To assess the relationship between the neutrophil-to-lymphocyte ratio (NLR) and related parameters to the severity of coronavirus disease 2019 (COVID-19) symptoms. Clinical data from 38 COVID-19 patients who were diagnosed, treated and discharged from the Qishan Hospital in Yantai over the period from January to February 2020 were analysed. NLR and procalcitonin (PCT) were determined in the first and fourth weeks after their admission, along with the clinical characteristics and laboratory test results of these patients. Based on results as obtained on the first and fourth weeks after admission, five indices consisting of NLR, white blood cells, neutrophils, lymphocytes (LY) and monocytes (MON) were selected to generate receiver operating characteristic curves, while optimal cutoff values, sensitivities and specificities were obtained according to the Yuden index. Statistically significant differences in neutrophils, LY and the NLR were present in the severe vs. moderate COVID-19 group from the first to the fourth week of their hospitalisation. The cut-off value of NLR for predicting the severity of COVID-19 was 4.425, with a sensitivity of 0.855 and a specificity of 0.979. A statistically significant positive correlation was present between PCT and NLR in the severe group as determined within the first week of admission. NLR can serve as a predictor of COVID-19 disease severity as patients' progress from the first to the fourth week of their hospitalisation. The statistically significant positive correlation between levels of NLR and PCT in severe patients indicated that increases in NLR were accompanied with gradual increases in PCT.

The current investigation was conducted with the objective to develop an epidemiological case definition of possible severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) re-infection and assess its magnitude in India. The epidemiological case definition for SARS-CoV-2 re-infection was developed from literature review of data on viral kinetics. For achieving second objective, the individuals who satisfied the developed case definition for SARS-CoV-2 re-infection were contacted telephonically. Taking available evidence into consideration, re-infection with SARS-CoV-2 in our study was defined as any individual who tested positive for SARS-CoV-2 on two separate occasions by either molecular tests or rapid antigen test at an interval of at least 102 days with one negative molecular test in between. In this archive based, telephonic survey, 58 out of 1300 individuals (4.5%) fulfilled the above-mentioned definition; 38 individuals could be contacted with healthcare workers (HCWs) accounting for 31.6% of the cases. A large proportion of participants was asymptomatic and had higher Ct value during the first episode. While SARS-CoV-2 re-infection is still a rare phenomenon, there is a need for epidemiological definition of re-infection for establishing surveillance systems and this study contributes to such a goal.

Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) re-infection is an emerging concern and there is a need to define it. Therefore, working epidemiological case definition for re-infection was developed and its magnitude was explored via archive-based, telephonic survey. Re-infection with SARS-CoV-2 was defined as two positive tests at an interval of at least 102 days with one interim negative test. Thirty-eight of the 58 eligible patients could be contacted with 12 (31.6%) being HCWs. Majority of the participants were asymptomatic and had higher Ct value during their first episode. To conclude, a working epidemiological case definition of SARS-CoV-2 re-infection is important to strengthen surveillance. The present investigation contributes to this goal and records reinfection in 4.5% of SARS-CoV-2 infected individuals in India.

We investigated a large gastroenteritis outbreak that occurred in Northern Greece in 2019. A case was defined as anyone presenting with diarrhoea and/or vomiting from 24 January 2019 to 04 February 2019. We conducted a case-control study (CCS) using random selection of participants >16 years of age, residents of town X, who visited the health care centre between 25 and 28 January 2019. Moreover, we conducted a retrospective cohort study (CS) at the four elementary schools of the town. We collected clinical and water samples and the water supply system was inspected. In total, we recorded 638 cases (53% female; median age was 44 years (range 0–93)). Forty-eight cases and 52 controls participated in the CCS and 236 students in the CS. Both CCS and CS indicated tap water as the most likely source (OR 10, 95% CI 2.09–93.4, explaining 95.7% of cases; RR = 2.22, 95% CI 1.42–3.46, respectively). More than one pathogen was detected from stool samples of 6 of the 11 cases tested (norovirus, Campylobacter jejuni, Enterohemorrhagic E. coli (EHEC) and Enteropathogenic E. coli (EPEC)). Water samples, collected after ad-hoc chlorination, tested negative. Technical failures of the water tanks' status were identified. Our results suggested a waterborne outbreak. We recommended regular monitoring of the water supply system and immediate repair of technical failures.

