Coronavirus disease 2019 (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with a limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13324X. We identified 564 high-quality SARS-CoV-2 variants. A total of 18 variants mapped to reverse transcription polymerase chain reaction primer/probe sites, and four variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (20A, 20B and 20C) (94%), whereas 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.

COVID-19 research has been produced at an unprecedented rate and managing what is currently known is in part being accomplished through synthesis research. Here we evaluated how the need to rapidly produce syntheses has impacted the quality of the synthesis research. Thus, we sought to identify, evaluate and map the synthesis research on COVID-19 published up to 10 July 2020. A COVID-19 literature database was created using pre-specified COVID-19 search algorithms carried out in eight databases. We identified 863 citations considered to be synthesis research for evaluation in this project. Four-hundred and thirty-nine reviews were fully assessed with A MeaSurement Tool to Assess systematic Reviews (AMSTAR-2) and rated as very low-quality (n = 145), low-quality (n = 80), medium-quality (n = 208) and high-quality (n = 151). The quality of these reviews fell short of what is expected for synthesis research with key domains being left out of the typical methodology. The increase in risk of bias due to non-adherence to systematic review methodology is unknown and prevents the reader from assessing the validity of the review. The responsibility to assure the quality is held by both producers and publishers of synthesis research and our findings indicate there is a need to equip readers with the expertise to evaluate the review conduct before using it for decision-making purposes.

The feasibility of non-pharmacological public health interventions (NPIs) such as physical distancing or isolation at home to prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in low-resource countries is unknown. Household survey data from 54 African countries were used to investigate the feasibility of SARS-CoV-2 NPIs in low-resource settings. Across the 54 countries, approximately 718 million people lived in households with ⩾6 individuals at home (median percentage of at-risk households 56% (95% confidence interval (CI), 51% to 60%)). Approximately 283 million people lived in households where ⩾3 people slept in a single room (median percentage of at-risk households 15% (95% CI, 13% to 19%)). An estimated 890 million Africans lack on-site water (71% (95% CI, 62% to 80%)), while 700 million people lacked in-home soap/washing facilities (56% (95% CI, 42% to 73%)). The median percentage of people without a refrigerator in the home was 79% (95% CI, 67% to 88%), while 45% (95% CI, 39% to 52%) shared toilet facilities with other households. Individuals in low-resource settings have substantial obstacles to implementing NPIs for mitigating SARS-CoV-2 transmission. These populations urgently need to be prioritised for coronavirus disease 2019 vaccination to prevent disease and to contain the global pandemic.

The Republic of Ireland (ROI) currently reports the highest incidence rates of Shiga-toxin producing Escherichia coli (STEC) enteritis and cryptosporidiosis in Europe, with the spatial distribution of both infections exhibiting a clear urban/rural divide. To date, no investigation of the role of socio-demographic profile on the incidence of either infection in the ROI has been undertaken. The current study employed bivariate analyses and Random Forest classification to identify associations between individual components of a national deprivation index and spatially aggregated cases of STEC enteritis and cryptosporidiosis. Classification accuracies ranged from 78.2% (STEC, urban) to 90.6% (cryptosporidiosis, rural). STEC incidence was (negatively) associated with a mean number of persons per room and percentage of local authority housing in both urban and rural areas, addition to lower levels of education in rural areas, while lower unemployment rates were associated with both infections, irrespective of settlement type. Lower levels of third-level education were associated with cryptosporidiosis in rural areas only. This study highlights settlement-specific disparities with respect to education, unemployment and household composition, associated with the incidence of enteric infection. Study findings may be employed for improved risk communication and surveillance to safeguard public health across socio-demographic profiles.

This study aimed to analyse the geographical distribution of coronavirus disease 2019 (COVID-19) and to identify high-risk areas in space and time for the occurrence of cases and deaths in the indigenous population of Brazil. This is an ecological study carried out between 24 March and 26 October 2020 whose units of analysis were the Special Indigenous Sanitary Districts. The Getis-Ord General G and Getis-Ord Gi* techniques were used to verify the spatial association of the phenomena and a retrospective space–time scan was performed. There were 32 041 confirmed cases of COVID-19 and 471 deaths. The non-randomness of cases (z score = 5.40; P < 0.001) and deaths (z score = 3.83; P < 0.001) were confirmed. Hotspots were identified for cases and deaths in the north and midwest regions of Brazil. Sixteen high-risk space–time clusters were identified for the occurrence of cases with a higher RR = 21.23 (P < 0.001) and four risk clusters for deaths with a higher RR = 80.33 (P < 0.001). These clusters were identified from 22 May and were active until 10 October 2020. The results indicate critical areas in the indigenous territories of Brazil and contribute to better directing the actions of control of COVID-19 in this population.

