The rapid evolution of SARS-CoV-2 has led to the emergence of variants of concern (VOCs) characterized by increased transmissibility, pathogenicity, and resistance to neutralizing antibodies. Identifying these variants is essential for guiding public health efforts to control COVID-19. Although whole genome sequencing (WGS) is the gold standard for variant identification, its implementation is often limited in developing countries due to resource constraints. In Bolivia, genomic surveillance is a challenge due to its limited technological infrastructure and resources. An RT-qPCR-based strategy was designed to address these limitations and detect the mutations associated with VOCs and variants of interest (VOIs). The multiplex RT-qPCR commercial kits AllplexTM Master and Variants I (Seegene®) and the ValuPanelTM (Biosearch®) were used to target mutations such as HV69/70del, E484K, N501Y, P681H, and K417N/T. They are characteristic of the Alpha (B.1.1.7), Beta (B.1.531), Gamma (P.1), Omicron (B.1.1.529), Mu (B.1.621), and Zeta (P.2) variants. A total of 157 samples collected in Cochabamba from January to November 2021 were evaluated, identifying 44 Gamma, 2 Zeta, 20 Mu, and 10 Omicron were identified. The strategy’s effectiveness was validated against WGS data generated with Oxford NanoporeTM technology, showing a concordance rate of 0.96. This highlights the value of the RT-qPCR strategy in guiding the selection of samples for WGS, enabling broader detection of new variants that cannot be identified by RT-qPCR alone.

Antimicrobial resistance (AMR) in intensive care units (ICUs) is a critical issue, which has been exacerbated by the coronavirus disease 2019 (COVID-19) pandemic. This study investigated AMR prevalence and its associated factors among ICU patients in two Vietnamese hospitals from January 2020 to June 2022. Electronic medical records of 1,296 patients with 2,432 non-duplicate bacterial isolates were collected in Phu Tho Hospital (Northern, rural, non-COVID-19 treatment) and 175 Hospital (Southern, urban, COVID-19 treatment centre). Antibiotic susceptibility testing was conducted using VITEK2, BD Phoenix 100, and disk diffusion methods. Logistic regression with 1,000 bootstrap resampling and cross-validation was used to examine factors linked to AMR. Results revealed Acinetobacter spp. (27.5%) as leading strains in Phu Tho Hospital, while Klebsiella spp. (28.0%) predominated in 175 Hospital, except during 2021when Acinetobacter spp. reached the peak. Alarmingly, Acinetobacter spp., Klebsiella spp., and Pseudomonas aeruginosa demonstrated the highest AMR rates and multidrug resistance rates (83.8%–95.8%) in both hospitals. Resistance to cephalosporins, carbapenems, and fluoroquinolones ranged from 75% to 100%. Significant associated factors included age, sex, location, initial admission diagnosis, and bacterial isolation month. This study highlights the urgent need for controlling AMR in ICUs during the pandemic.

The Alpha, Delta, and Omicron variants of the SARS-CoV-2 virus have been deemed as variants of concern (VOCs) by the WHO due to their increased transmissibility, severity of illness, and resilience against treatments. Geographically tracking the spread of these variants can help us implement effective control measures. RNA from 8,154 SARS-CoV-2 positive nasal swab samples from a Central Texas hospital collected between March 2020 and April 2023 were sequenced in Temple, TX. Global and U.S. sequencing metadata was obtained from the GISAID database on 3 April 2023. Using sequencing metadata, the growth rate of Alpha, Delta, and the first subvariant of Omicron (BA.1) were obtained as 0.27, 0.3, and 1.08 each. The average time in days to penetrate the US for Alpha, Delta, and Omicron were 269.2, 326.2, and 27.3 days, respectively. Viral sequencing data can be a useful tool to examine the spread of viruses. Each emerging SARS-CoV-2 variant penetrated cities more rapidly as the pandemic progressed. With a high logarithmic growth rate, the Omicron variant penetrated the US more rapidly as the pandemic progressed.

The Secretary of the US Department of Health & Human Services, Robert Kennedy Jr is leading a political agenda against vaccination. This is undermining the delivery of life-saving vaccination programmes and provision of evidence-based information on the safety and effectiveness of vaccines for the public and health professionals. Inconsistent and conflicting messaging between health practitioners and government health agencies erodes trust in public health programmes, creating a vacuum which is often filled with mis/disinformation that presents severe consequences for families. Due to the transnational spread of diseases, we consider the implications of events in the US for routine childhood vaccination programmes in the UK. Public health agencies across the world need to be ‘Kennedy ready’; pragmatic steps must be taken to mitigate threats posed to vaccine confidence and the control of vaccine preventable diseases.

