Prioritizing COVID-19 vaccine allocation in resource poor settings: Towards an Artificial Intelligence-enabled and Geospatial-assisted decision support framework.

OBJECTIVES: To propose a novel framework for COVID-19 vaccine allocation based on three components of Vulnerability, Vaccination, and Values (3Vs). METHODS: A combination of geospatial data analysis and artificial intelligence methods for evaluating vulnerability factors at the local level and allocate vaccines according to a dynamic mechanism for updating vulnerability and vaccine uptake. RESULTS: A novel approach is introduced including (I) Vulnerability data collection (including country-specific data on demographic, socioeconomic, epidemiological, healthcare, and environmental factors), (II) Vaccination prioritization through estimation of a unique Vulnerability Index composed of a range of factors selected and weighed through an Artificial Intelligence (AI-enabled) expert elicitation survey and scientific literature screening, and (III) Values consideration by identification of the most effective GIS-assisted allocation of vaccines at the local level, considering context-specific constraints and objectives. CONCLUSIONS: We showcase the performance of the 3Vs strategy by comparing it to the actual vaccination rollout in Kenya. We show that under the current strategy, socially vulnerable individuals comprise only 45% of all vaccinated people in Kenya while if the 3Vs strategy was implemented, this group would be the first to receive vaccines.

Determinants of influenza and pneumococcal vaccine uptake among preschool children in Singapore.

Young children are at increased risk of severe illness from influenza and pneumococcal infections. The World Health Organization (WHO) recommends vaccination with influenza and pneumococcal conjugate vaccine (PCV). However, in Singapore, vaccine uptake remains suboptimal relative to other routine childhood immunisations. Limited information exists regarding determinants of influenza and pneumococcal vaccine uptake in children. We estimated vaccine uptake and investigated factors associated with influenza and pneumococcal vaccination status by age group using data from a cohort study on acute respiratory infections in children attending preschools in Singapore. We recruited children aged two to six years at 24 participating preschools from June 2017 to July 2018. We determined the proportion of children immunised with influenza vaccine and PCV, and investigated socio-demographic factors associated with vaccine uptake using logistic regression models. Among 505 children, 77.5% were of Chinese ethnicity, and 53.1% were male. History of influenza vaccination was 27.5% of which 11.7% had been vaccinated within the past 12 months. In multivariable analyses, factors associated with influenza vaccine uptake were 'children living in landed property' (aOR = 2.25, 95% CI [1.07-4.67]) and 'history of hospitalisation due to cough' (aOR = 1.85, 95% CI [1.00-3.36]). Nearly three-quarters of participants (70.7% 95%CI: [66.6-74.5]) reported prior PCV vaccination. PCV uptake was higher for younger children. 'Higher parental education' (OR = 2.83, 95% CI [1.51,5.32]), 'household income' (OR = 1.26, 95% CI [1.08,1.48]) and 'smokers in household' (OR = 0.48, 95% CI [0.31,0.74]) were significantly associated with PCV uptake in univariable analyses. Only 'smokers in household' remained significantly associated with PCV uptake (aOR = 0.55, 95% CI [0.33,0.91]) in the adjusted model. Our results indicate that episodes of severe respiratory illness are a cue to influenza vaccination suggesting that doctors are more likely to recommend influenza vaccines to high-risk children. For PCV, our findings suggest overall greater awareness and education on the benefit of PCV vaccination is required.

Adolescent girls' recommendations for the design of a human papillomavirus vaccination program in Sindh, Pakistan: a qualitative study.

PURPOSE: Vaccination of adolescent girls against human papillomavirus (HPV) significantly reduces the incidence of cervical cancer. HPV vaccines are available in Pakistan but plans to develop HPV vaccination program are at a nascent stage. We conducted a formative study to explore adolescent girls' knowledge and perspectives on HPV and cervical cancer and collect their recommendations for implementing an HPV vaccination program in their community. METHODS: Using qualitative exploratory study design, we conducted four focus group discussions (FGDs) with 12 adolescent girls per group in District West, Karachi. We recruited unmarried girls aged 16-19 years from schools and community settings between May-December 2020. Data analysis was done using NVivo. RESULTS: Overall, participants displayed a positive attitude toward HPV vaccine. However, they were unfamiliar with basic concepts related to female reproductive health. Female relatives were indicated as girls' preferred point of contact for discussions on HPV and cervical cancer, but fathers were portrayed as decision-making authority on vaccination. Participants indicated vaccine hesitancy among parents may affect HPV vaccination uptake. Girls suggested individual household visits and community-based camps as strategies for successful implementation of HPV vaccination program. A solid foundation of trust between girls' families, program managers, and other stakeholders emerged as a key asset for the program's success. CONCLUSION: Adolescent girls' suggestions of informing key decision-makers in the family (particularly fathers) of the benefits of HPV vaccination, establishing trust with vaccine providers, and increasing accessibility of vaccinations should be explored for successful implementation of an HPV vaccination program in Pakistan.

