs. 0.50, p <0.01) than the northern divisions. Festival-related travel along with meteorological factors and urbanization are likely to have contributed to the shift of dengue from Dhaka to different districts in Bangladesh.


Monthly HAstV positivity rates from January 2015 to December 2022 (n = 202,769). The figure represents the monthly HAstV positivity for the two laboratories from 2015 to 2022. Up until 2021, there was no evident seasonality, and the peak positivity rates remained below 6%. A notable and abrupt increase in HAstV positivity rates was observed between June and August 2022. Abbreviation: HAstV, human astrovirus.
Phylogenetic analysis of HAstVs collected in 2022 and reference strains in GenBank. Phylogenetic trees were constructed using the maximum-likelihood method, using MEGA version 11. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Branch lengths are shown above the branches. Black circles indicate the strains from this study. All HAstVs detected in 2022 belong to the same HastV-1 type, exhibiting minimal sequence variation. Abbreviation: HAstV, human astrovirus.
Age distribution of HAstV positivity in patients from two laboratories in 2022
Surge of human astrovirus type 1 infection in summer 2022 in Korea

January 2025

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6 Reads

As astroviral infection rapidly increased in the summer of 2022 in Korea, this study aimed to determine the cause and genotype of astroviruses during this period. From January to December 2022, we tested 43,312 stool samples from patients with acute gastroenteritis utilizing multiplex PCR to detect HAstV. For the HAstV-positive samples, we determined the genotypes of the HAstVs by PCR and sequencing. The monthly positive rate from 2015 to 2022 showed a notable and abrupt increase of HAstV infection between June and August 2022, peaking at 9.8% in July 2022. The annual positivity rate of HAstV remained at 2–3% between 2015 and 2019, and then decreased to 0.5% in 2020, followed by an increase to 1.5% in 2021 and 3.6% in 2022.The genotyped astroviruses in 2022 were all identified as HAstV-1 type, and the nucleotide identity% among them was >99%. The GenBank accession number for the strain genetically closest to the strains identified in our study was ON571597.1, which was HAstV-1 isolated from Pingtan in 2019. Our results provide recent epidemiological data on HAstVs in Korea. The decline and surge in astrovirus positivity in recent years may be related to the COVID-19 pandemic.


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