Contact tracing is an effective public health policy to put the fast-spreading epidemic under control. The government tracks the contacts of confirmed SARS-CoV-2 cases, recommends testing, encourages self-quarantine, and monitors symptoms of contacts. In developing and less-developed countries with limited resources for widespread SARS-CoV-2 testing, it remains essential to identify and quarantine positive contacts to control outbreaks. Therefore, analysing recall and precision when implementing testing policies for these contacts is necessary. We analysed a contact tracing dataset from a cohort of 827 index patients infected with SARS-CoV-2 and their 14814 close contacts from Jan 2020 to July 2020 in a province in eastern China. We constructed a network from the data and used a Graph Convolutional Network to predict each contact’s infection status. To the best of our knowledge, this is the first method to use population-based contact tracing data for predicting the infection status using graph neural networks. Despite limited information, our model achieves competitive Area Under the Receiver Operating Characteristic Curve (ROC AUC) compared to hospital-onset scenarios. Based on the risk scores, we propose several contact testing policy adaptations that balance resource efficiency and effective pandemic control.

Investigating risk factors for mpox’s infectious period is vital for preventing this emerging disease, yet evidence remains scarce. This study aimed to identify risk factors associated with the duration of mpox infectiousness among mpox cases in Vietnam. The primary outcome was the duration of the mpox infectiousness, defined between symptom onset and the first negative test result for the mpox virus. Fine and Gray’s regression models were employed to assess the associations between the infectious period and several risk factors while accounting for competing risks of death by mpox. Most mpox cases recovered within 30 days. Patients with HIV or treated at multiple facilities for mpox had lower incidence rates of cleared infection compared to those who were HIV-negative or treated at a single facility. In regression models, patients with mpox symptoms of rash or mucosal lesions (sub-distribution hazard ratios = 0.62, 95% confidence interval = 0.46–0.83), ulcers (0.57, 0.41–0.80), or fever (0.62, 0.46–0.83) had significantly prolonged infectious periods than those without such symptoms. Our findings provided insights for managing mpox cases, especially those vulnerable to prolonged infectious periods in settings with sporadic cases reported.

Lower COVID-19 vaccination coverage was observed among some populations with a migration background in the Netherlands. This study examined determinants of being unvaccinated against COVID-19 in the primary vaccination round in adults and in the 2022 autumn booster round in persons aged ≥60 years, among four populations of non-Dutch origin with below average vaccination coverage: Moroccan, Turkish, Surinamese and Dutch-Caribbean, and persons of Dutch origin. We performed a population-wide register-based study, examining associations between potential determinants and being unvaccinated using multivariable logistic regression and computing population attributable fractions. Being a migrant with two foreign-born parents, younger age, living in highly/extremely urban areas and having a lower income, lower education level and low medical risk for severe COVID-19 were risk factors for being unvaccinated in all populations. Substantial differences in the (strength of) determinants and population attributable fractions between populations were also observed. Socioeconomic status only partially mediated the association with being a migrant with two foreign-born parents. These findings illustrate that interventions targeting specific ethnic minority and migrant populations need further study with the aim to optimize the impact of vaccination programmes and improve health equity. To understand reasons behind non-uptake and design (community-based) interventions, qualitative and survey-based research is needed.

This study analyzed standardized excess mortality due to specific causes during the Covid-19 pandemic across 33 European countries, using Eurostat data (2016–2021) and Our World in Data databases. Causes included circulatory and respiratory diseases, neoplasms, transport accidents, and “other” causes (e.g., diabetes, dementia, ill-defined conditions). Additional variables such as vaccination rates, economic and health indicators, demographics, and government stringency measures were also examined. Key findings include: (1) Most European countries (excluding Central and Eastern Europe), recorded lower than expected excess mortality from circulatory and respiratory diseases, neoplasms, and transport accidents. Ireland had the lowest excess respiratory mortality in both 2020 and 2021; (2) Croatia, Cyprus, Malta, and Turkey showed significant positive excess mortality from “other” causes, potentially linked to public health restrictions, with Turkey as an exception; (3) Regression analysis found that higher human development index and vaccination rates were associated with lower excess mortality. Policy Implications are: (1) Statistically significant positive or negative cause-specific excess mortality may indicate future health trends; (2) The pandemic and government stringency measures negatively affected mortality from “other” causes; (3) Strengthening health system resilience, investing in digital medicine, directing aid to countries with weaker systems, and supporting disadvantaged groups are key recommendations.