Establishing accurate population size estimates (PSE) is important for prioritising and planning provision of services. Multiple source capture−recapture sampling method increases PSE accuracy and reliability. In August 2018, the three-source capture−recapture (3S-CRC) method was employed with a stringent assumption of sample independence to estimate the number of female sex workers (FSW) in Rwanda. Using Rwanda 2017 FSW hotspots mapping data, street and venue-based FSW were sampled at the sector level of each province and tagged with two unique gifts. Each capture was completed within one week to minimise FSW migration between provinces and recall bias. The three captures had 1042, 1204 and 1488 FSW. There were 111 FSW recaptured between captures 1 and 2; 237 between captures 2 and 3; 203 between captures 1 and 3 and 46 captured in all three. The PSE for street and venue-based FSW in Rwanda lies within 95% credible set: 8328–22 806 with corresponding median of 13 716 FSW. The 3S-CRC technique was low-cost and relatively easy to use for PSE in hard-to-reach populations. This estimate provides the basis for determining the denominators to assess HIV programme performance towards FSW and epidemic control and warrants further PSE for home- and cyber-based FSW in Rwanda.

Since 1993, reports on tuberculosis (TB) outbreaks have been collected in Japan; however, there has never been an overall analysis of these TB outbreaks. We aim to provide one here. The TB outbreak data were obtained from the Ministry of Health, Labour and Welfare and are described in terms of time, place and transmission site. The average number of TB cases and latent tuberculosis infection (LTBI) were compared by the transmission site. Some 605 TB outbreaks with 3491 TB cases were reported in 1993–2015 with an increasing trend (r = 0.45), during which time 728 777 TB cases were reported nationwide. On an average, TB outbreaks occurred more often in April to May (5.5 outbreaks per 2 months) than in December to January (3.4). The most common transmission sites were workplaces (n = 255), followed by health facilities (n = 144), schools (n = 60) and welfare facilities (n = 48). Psychiatric hospitals and nursing homes had the highest average number of TB cases per outbreak (8.5 each), whereas schools and prisons had the highest numbers of LTBI cases (29.1 and 38.9, respectively). Countries, particularly those that have resources to investigate TB outbreaks, should collect and analyse findings of TB outbreaks, as it informs surveillance systems and eventually strengthens general health systems.

In this paper, we present a method to estimate the risk of reopening of schools illustrated with the case of the State of São Paulo, Brazil. The model showed that, although no death of children would result from the reopening of the schools in the three cities analysed, the risk of asymptomatic and symptomatic cases and secondary cases among teachers, school staff and relatives of the children is not negligible. Although the epidemic hit different regions with different intensities, our model shows that, for regions where the incidence profile is similar to the cities analysed, the risk of reopening of schools is still too high. This in spite of the fact that incidences in these cities were declining in the period of the time considered. Therefore, although we cannot extend the result to the entire country, the overall conclusion is valid for regions with a declining incidence and it is even more valid for regions where incidence is increasing. We assumed a very conservative level of infection transmissibility of children of just 10% as that of adults. In spite of the very low level of transmissibility is assumed, the number of secondary cases caused by infected children among teachers, school staff and relatives varied from 2 to 85. It is, therefore, too soon to have any degree of confidence that reopening of schools before the advent of a vaccine is the right decision to take. The purpose of our model and simulations is to provide a method to estimate the risk of school reopening, although we are sure it could be applied as a guide to public health strategies.

Europe is in the midst of a COVID-19 epidemic and a number of non-pharmaceutical public health and social measures have been implemented, in order to contain the transmission of severe acute respiratory syndrome coronavirus 2. These measures are fundamental elements of the public health approach to controlling transmission but have proven not to be sufficiently effective. Therefore, the European Centre for Disease Prevention and Control has conducted an assessment of research gaps that can help inform policy decisions regarding the COVID-19 response. We have identified research gaps in the area of non-pharmaceutical measures, physical distancing, contact tracing, transmission, communication, mental health, seasonality and environment/climate, surveillance and behavioural aspects of COVID-19. This prioritisation exercise is a step towards the global efforts of developing a coherent research road map in coping with the current epidemic but also developing preparedness measures for the next unexpected epidemic.