This study characterises changes in the incidence and mortality of hepatitis A in different age groups and provinces of China from 1990 to 2018, and evaluates the effect of the nation-wide expanded programme on immunisation (EPI). A mathematical model was used to estimate the relative change in incidence and mortality in different provinces and age groups. Interrupted time series regression was applied to evaluate the impacts of the inclusion of vaccination in the EPI during 2007–2018. The geographic clustering of hepatitis A incidence was assessed using global Moran's I and changing trends over time were estimated using joinpoint regression analysis. Both the incidence (odds ratio (OR) for overall relative change: 0.86; 95% confidence interval (CI): 0.85–0.87; P < 0.0001) and the mortality rate (OR for overall relative change: 0.84; 95% CI: 0.83–0.85; P < 0.0001) decreased. Most age groups had significant declines in reported incidence over time. The incidence and mortality of hepatitis A significantly reduced after inclusion of hepatitis A vaccine in EPI, showing that the EPI strategy had a continuous effect on the decreasing trend of hepatitis A burden. Increasing the coverage rate of the vaccine and improving hygiene conditions are the key measures for the control of hepatitis A in China.

We update our previous insights into COVID-19 vaccine acceptance and hesitancy in Finland. Vaccine acceptance increased from 64% (November/December 2020) to 74% (April 2021). However, there was a group of participants that were preferring to wait to get vaccinated ranging from 6% of over-64-years-olds to 29% of under-30-years-olds. The previously identified enablers convenience (below-50-years-olds), worry about severe disease and protection for oneself (above-50-years-olds) were no longer significantly associated with increased vaccine acceptance. Understanding barriers and enablers behind vaccine acceptance is decisive in ensuring a successful implementation of COVID-19 vaccination programs, which will be key to ending the pandemic.

In 2015–2016, simultaneous circulation of dengue, Zika and chikungunya in the municipality of Rio de Janeiro (Brazil) was reported. We conducted an ecological study to analyse the spatial distribution of dengue, Zika and chikungunya cases and to investigate socioeconomic factors associated with individual and combined disease incidence in 2015–2016. We then constructed thematic maps and analysed the bivariate global Moran indices. Classical and spatial models were used. A distinct spatial distribution pattern for dengue, Zika and chikungunya was identified in the municipality of Rio de Janeiro. The bivariate global Moran indices (P < 0.05) revealed negative spatial correlations between rates of dengue, Zika, chikungunya and combined arboviruses incidence and social development index and mean income. The regression models (P < 0.05) identified a negative relationship between mean income and each of these rates and between sewage and Zika incidence rates, as well as a positive relationship between urban areas and chikungunya incidence rates. In our study, spatial analysis techniques helped to identify high-risk and social determinants at the local level for the three arboviruses. Our findings may aid in backing effective interventions for the prevention and control of epidemics of these diseases.

Varicella is a highly infectious contagious disease, and Chongqing is one of the high incidence areas in China. To understand the epidemic regularity and predict the epidemic trend of varicella is of great significance to the risk analysis and health resource allocation in the health sector. First, we used the ‘STL’ function to decompose the incidence of varicella to understand its trend and seasonality. Second, we established SARIMA model for linear fitting, and then took the residual of the SARIMA model as the sample to fit the LS-SVM model, to explain the non-linearity of the residuals. The monthly varicella incidence peaks in April to June and October to December. Mixed model was compared to SARIMA model, the prediction error of the hybrid model was smaller, and the RMSE and MAPE values of the hybrid model were 0.7525 and 0.0647, respectively, the mixed model had a better prediction effect. Based on the study, the incidence of varicella in Chongqing has an obvious seasonal trend, and a hybrid model can also predict the incidence of varicella well. Thus, hybrid model analysis is a feasible and simple method to predict varicella in Chongqing.