Tuberculosis (TB) remains a significant public health concern in China. Using data from the Global Burden of Disease (GBD) study 2021, we analyzed trends in age-standardized incidence rate (ASIR), prevalence rate (ASPR), mortality rate (ASMR), and disability-adjusted life years (DALYs) for TB from 1990 to 2021. Over this period, HIV-negative TB showed a marked decline in ASIR (AAPC = −2.34%, 95% CI: −2.39, −2.28) and ASMR (AAPC = −0.56%, 95% CI: −0.62, −0.59). Specifically, drug-susceptible TB (DS-TB) showed reductions in both ASIR and ASMR, while multidrug-resistant TB (MDR-TB) showed slight decreases. Conversely, extensively drug-resistant TB (XDR-TB) exhibited upward trends in both ASIR and ASMR. TB co-infected with HIV (HIV-DS-TB, HIV-MDR-TB, HIV-XDR-TB) showed increasing trends in recent years. The analysis also found an inverse correlation between ASIRs and ASMRs for HIV-negative TB and the Socio-Demographic Index (SDI). Projections from 2022 to 2035 suggest continued increases in ASIR and ASMR for XDR-TB, HIV-DS-TB, HIV-MDR-TB, and HIV-XDR-TB. The rising burden of XDR-TB and HIV-TB co-infections presents ongoing challenges for TB control in China. Targeted prevention and control strategies are urgently needed to mitigate this burden and further reduce TB-related morbidity and mortality.

Hepatitis B virus vaccination is currently recommended in Australia for adults at an increased risk of acquiring infection or at high risk of complications from infection. This retrospective cohort study used data from an Australian sentinel surveillance system to assess the proportion of individuals who had a recorded test that indicated being susceptible to hepatitis B infection in six priority populations, as well as the proportion who were then subsequently vaccinated within six months of being identified as susceptible. Priority populations included in this analysis were people born overseas in a hepatitis B endemic country, people living with HIV, people with a recent hepatitis C infection, gay, bisexual and other men who have sex with men, people who have ever injected drugs, and sex workers. Results of the study found that in the overall cohort of 43,335 individuals, 14,140 (33%) were identified as susceptible to hepatitis B, and 5,255 (37%) were subsequently vaccinated. Between 26% and 33% of individuals from priority populations were identified as susceptible to hepatitis B infection, and the proportion of these subsequently vaccinated within six months was between 28% and 42% across the groups. These findings suggest further efforts are needed to increase the identification and subsequent vaccination of susceptible individuals among priority populations recommended for hepatitis B vaccination, including among people who are already engaged in hepatitis B care.

Mosquito-borne California serogroup orthobunyaviruses Inkoo (INKV) and Chatanga (CHATV) are known to be endemic in Finland with a high seroprevalence. We developed a novel multiplexed reverse transcription quantitative polymerase chain reaction method for discriminating between the INKV and CHATV. This assay was used along with traditional serological tests to study a set of summertime patients during the years 2021, 2023, and 2024 to assess the epidemiology and prevalence of acute INKV and CHATV infections in Finland. Altogether, 1470 samples were screened, and there were 16 patients who had an acute infection based on serological findings and/or nucleic acid test. The orthobunyavirus-IgG seroprevalences were 18% (2021), 20% (2023), and 30% (2024), being lower than that in studies from 20 years ago. Neutralization tests were carried out, and all but one acute case had more than four-fold higher titre to INVK vs. CHATV, indicating specificity to INKV infection. The results suggest that epidemiology has changed from previous studies, and INKV should be considered a causative agent of summertime infections in Finland. The symptom diversity in mild disease outcomes should be studied to guide orthobunyavirus recognition by clinicians. The use of molecular assay discriminating INKV and CHATV aids in understanding disease associations.