Provision of high-quality care and ensuring retention of children on antiretroviral therapy (ART) are essential to reduce human immunodeficiency virus (HIV)-associated morbidity and mortality. Virological non-suppression (≥1000 viral copies/ml) is an indication of suboptimal HIV care and support. This retrospective cohort study included ART-naïve children who initiated first-line ART between July 2015 and August 2017 in Johannesburg and rural Mopani district. Of 2739 children started on ART, 29.5% (807/2739) were lost to care at the point of analysis in August 2018. Among retained children, overall virological non-suppression was 30.2% (469/1554). Virological non-suppression was associated with higher loss to care 30.3% (229/755) compared with suppressed children (9.7%, 136/1399, P < 0.001). Receiving treatment in Mopani was associated with virological non-suppression in children under 5 years (adjusted odds ratio (aOR) 1.7 (95% confidence interval (CI) 1.1–2.4), 5–9 years (aOR 1.8 (1.1–3.0)) and 10–14 years (aOR 1.9 (1.2–2.8)). Virological non-suppression was associated with lower CD4 count in children 5–9 years (aOR 2.1 (1.1–4.1)) and 10–14 years (aOR 2.1 (1.2–3.8)). Additional factors included a shorter time on ART (<5 years aOR 1.8–3.7 (1.3–8.2)), and male gender (5–9 years, aOR1.5 (1.01–2.3)), and receiving cotrimoxazole prophylaxis (10–14 years aOR 2.0 (1.2–3.6)). In conclusion, virological non-suppression is a factor of subsequent programme loss in both regions, and factors affecting the quality of care need to be addressed to achieve the third UNAIDS 90 in paediatric HIV.

Toxoplasma gondii (T. gondii) is an important human disease-causing parasite. In the USA, T. gondii infects >10% of the population, accrues economic losses of US$3.6 billion/year, and ranks as the second leading culprit of foodborne illness-related fatalities. We assessed toxoplasmosis risk among the Old Order Amish, a mostly homogenous population with a high prevalence of T. gondii seropositivity, using a questionnaire focusing on food consumption/preparation behaviours and environmental risk factors. Analyses were conducted using multiple logistic regression. Consuming raw meat, rare meat, or unpasteurised cow or goat milk products was associated with increased odds of seropositivity (unadjusted Odds Ratios: 2.192, 1.613, and 1.718 , respectively). In separate models by sex, consuming raw meat, or consuming unpasteurised cow or goat milk products, was associated with increased odds of seropositivity among women; washing hands after touching meat with decreased odds of seropositivity among women (adjusted OR (AOR): 0.462); and cleaning cat litterbox with increased odds of seropositivity among men (AOR: 5.241). This is the first study to assess associations between behavioural and environmental risk factors and T. gondii seropositivity in a US population with high seroprevalence for T. gondii. Our study emphasises the importance of proper food safety behaviours to avoid the risk of infection.

Invasive meningococcal disease has high morbidity and mortality, with infants and young children among those at greatest risk. This phase III, open-label, randomised study in toddlers aged 12–23 months evaluated the immunogenicity and safety of meningococcal tetanus toxoid-conjugate vaccine (MenACYW-TT), a tetanus toxoid conjugated vaccine against meningococcal serogroups A, C, W and Y, when coadministered with paediatric vaccines (measles, mumps and rubella [MMR]; varicella [V]; 6-in-1 combination vaccine against diphtheria, tetanus, pertussis, polio, hepatitis B and Haemophilus influenzae type b [DTaP-IPV-HepB-Hib] and pneumococcal conjugate vaccine [PCV13])(NCT03205371). Immunogenicity to each meningococcal serogroup was assessed by serum bactericidal antibody assay using human complement (hSBA). Vaccine safety profiles were described up to 30 days post-vaccination. A total of 1183 participants were enrolled. The proportion with seroprotection (hSBA ≥1:8) to each meningococcal serogroup at Day 30 was comparable between the MenACYW-TT and MenACYW-TT + MMR + V groups (≥92 and ≥96%, respectively), between the MenACYW-TT and MenACYW-TT + DTaP-IPV-HepB-Hib groups (≥90% for both) and between the MenACYW-TT and MenACYW-TT + PCV13 groups (≥91 and ≥84%, respectively). The safety profiles of MenACYW-TT, and MMR + V, DTaP-IPV-HepB-Hib, and PCV13, with or without MenACYW-TT, were generally comparable. Coadministration of MenACYW-TT with paediatric vaccines in toddlers had no clinically relevant effect on the immunogenicity and safety of any of the vaccines.

An outbreak of SARS-CoV2 infection in a Barcelona prison was studied. One hundred and forty-eight inmates and 36 prison staff were evaluated by rt-PCR, and 24.1% (40 prisoners, two health workers and four non-health workers) tested positive. In all, 94.8% of cases were asymptomatic. The inmates were isolated in prison module 4, which was converted into an emergency COVID unit. There were no deaths. Generalised screening and the isolation and evaluation of the people infected were key measures. Symptom-based surveillance must be supplemented by rapid contact-based monitoring in order to avoid asymptomatic spread among prisoners and the community at large.