About 800 foodborne disease outbreaks are reported in the United States annually. Few are associated with food recalls. We compared 226 outbreaks associated with food recalls with those not associated with recalls during 2006–2016. Recall-associated outbreaks had, on average, more illnesses per outbreak and higher proportions of hospitalisations and deaths than non-recall-associated outbreaks. The top confirmed aetiology for recall-associated outbreaks was Salmonella. Pasteurised and unpasteurised dairy products, beef and molluscs were the most frequently implicated foods. The most common pathogen−food pairs for outbreaks with recalls were Escherichia coli-beef and norovirus-molluscs; the top pairs for non-recall-associated outbreaks were scombrotoxin-fish and ciguatoxin-fish. For outbreaks with recalls, 48% of the recalls occurred after the outbreak, 27% during the outbreak, 3% before the outbreak, and 22% were inconclusive or had unknown recall timing. Fifty per cent of recall-associated outbreaks were multistate, compared with 2% of non-recall-associated outbreaks. The differences between recall-associated outbreaks and non-recall-associated outbreaks help define the types of outbreaks and food vehicles that are likely to have a recall. Improved outbreak vehicle identification and traceability of rarely recalled foods could lead to more recalls of these products, resulting in fewer illnesses and deaths.

The prevalence of human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) is increasing day by day in the region, including Turkey. The study aimed to examine AIDS-related deaths in Turkey between 2009 and 2018 according to the national death registration system records. In this descriptive study, data on AIDS-related deaths were obtained from the Turkish Statistical Institute. The data consist of the cause of death codes, year of death, age and gender. Findings were presented using numbers and percentages. Seven hundred twenty-one AIDS-related deaths were reported in Turkey between 2009 and 2018. AIDS-related deaths in Turkey increased more than twice at the end of 10 years. The male/female death ratio is 4.5. Deaths under the age of 15 were 4.2% in total; however, they were increased to 10.2% in 2018. AIDS-related deaths are decreasing in the world but increasing in Turkey. The data from the Ministry of Health do not match the data of the national death registration system. Establishing a strong and accurate HIV/AIDS reporting system and identifying the causes and risk groups of this increase in AIDS-related deaths are critical.

To investigate temporal trends in coronavirus disease 2019 (COVID-19)-related outcomes and to evaluate whether the impacts of potential risk factors and disparities changed over time, we conducted a retrospective cohort study with 249 075 patients tested or treated for COVID-19 at Michigan Medicine (MM), from 10 March 2020 to 3 May 2021. Among these patients, 26 289 were diagnosed with COVID-19. According to the calendar time in which they first tested positive, the COVID-19-positive cohort were stratified into three-time segments (T1: March–June, 2020; T2: July–December, 2020; T3: January–May, 2021). Potential risk factors that we examined included demographics, residential-level socioeconomic characteristics and preexisting comorbidities. The main outcomes included COVID-19-related hospitalisation and intensive care unit (ICU) admission. The hospitalisation rate for COVID-positive patients decreased from 36.2% in T1 to 14.2% in T3, and the ICU admission rate decreased from 16.9% to 2.9% from T1 to T3. These findings confirm that COVID-19-related hospitalisation and ICU admission rates were decreasing throughout the pandemic from March 2020 to May 2021. Black patients had significantly higher (compared to White patients) hospitalisation rates (19.6% vs. 11.0%) and ICU admission rates (6.3% vs. 2.8%) in the full COVID-19-positive cohort. A time-stratified analysis showed that racial disparities in hospitalisation rates persisted over time and the estimates of the odds ratios (ORs) stayed above unity in both unadjusted [full cohort: OR = 1.98, 95% confidence interval (CI) (1.79, 2.19); T1: OR = 1.70, 95% CI (1.36, 2.12); T2: OR = 1.40, 95% CI (1.17, 1.68); T3: OR = 1.55, 95% CI (1.29, 1.86)] and adjusted analysis, accounting for differences in demographics, socioeconomic status, and preexisting comorbid conditions (full cohort: OR = 1.45, 95% CI (1.25, 1.68); T1: OR = 1.26, 95% CI (0.90, 1.76); T2: OR = 1.29, 95% CI (1.01, 1.64); T3: OR = 1.29, 95% CI (1.00, 1.67)).