Population anxiety and positive behaviour change during the COVID-19 epidemic: Cross-sectional surveys in Singapore, China and Italy.

BACKGROUND: On 31 December 2019, an epidemic of pneumonia of unknown aetiology was first reported in the city of Wuhan, Hubei Province, People's Republic of China. A rapidly progressing epidemic of COVID-19 ensued within China, with multiple exportations to other countries. We aimed to measure perceptions and responses towards COVID-19 in three countries to understand how population-level anxiety can be mitigated in the early phases of a pandemic. METHODS: Between February and March 2020, we conducted online surveys in Singapore, China and Italy with a total of 4505 respondents to measure respondents' knowledge, perceptions, anxiety and behaviours towards the COVID-19 epidemic, and identified factors associated with lower anxiety and more positive behavioural responses. RESULTS: Respondents reported high awareness of COVID-19 and its accompanying symptoms, comparable information-seeking habits and similarly high levels of information sufficiency, adherence to and acceptance of public health control measures. Higher self-efficacy was associated with lower anxiety levels in all three countries, while willingness to comply with restrictive measures and greater information sufficiency were associated with more positive behavioural changes to reduce spread of infection. CONCLUSION: Population-level anxiety and behavioural responses to an outbreak can be influenced by information provided. This should be used to inform future outbreak preparedness plans, taking into account the importance of increasing population-level self-efficacy and information sufficiency to reduce anxiety and promote positive behavioural changes.

Acceptance and feasibility of school-based seasonal influenza vaccination in Singapore: A qualitative study.

INTRODUCTION: Influenza is a major cause of disease in children. School-based seasonal influenza vaccination can be a cost-effective tool to improve vaccine uptake among children, and can bring substantial health and economic benefits to the broader community. The acceptance and feasibility of school-based influenza vaccination are likely to be highly context-specific, but limited data exist from tropical settings with year-round influenza transmission. We conducted a qualitative study to assess acceptability and feasibility of a school-based seasonal influenza vaccination programme in Singapore. METHODS: We conducted qualitative in-depth interviews with key stakeholders, including healthcare professionals, representatives of relevant ministries, preschool principals and parents to understand their perspectives on a proposed school-based seasonal influenza vaccination programme. Interviews were transcribed verbatim and analysed using thematic analysis. RESULTS: We conducted 40 interviews. Although preschool-aged children are currently the recommended age group for vaccination, stakeholders suggested introducing the programme in primary and/or secondary schools, where existing vaccination infrastructure would facilitate delivery. However, more comprehensive evidence on the local influenza burden and transmission patterns among children is required to develop an evidence-based, locally relevant rationale for a school-based vaccination programme and effectively engage policy-makers, school staff, and parents. Extensive, age-appropriate public education and awareness campaigns would increase the acceptability of the programme among stakeholders. Stakeholders indicated that an opt-out programme with free or subsidised vaccination would be the most likely to achieve high vaccine coverage and make access to vaccination more equitable. CONCLUSIONS: Overall, participants were supportive of a free or subsidised school-based influenza vaccination programme in primary and/or secondary schools, although children in this age group are not currently a recommended group for vaccination. However, a better informed, evidence-based rationale to estimate the programme's impact in Singapore is currently lacking. Extensive, age-appropriate public education and awareness campaigns will help ensure full support across key stakeholder groups.

Coverage and determinants of influenza vaccine among pregnant women: a cross-sectional study.