Case identification is an ongoing issue for the COVID-19 epidemic, in particular for outpatient care where physicians must decide which patients to prioritise for further testing. This paper reports tools to classify patients based on symptom profiles based on 236 severe acute respiratory syndrome coronavirus 2 positive cases and 564 controls, accounting for the time course of illness using generalised multivariate logistic regression. Significant symptoms included abdominal pain, cough, diarrhoea, fever, headache, muscle ache, runny nose, sore throat, temperature between 37.5 and 37.9 °C and temperature above 38 °C, but their importance varied by day of illness at assessment. With a high percentile threshold for specificity at 0.95, the baseline model had reasonable sensitivity at 0.67. To further evaluate accuracy of model predictions, leave-one-out cross-validation confirmed high classification accuracy with an area under the receiver operating characteristic curve of 0.92. For the baseline model, sensitivity decreased to 0.56. External validation datasets reported similar result. Our study provides a tool to discern COVID-19 patients from controls using symptoms and day from illness onset with good predictive performance. It could be considered as a framework to complement laboratory testing in order to differentiate COVID-19 from other patients presenting with acute symptoms in outpatient care.

The global outbreak of coronavirus disease 2019 (COVID-19) is greatly threatening the public health in the world. We reconstructed global transmissions and potential demographic expansions of severe acute respiratory syndrome coronavirus 2 based on genomic information. We found that intercontinental transmissions were rare in January and early February but drastically increased since late February. After world-wide implements of travel restrictions, the transmission frequencies decreased to a low level in April. We identified a total of 88 potential demographic expansions over the world based on the star-radiative networks and 75 of them were found in Europe and North America. The expansion numbers peaked in March and quickly dropped since April. These findings are highly concordant with epidemic reports and modelling results and highlight the significance of quarantine validity on the global spread of COVID-19. Our analyses indicate that the travel restrictions and social distancing measures are effective in containing the spread of COVID-19.

The present study attempted to analyse human papillomavirus (HPV) genotype distribution and its association with cervical cytology results in women in western China. The present retrospective analysis was performed in 1089 female outpatients with a positive HPV test result who had undergone a cervical cytology test at the gynaecological clinic, West China Second Hospital, Sichuan University, China, between January 2014 and December 2016. Of the 1089 patients with HPV infection, multiple HPV genotypes were detected in 220 patients (20.20%). Among the 1368 HPV genotypes detected, 1145 (83.70%) were high-risk subtypes. The most common genotypes were HPV-52 (18.64%), HPV-16 (16.59%), HPV-58 (13.23%), HPV-18 (6.80%), HPV-56 (5.56%) and HPV-59 (5.56%). Cervical cytology revealed abnormal cells in 430 (39.49%) patients. The most common diagnoses were atypical squamous cells of undetermined significance (ASC-US; 236 cases, 54.88%), low-grade squamous intraepithelial lesions (LSIL; 151 cases, 35.12%), high-grade squamous intraepithelial lesions (HSIL; 63 cases, 14.65%) and atypical glandular cells (AGC; 21 cases, 4.88%). HPV-66 was significantly associated (P = 0.037) with ASC; HPV-52 and HPV-56 were significantly associated with LSIL (P = 0.009 and 0.026, respectively); HPV-16 (P < 0.001), HPV-33 (P = 0.014) and HPV-58 (P = 0.003) were significantly associated with HSIL; and HPV-16 (P = 0.005) was significantly associated with AGC. HPV-16, HPV-52 and HPV-58 are associated with different diagnoses in patients with positive cervical cytological findings.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pandemic. Prevention and control strategies require an improved understanding of SARS-CoV-2 dynamics. We did a rapid review of the literature on SARS-CoV-2 viral dynamics with a focus on infective dose. We sought comparisons of SARS-CoV-2 with other respiratory viruses including SARS-CoV-1 and Middle East respiratory syndrome coronavirus. We examined laboratory animal and human studies. The literature on infective dose, transmission and routes of exposure was limited specially in humans, and varying endpoints were used for measurement of infection. Despite variability in animal studies, there was some evidence that increased dose at exposure correlated with higher viral load clinically, and severe symptoms. Higher viral load measures did not reflect coronavirus disease 2019 severity. Aerosol transmission seemed to raise the risk of more severe respiratory complications in animals. An accurate quantitative estimate of the infective dose of SARS-CoV-2 in humans is not currently feasible and needs further research. Our review suggests that it is small, perhaps about 100 particles. Further work is also required on the relationship between routes of transmission, infective dose, co-infection and outcomes.