Cryptosporidium parvum is a well-established cause of gastrointestinal illness in both humans and animals and often causes outbreaks at animal contact events, despite the availability of a code of practice that provides guidance on the safe management of these events. We describe a large C. parvum outbreak following a lamb-feeding event at a commercial farm in Wales in 2024, alongside findings from a cohort study to identify high-risk exposures. Sixty-seven cases were identified, 57 were laboratory-confirmed C. parvum, with similar genotypes. Environmental investigations found a lack of adherence to established guidance. The cohort study identified 168 individuals with cryptosporidiosis-like illness from 540 exposure questionnaires (distributed via email to 790 lead bookers). Cases were more likely to have had closer contact with lambs (odds ratio (OR) kissed lambs = 2.4, 95% confidence interval (95% CI): 1.2–4.8). A multivariable analysis found cases were more likely to be under 10 years (adjusted OR (aOR) = 4.5, 95% CI: 2.0–10.0) and have had visible faeces on their person (aOR = 3.6, 95% CI: 2.1–6.2). We provide evidence that close contact at lamb-feeding events presents an increased likelihood of illness, suggesting that farms should limit animal contact at these events and that revisions to established codes of practice may be necessary. Enhancing risk awareness among farmers and visitors is needed, particularly regarding children.

In March 2024, the East Midlands Health Protection Team was notified of a case of invasive Group A Streptococcus (iGAS) infection in an elderly care home resident. Twenty-two days later, another case in a resident from the same floor of the care home was notified. In accordance with national guidelines, an outbreak was declared, and a multidisciplinary outbreak control team (OCT) was urgently convened. Screening for GAS throat carriage was undertaken for staff and residents, excluding those receiving end-of-life care. All isolates were strain typed and characterised. Infection prevention and control (IPC) visits were undertaken to provide ongoing support. Screening identified five residents and five staff members positive for GAS. Antibiotic prophylaxis was provided to all staff throughout the setting (n = 74) and all residents on the affected floor (n = 35). Three individuals were positive on repeat screening. All staff and residents screened negative after 4 months and the two clinical cases recovered. Eleven of the 12 GAS isolates were identified as emm 3.93. This outbreak highlighted the importance of rapid screening, possible only through the deployment of a dedicated team, and rescreening post-decolonising treatment, as a means to contain such outbreaks.

The aim of this study was to describe how the detection of protozoan and helminth parasites has been affected by the introduction of polymerase chain reaction (PCR) and changes in test algorithms. We extracted data about faecal samples tested for parasites (n = 114839) at five Norwegian clinical microbiology laboratories. Samples were classified into prePCR or postPCR depending on whether they were submitted before or after the introduction of PCR, and into diagnostic episodes (n = 99320). The number of diagnostic episodes increased 3.7-fold from prePCR to postPCR. Giardia positive episodes doubled, the positivity rate decreased from 2.0% to 1.3%. Cryptosporidium was hardly detected prePCR and increased to a positivity rate of 1.2%. Entamoeba histolytica was rarely found. Episodes examined for helminths decreased 51%, the number of positive episodes decreased 34%. Samples from immigrants were more likely to be positive for Giardia, E. histolytica, or helminths and less likely to be Cryptosporidium positive. During the COVID-19 pandemic, the number of Giardia and helminth-positive episodes decreased. Cryptosporidium-positive episodes remained unchanged. The implementation of multiplex PCR for protozoa led to a doubling of Giardia cases and a better test for Cryptosporidium. Fewer microscopy examinations raise concerns that helminth infections may be overlooked.

Monkeypox (mpox) has re-emerged as global public health concern including in several non-endemic countries. This study aims to characterize monkeypox virus (MPXV) genomes in Indonesia, to explore viral evolution and transmission. Genomic analysis was conducted on 53 isolates from Indonesian mpox patients between 2023 and 2024. All sequences belonged to Clade IIb, with identified sub-clades including A.1.1, B.1, B.1.3, and C.1 – of which C.1 became dominant during this period. Out of 87 mpox-confirmed cases, 60.9% (53/87) were successfully sequenced and submitted to the Global Initiative on Sharing All Influenza Data (GISAID). The majority of cases in Indonesia occurred among males (95.4%), men who have sex with men (59.8%), and people living with HIV/AIDS (71.3%). Notably, a large portion of cases had no travel history, suggesting local transmission. Initially, only clade IIb (B.1) was detected in October 2022. By August 2023, lineage diversity had increased, with B.1.3 and C.1 emerging as the predominant sub-clades. A time–calibrated phylogenetic tree revealed genetic relatedness and shared ancestry within clade IIb. Integrating genomic and epidemiological data offers valuable insights to improve mpox surveillance and public health response in Indonesia and the broader region