There is a paucity of evidence about the prevalence and risk factors for symptomatic infection among children. This study aimed to describe the prevalence of symptomatic coronavirus disease 2019 (COVID-19) and its risk factors in children and adolescents aged 0–18 years in Qatar. We conducted a cross-sectional study of all children aged 0–18 years diagnosed with COVID-19 using polymerase chain reaction in Qatar during the period 1st March to 31st July 2020. A generalised linear model with a binomial family and identity link was used to assess the association between selected factors and the prevalence of symptomatic infection. A total of 11 445 children with a median age of 8 years (interquartile range (IQR) 3–13 years) were included in this study. The prevalence of symptomatic COVID-19 was 36.6% (95% confidence interval (CI) 35.7–37.5), and it was similar between children aged <5 years (37.8%), 5–9 years (34.3%) and 10 + years (37.3%). The most frequently reported symptoms among the symptomatic group were fever (73.5%), cough (34.8%), headache (23.2%) and sore throat (23.2%). Fever (82.8%) was more common in symptomatic children aged <5 years, while cough (38.7%) was more prevalent in those aged 10 years or older, compared to other age groups. Variables associated with an increased risk of symptomatic infection were; contact with confirmed cases (RD 0.21; 95% CI 0.20–0.23; P = 0.001), having visited a health care facility (RD 0.54; 95% CI 0.45–0.62; P = 0.001), and children aged under 5 years (RD 0.05; 95% CI 0.02–0.07; P = 0.001) or aged 10 years or older (RD 0.04; 95% CI 0.02–0.06; P = 0.001). A third of the children with COVID-19 were symptomatic with a higher proportion of fever in very young children and a higher proportion of cough in those between 10 and 18 years of age.

Estimating the spread of SARS-CoV-2 infection in communities is critical. We surveyed 2244 stratified random sample community members of the Gardena valley, a winter touristic area, amidst the first expansion phase of the COVID-19 pandemic in Europe. We measured agreement between Diasorin and Abbott serum bioassay outputs and the Abbott optimal discriminant threshold of serum neutralisation titres with recursive receiver operating characteristic curve. We analytically adjusted serum antibody tests for unbiased seroprevalence estimate and analysed the determinants of infection with non-response weighted multiple logistic regression. SARS-CoV-2 seroprevalence was 26.9% (95% CI 25.2–28.6) by June 2020. The bioassays had a modest agreement with each other. At a lower threshold than the manufacturer's recommended level, the Abbott assay reflected greater discrimination of serum neutralisation capacity. Seropositivity was associated with place and economic activity, not with sex or age. Symptoms like fever and weakness were age-dependent. SARS-CoV-2 mitigation strategies should account for context in high prevalence areas.

Our population-based study objectives were to describe characteristics and outcomes of Escherichia coli bloodstream infections (BSIs), and to evaluate factors associated with outcomes. We included incident E. coli BSIs from western interior residents (British Columbia, Canada; 04/2010–03/2020). We obtained data including patient demographics, location of onset, infection focus, Charlson comorbidity index (CCI), antimicrobial resistance, 30-day all-cause mortality and length of hospital stay (LOS). Using multivariable logistic regression models fitted with generalised estimating equations, we estimated factors associated with 30-day mortality and long post-infection LOS (>75th percentile). We identified 1080 incident E. coli BSIs in 1009 patients. The crude incidence and 30-day mortality rates were 59.1 BSIs and 6.8 deaths/100 000 person-years, respectively. The 30-day case fatality risk was 11.5%. Compared to community-acquired E. coli BSIs, either healthcare-associated or nosocomial cases had higher odds of 30-day mortality. Older cases, non-urogenital BSI foci and CCI ⩾ 3 had higher odds of 30-day mortality compared to younger cases, urogenital foci and CCI < 3. In patients that survived to discharge, those with extended-spectrum β-lactamase (ESBL)-producing E. coli BSIs, nosocomial BSIs, and CCI ⩾ 3 had higher odds of long post-infection LOS compared to those with non-ESBL-producing, community-acquired and healthcare-associated, and CCI < 3. There is a substantial disease burden from E. coli BSIs.

This study aimed to evaluate the performance of Cobas human papillomavirus (HPV) test in cervical cancer screening. A total of 3442 women aged ⩾20 years used Cobas HPV and hybrid capture 2 (HC2) tests were included in this study. Women with any positive result were examined by liquid-based cytology (LBC) test. Then subjects with abnormal LBC or positive Cobas HPV16/18 were further checked by colposcopy to observe the visible lesions to perform the pathological examination. Of these 3442 women, 328 cases were Cobas HPV positive, and the positive rate was 9.53% (95% confidence interval (CI) 8.50–10.53). The positive rate of HPV16, HPV18, and other 12 types of high-risk HPV were 1.54% (95% CI 1.12–1.95), 0.55% (95% CI 0.30–0.80), and 7.44% (95% CI 6.56–8.32), respectively. The coincidence rate of Cobas HPV test and HC2 test was 90% (95% CI 89.00–91.00; Kappa = 0.526) in the primary screening. Age had a non-linear relationship with Cobas HPV positive rate (χ2 = 4.240, P = 0.040) and HPV16/18 typing positive rate (χ2 = 6.610, P = 0.010). Compared with the LBC test, the Cobas HPV test had higher sensitivity when detecting patients with high cervical intraepithelial neoplasia (CIN2+ and CIN3+).