European orthohantaviruses (Puumala orthohantavirus (PUUV); Dobrava-Belgrade orthohantavirus (DOBV), genotype Kurkino; Tula orthohantavirus (TULV)), and Leptospira spp. are small mammal-associated zoonotic pathogens that cause diseases with potentially similar symptoms in humans. We investigated the frequency of Leptospira spp. and hantavirus single and double infections in small mammals from 22 sites in Thuringia, central Germany, during 2017. TULV infections were detected at 18 of 22 sites (mean prevalence 13.8%, 93/674). PUUV infections were detected at four of 22 sites (mean prevalence 1.5%, 7/471), and respective PUUV sequences formed a novel phylogenetic clade, but DOBV infections were not detected at all. Leptospira infections were detected at 21 of 22 sites with the highest overall prevalence in field voles (Microtus agrestis) with 54.5% (6/11) and common voles (Microtus arvalis) with 30.3% (205/676). Leptospira–hantavirus coinfections were found in 6.6% (44/671) of common voles but only in two of 395 bank voles. TULV and Leptospira coinfection probability in common voles was driven by individual (age) and population-level factors. Coinfections seemed to be particularly associated with sites where Leptospira spp. prevalence exceeded 35%. Future investigations should evaluate public health consequences of this strong spatial clustering of coinfections.

Monitoring and evaluation (M&E) is an essential component of public health emergency response. In the WHO African region (WHO AFRO), over 100 events are detected and responded to annually. Here we discuss the development of the M&E for COVID-19 that established a set of regional and country indicators for tracking the COVID-19 pandemic and response measures. An interdisciplinary task force used the 11 pillars of strategic preparedness and response to define a set of inputs, outputs, outcomes and impact indicators that were used to closely monitor and evaluate progress in the evolving COVID-19 response, with each pillar tailored to specific country needs. M&E data were submitted electronically and informed country profiles, detailed epidemiological reports, and situation reports. Further, 10 selected key performance indicators were tracked to monitor country progress through a bi-weekly progress scoring tool used to identify priority countries in need of additional support from WHO AFRO. Investment in M&E of health emergencies should be an integral part of efforts to strengthen national, regional and global capacities for early detection and response to threats to public health security. The development of an adaptable M&E framework for health emergencies must draw from the lessons learned throughout the COVID-19 response.

Serology data are an increasingly important tool in malaria surveillance, especially in low transmission settings where the estimation of parasite-based indicators is often problematic. Existing methods rely on the use of thresholds to identify seropositive individuals and estimate transmission intensity, while making assumptions about the temporal dynamics of malaria transmission that are rarely questioned. Here, we present a novel threshold-free approach for the analysis of malaria serology data which avoids dichotomization of continuous antibody measurements and allows us to model changes in the antibody distribution across age in a more flexible way. The proposed unified mechanistic model combines the properties of reversible catalytic and antibody acquisition models, and allows for temporally varying boosting and seroconversion rates. Additionally, as an alternative to the unified mechanistic model, we also propose an empirical approach to analysis where modelling of the age-dependency is informed by the data rather than biological assumptions. Using serology data from Western Kenya, we demonstrate both the usefulness and limitations of the novel modelling framework.

Brazil ranks second in the number of confirmed cases of COVID-19 worldwide. In spite of this, coping measures differ throughout the national territory, as does the disease's impact on the population. This cross-sectional observational study, with 59 695 cases of COVID-19 registered in the state of Alagoas between March and August 2020, analysed clinical-epidemiological variables, incidence rate, mortality rate, case fatality rate (CFR) and the social indicators municipal human development index (MHDI) and social vulnerability index (SVI). Moran statistics and regression models were applied. Logistic regression analysis was applied to determine the predictors of death. The incidence rate was 1788.7/100 000 inhabitants; mortality rate was 48.0/100 000 and CFR was 2.7%. The highest incidence rates were observed in municipalities with better human development (overall MHDI (I = 0.1668; p = 0.002), education MHDI (I = 0.1649; p = 0.002) and income MHDI (I = 0.1880; p = 0.005)) and higher social vulnerability (overall SVI (I = 0.0599; p = 0.033)). CFR was associated with higher social vulnerability (SVI human capital (I = 0.0858; p = 0.004) and SVI urban infrastructure (I = 0.0985; p = 0.040)). Of the analysed cases, 55.4% were female; 2/3 were Black or Brown and the median age was 41 years. Among deaths, most were male (919; 57.4%) and elderly (1171; 73.1%). The predictors of death were male sex, advanced age and the presence of comorbidities. In Alagoas, Brazil, the disease has undergone a process of interiorisation and caused more deaths in poorer municipalities. The presence of comorbidities and advanced age were predictors of death.