BACKGROUND: Pregnant women are at increased risk of influenza-related complications. The World Health Organisation recommends influenza vaccination to this high-risk population as highest priority. However, achieving high influenza vaccine coverage among pregnant women remains challenging. We conducted a cross-sectional survey to estimate the coverage and determinants of influenza vaccination among pregnant women in Singapore. METHODS: Between September and November 2017, pregnant women aged ≥21 years were recruited at two public hospitals in Singapore. Participants completed an anonymous, self-administered online questionnaire assessing participants' influenza vaccination uptake, knowledge of and attitudes towards influenza and the influenza vaccine, vaccination history, willingness to pay for the influenza vaccine, and external cues to vaccination. We estimated vaccine coverage and used multivariable Poisson models to identify factors associated with vaccine uptake. RESULTS: Response rate was 61% (500/814). Only 49 women (9.8, 95% Confidence Interval (CI): 7.3-12.7%) reported receiving the vaccine during their current pregnancy. A few misconceptions were identified among participants, such as the belief that influenza can be treated with antibiotics. The most frequent reason for not being vaccinated was lack of recommendation. Women who were personally advised to get vaccinated against influenza during pregnancy were 7 times more likely to be vaccinated (prevalence ratio (PR) = 7.11; 95% CI: 3.92-12.90). However, only 12% of women were personally advised to get vaccinated. Other factors associated with vaccine uptake were vaccination during a previous pregnancy (PR = 2.51; 95% CI: 1.54-4.11), having insurance to cover the cost of the vaccine (PR = 2.32; 95% CI: 1.43-3.76), and higher vaccine confidence (PR = 1.62; 95% CI: 1.30-2.01). CONCLUSIONS: Influenza vaccination uptake among pregnant women in Singapore is low. There is considerable scope for improving vaccination coverage in this high-risk population through vaccination recommendations from healthcare professionals, and public communication targeting common misconceptions about influenza and influenza vaccines.

Epidemiology and Transmission of Respiratory Infections in Thai Army Recruits: A Prospective Cohort Study.

Military recruits are at high risk of respiratory infections. However, limited data exist on military populations in tropical settings, where the epidemiology of respiratory infections differs substantially from temperate settings. We enrolled recruits undertaking a 10-week military training at two Royal Thai Army barracks between May 2014 and July 2015. We used a multiplex respiratory panel to analyze nose and throat swabs collected at the start and end of the training period, and from participants experiencing respiratory symptoms during follow-up. Paired sera were tested for influenza seroconversion using a hemagglutinin inhibition assay. Overall rates of upper respiratory illness and influenza-like illness were 3.1 and 2.0 episodes per 100 person-weeks, respectively. A pathogen was detected in 96% of samples. The most commonly detected microbes were Haemophilus influenzae type B (62.7%) or non-type B (58.2%) and rhinovirus (22.4%). At baseline, bacterial colonization was high and included H. influenzae type B (82.3%), H. influenzae non-type B (31.5%), Klebsiella pneumoniae (14.6%), Staphylococcus aureus (8.5%), and Streptococcus pneumoniae (8.5%). At the end of follow-up, colonization with H. influenzae non-type B had increased to 74.1%, and S. pneumoniae to 33.6%. In the serology subset, the rate of influenza infection was 3.4 per 100 person-months; 58% of influenza infections resulted in clinical disease. Our study provides key data on the epidemiology and transmission of respiratory pathogens in tropical settings. Our results emphasize the need for improved infection prevention and control in military environments, given the high burden of illness and potential for intense transmission of respiratory pathogens.

Association between semi-quantitative microbial load and respiratory symptoms among Thai military recruits: a prospective cohort study.

BACKGROUND: Multiplex real-time polymerase chain reaction assays have improved diagnostic sensitivity for a wide range of pathogens. However, co-detection of multiple agents and bacterial colonization make it difficult to distinguish between asymptomatic infection or illness aetiology. We assessed whether semi-quantitative microbial load data can differentiate between symptomatic and asymptomatic states for common respiratory pathogens. METHODS: We obtained throat and nasal swab samples from military trainees at two Thai Army barracks. Specimens were collected at the start and end of 10-week training periods (non-acute samples), and from individuals who developed upper respiratory tract infection during training (acute samples). We analysed the samples using a commercial multiplex respiratory panel comprising 33 bacterial, viral and fungal targets. We used random effects tobit models to compare cycle threshold (Ct) value distributions from non-acute and acute samples. RESULTS: We analysed 341 non-acute and 145 acute swab samples from 274 participants. Haemophilus influenzae type B was the most commonly detected microbe (77.4% of non-acute and 64.8% of acute samples). In acute samples, nine specific microbe pairs were detected more frequently than expected by chance. Regression models indicated significantly lower microbial load in non-acute relative to acute samples for H. influenzae non-type B, Streptococcus pneumoniae and rhinovirus, although it was not possible to identify a Ct-value threshold indicating causal etiology for any of these organisms. CONCLUSIONS: Semi-quantitative measures of microbial concentration did not reliably differentiate between illness and asymptomatic colonization, suggesting that clinical symptoms may not always be directly related to microbial load for common respiratory infections.