Estimating the case fatality ratio (CFR) for COVID-19 is an important aspect of public health. However, calculating CFR accurately is problematic early in a novel disease outbreak, due to uncertainties regarding the time course of disease and difficulties in diagnosis and reporting of cases. In this work, we present a simple method for calculating the CFR using only public case and death data over time by exploiting the correspondence between the time distributions of cases and deaths. The time-shifted distribution (TSD) analysis generates two parameters of interest: the delay time between reporting of cases and deaths and the CFR. These parameters converge reliably over time once the exponential growth phase has finished. Analysis is performed for early COVID-19 outbreaks in many countries, and we discuss corrections to CFR values using excess-death and seroprevalence data to estimate the infection fatality ratio (IFR). While CFR values range from 0.2% to 20% in different countries, estimates for IFR are mostly around 0.5–0.8% for countries that experienced moderate outbreaks and 1–3% for severe outbreaks. The simplicity and transparency of TSD analysis enhance its usefulness in characterizing a new disease as well as the state of the health and reporting systems.

We investigated whether household to clinic distance was a risk factor for death on tuberculosis (TB) treatment in Malawi. Using enhanced TB surveillance data, we recorded all TB treatment initiations and outcomes between 2015 and 2018. Household locations were geolocated, and distances were measured by a straight line or shortest road network. We constructed Bayesian multi-level logistic regression models to investigate associations between distance and case fatality. A total of 479/4397 (10.9%) TB patients died. Greater distance was associated with higher (odds ratio (OR) 1.07 per kilometre (km) increase, 95% credible interval (CI) 0.99–1.16) odds of death in TB patients registered at the referral hospital, but not among TB patients registered at primary clinics (OR 0.98 per km increase, 95% CI 0.92–1.03). Age (OR 1.02 per year increase, 95% CI 1.01–1.02) and HIV-positive status (OR 2.21, 95% CI 1.73–2.85) were also associated with higher odds of death. Model estimates were similar for both distance measures. Distance was a risk factor for death among patients at the main referral hospital, likely due to delayed diagnosis and suboptimal healthcare access. To reduce mortality, targeted community TB screening interventions for TB disease and HIV, and expansion of novel sensitive diagnostic tests are required.

Adenovirus pneumonia can occur in immunocompetent youths and adults. We conducted a retrospective analysis on five immunocompetent patients (aged ⩾14 years) with adenovirus pneumonia who visited our fever clinic between 1 February 2020 and 29 February 2020. The symptoms at clinical onset were fever, with cough and phlegm production either absent or appearing several days after disease onset. One patient with severe disease exhibited dyspnoea and a rapid development of respiratory failure. A subset of patients had concurrent gastrointestinal symptoms. The results of blood tests revealed normal leukocyte counts, decreased lymphocyte counts and increased C-reactive protein levels. The imaging findings resembled those of bacterial pneumonia, and pleural effusions were present in some cases. Most patients had a good prognosis with symptomatic treatment and supportive care. However, one patient with severe disease and a MuLBSTA score of >12 had a poor prognosis and ultimately died. Immunocompetent youths and adults may develop adenovirus pneumonia, and severe cases are at the risk of death. Since no effective treatments for adenovirus pneumonia are currently known, the early diagnosis and provision of symptomatic treatment and supportive care should be adopted to prevent the development and progression of severe disease.

We report a familial cluster of 24 individuals infected with severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The index case had a travel history and spent 24 days in the house before being tested and was asymptomatic. Physical overcrowding in the house provided a favourable environment for intra-cluster infection transmission. Restriction of movement of family members due to countrywide lockdown limited the spread in community. Among the infected, only four individuals developed symptoms. The complete genome sequences of SARS-CoV-2 was retrieved using next-generation sequencing from eight clinical samples which demonstrated a 99.99% similarity with reference to Wuhan strain and the phylogenetic analysis demonstrated a distinct cluster, lying in the B.6.6 pangolin lineage.