Dengue, the most prevalent urban arbovirus in the world, has triggered recurrent epidemics in Rio de Janeiro, Brazil, since the 1980s. This study aimed to describe the spatial–temporal patterns of dengue spread during the epidemic years of 2002, 2008, 2011, 2012, 2013, and 2024 in Rio de Janeiro. This is an ecological study using secondary data on notified confirmed dengue cases aggregated by neighbourhood. The incidence rates were estimated via the local empirical Bayes method. The local spatial autocorrelation indicators assessed incidence clusters, and the monthly geographic trajectory was outlined for each year. The results revealed changes in the spatial distribution of dengue over time, with clusters of high incidences predominating in the northern and central neighbourhoods in 2002 and 2008, and in the western zone in 2011, 2012, and 2013. In 2024, the distribution was predominant throughout the city, with emphasis in the central and western zones. The monthly geographic centre of dengue cases shifted from the west to the north during the peak of the epidemic. These results highlight the heterogeneous nature of dengue transmission in Rio de Janeiro. The incorporation of spatial and temporal analyses in epidemiological studies can enhance targeted and localized dengue control strategies.

Case-control studies can provide attribution estimates of the likely sources of zoonotic pathogens. We applied a meta-analytical model within a Bayesian estimation framework to pool population attributable fractions (PAFs) from European case-control studies of sporadic campylobacteriosis and salmonellosis. The input data were obtained from two existing systematic reviews, supplemented with additional literature searches, covering the period 2000–2021. In total, 12 studies on Campylobacter providing data for 180 PAFs referring to 5983 cases and 13213 controls, and five studies on Salmonella providing data for 75 PAFs referring to 2908 cases and 5913 controls, were included. All these studies were conducted in Western or Northern European countries. Both pathogens were estimated as being predominantly linked to food- and waterborne transmission, which explained nearly half of the cases, with Campylobacter being mainly attributable to poultry (meat), and Salmonella to poultry (eggs and meat) and pig (meat), as specific foodborne exposures. When also considering contact with animals, around 60% of cases could be explained by the larger group of zoonotic transmission pathways. While environmental transmission was also sizeable (around 10%), about a quarter of cases could be explained by factors such as travel, underlying diseases/medicine use, person-to-person transmission and occupational exposure.

Invasive Group B Streptococcus (GBS) infection caused by the highly virulent Sequence Type 283 (ST283) strain has been linked to consumption of raw freshwater fish. In late summer 2024, enhanced surveillance in Hong Kong detected a surge of invasive ST283 cases.

A retrospective case–control study was conducted involving all invasive GBS patients reported during August to September 2024. Data were collected through standardised interviewer-administered questionnaires. Cases were defined as patients infected with the ST283 strain, while controls had non-ST283 strains. A multivariate logistic regression analysis was conducted to determine the risk factors.

Among 170 invasive GBS patients, 131 (77%) were identified as cases and 39 (23%) as controls. Physical handling of raw freshwater fish was found to be the strongest risk factor for ST283 infection (adjusted odds ratio: 8.4, 95% confidence interval: 1.4–50.1).

This study represents the first epidemiological evidence specifically linking physical contact with raw freshwater fish to an increased risk of invasive GBS ST283 infection. Effective interdepartmental coordination, intensive public health education, active surveillance, and prompt environmental interventions effectively mitigated this large outbreak. The findings underscore the need for sustainable preventive strategies targeting high-risk fish handling practices, particularly during warm periods favouring environmental proliferation of ST283.

This systematic review synthesized evidence on the viral load of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) shedding in exhaled material to understand how the exhaled SARS-CoV-2 viral load of infected individuals varies with days since exposure. Medline, Scopus, and Web of Science databases were searched using a combination of search terms to identify articles that tested exhaled material from SARS-CoV-2 infected patients. Records were systematically screened and assessed for eligibility, following which reference lists of eligible articles were hand-searched to identify further relevant studies. Data extraction and quality assessment of individual studies were conducted prior to synthesizing the evidence. Forty-five articles that sampled exhaled breath, exhaled breath condensate, face masks, and cough samples were reviewed. The variation in the SARS-CoV-2 viral load in these materials was considerable with the detection of viral RNA shed during breathing as far as 43 days after symptom onset. The replication-competent virus was present in all four sample types, with the majority isolated during the first week of symptoms onset. Variations in the sample types and testing protocols precluded meta-analysis. High heterogeneity in exhaled SARS-CoV-2 viral load is likely due to host and viral factors as well as variations in sampling and diagnostic methodologies. Evidence on SARS-CoV-2 shedding in exhaled material is scarce and more controlled fundamental studies are needed to assess this important route of viral shedding.