Effectiveness of Masks and Respirators Against Respiratory Infections in Healthcare Workers: A Systematic Review and Meta-Analysis.

This systematic review and meta-analysis quantified the protective effect of facemasks and respirators against respiratory infections among healthcare workers. Relevant articles were retrieved from Pubmed, EMBASE, and Web of Science. Meta-analyses were conducted to calculate pooled estimates. Meta-analysis of randomized controlled trials (RCTs) indicated a protective effect of masks and respirators against clinical respiratory illness (CRI) (risk ratio [RR] = 0.59; 95% confidence interval [CI]:0.46-0.77) and influenza-like illness (ILI) (RR = 0.34; 95% CI:0.14-0.82). Compared to masks, N95 respirators conferred superior protection against CRI (RR = 0.47; 95% CI: 0.36-0.62) and laboratory-confirmed bacterial (RR = 0.46; 95% CI: 0.34-0.62), but not viral infections or ILI. Meta-analysis of observational studies provided evidence of a protective effect of masks (OR = 0.13; 95% CI: 0.03-0.62) and respirators (OR = 0.12; 95% CI: 0.06-0.26) against severe acute respiratory syndrome (SARS). This systematic review and meta-analysis supports the use of respiratory protection. However, the existing evidence is sparse and findings are inconsistent within and across studies. Multicentre RCTs with standardized protocols conducted outside epidemic periods would help to clarify the circumstances under which the use of masks or respirators is most warranted.

High Sporozoite Antibody Titers in Conjunction with Microscopically Detectable Blood Infection Display Signatures of Protection from Clinical Malaria.

Immunoepidemiological studies typically reveal slow, age-dependent acquisition of immune responses against Plasmodium falciparum sporozoites. Naturally acquired immunity against preerythrocytic stages is considered inadequate to confer protection against clinical malaria. To explore previously unrecognized antisporozoite responses, we measured serum levels of naturally acquired antibodies to whole Plasmodium falciparum sporozoites (Pfspz) and the immunodominant (NANP)5 repeats of the major sporozoite surface protein, circumsporozoite protein, in a well-characterized Kenyan cohort. Sera were sampled at the start of the malaria transmission season, and all subjects were prospectively monitored for uncomplicated clinical malaria in the ensuing 6 months. We used Kaplan-Meier analysis and multivariable regression to investigate the association of antisporozoite immunity with incidence of clinical malaria. Although naturally acquired humoral responses against Pfspz and (NANP)5 were strongly correlated (p < 0.0001), 37% of Pfspz responders did not recognize (NANP)5. The prevalence and magnitude of antisporozoite responses increased with age, although some high Pfspz responders were identified among children. Survival analysis revealed a reduced risk of and increased time to first or only episode of clinical malaria among Pfspz or (NANP)5 responders carrying microscopically detectable Plasmodium falciparum (Pf) parasitemia at the start of the transmission season (p < 0.03). Our Cox regression interaction models indicated a potentially protective interaction between high anti-Pfspz (p = 0.002) or anti-(NANP)5 (p = 0.001) antibody levels and microscopically detectable Pf parasitemia on the risk of subsequent clinical malaria. Our findings indicate that robust antisporozoite immune responses can be naturally acquired already at an early age. A potentially protective role of high levels of anti-Pfspz antibodies against clinical episodes of uncomplicated malaria was detected, suggesting that antibody-mediated preerythrocytic immunity might indeed contribute to protection in nature.

The Plasmodium protein P113 supports efficient sporozoite to liver stage conversion in vivo.

Invasive stages of Plasmodium parasites possess distinct integral and peripheral membrane proteins that mediate host cell attachment and invasion. P113 is an abundant protein in detergent-resistant high molecular weight complexes in Plasmodium schizonts, but is unusual since expression extends to gametocytes and sporozoites. In this study, we tested whether P113 performs important functions for parasite propagation in Plasmodium berghei. We show that pre-erythrocytic expression of P113 displays key signatures of upregulated in infectious sporozoites (UIS) genes, including control by the liver stage master regulator SLARP. Targeted gene deletion resulted in viable blood stage parasites that displayed no signs of blood stage growth defects. p113(-) parasites propagated normally through the life cycle until mature sporozoites, but displayed defects during natural sporozoite transmission, leading to a delay to patency in infected animals. By comparative in vitro and in vivo analysis of pre-erythrocytic development and using a xeno-diagnostic test we show that ablation of P113 results in lower sporozoite to liver stage conversion and, as a consequence, reduced merozoite output in vivo, without delaying liver stage development. We conclude that p113 is dispensable for Plasmodium life cycle progression and plays auxiliary roles during pre-erythrocytic development.

A protocol for the identification of protein-protein interactions based on 15N metabolic labeling, immunoprecipitation, quantitative mass spectrometry and affinity modulation.

Protein-protein interactions are fundamental for many biological processes in the cell. Therefore, their characterization plays an important role in current research and a plethora of methods for their investigation is available. Protein-protein interactions often are highly dynamic and may depend on subcellular localization, post-translational modifications and the local protein environment. Therefore, they should be investigated in their natural environment, for which co-immunoprecipitation approaches are the method of choice. Co-precipitated interaction partners are identified either by immunoblotting in a targeted approach, or by mass spectrometry (LC-MS/MS) in an untargeted way. The latter strategy often is adversely affected by a large number of false positive discoveries, mainly derived from the high sensitivity of modern mass spectrometers that confidently detect traces of unspecifically precipitating proteins. A recent approach to overcome this problem is based on the idea that reduced amounts of specific interaction partners will co-precipitate with a given target protein whose cellular concentration is reduced by RNAi, while the amounts of unspecifically precipitating proteins should be unaffected. This approach, termed QUICK for QUantitative Immunoprecipitation Combined with Knockdown, employs Stable Isotope Labeling of Amino acids in Cell culture (SILAC) and MS to quantify the amounts of proteins immunoprecipitated from wild-type and knock-down strains. Proteins found in a 1:1 ratio can be considered as contaminants, those enriched in precipitates from the wild type as specific interaction partners of the target protein. Although innovative, QUICK bears some limitations: first, SILAC is cost-intensive and limited to organisms that ideally are auxotrophic for arginine and/or lysine. Moreover, when heavy arginine is fed, arginine-to-proline interconversion results in additional mass shifts for each proline in a peptide and slightly dilutes heavy with light arginine, which makes quantification more tedious and less accurate. Second, QUICK requires that antibodies are titrated such that they do not become saturated with target protein in extracts from knock-down mutants. Here we introduce a modified QUICK protocol which overcomes the abovementioned limitations of QUICK by replacing SILAC for (15)N metabolic labeling and by replacing RNAi-mediated knock-down for affinity modulation of protein-protein interactions. We demonstrate the applicability of this protocol using the unicellular green alga Chlamydomonas reinhardtii as model organism and the chloroplast HSP70B chaperone as target protein (Figure 1). HSP70s are known to interact with specific co-chaperones and substrates only in the ADP state. We exploit this property as a means to verify the specific interaction of HSP70B with its nucleotide exchange factor CGE1.

Naturally acquired immune responses against Plasmodium falciparum sporozoites and liver infection.

Malaria is a vector-borne infectious disease caused by infection with eukaryotic pathogens termed Plasmodium. Epidemiological hallmarks of Plasmodium falciparum malaria are continuous re-infections, over which time the human host may experience several clinical malaria episodes, slow acquisition of partial protection against infection, and its partial decay upon migration away from endemic regions. To overcome the exposure-dependence of naturally acquired immunity and rapidly elicit robust long-term protection are ultimate goals of malaria vaccine development. However, cellular and molecular correlates of naturally acquired immunity against either parasite infection or malarial disease remain elusive. Sero-epidemiological studies consistently suggest that acquired immunity is primarily directed against the asexual blood stages. Here, we review available data on the relationship between immune responses against the Anopheles mosquito-transmitted sporozoite and exo-erythrocytic liver stages and the incidence of malaria. We discuss current limitations and research opportunities, including the identification of additional sporozoite antigens and the use of systematic immune profiling and functional studies in longitudinal cohorts to look for pre-erythrocytic signatures of naturally acquired immunity.