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Special Issue "Coronavirus and Influenza Epidemiology. Coronavirus Vaccine Studies and Influenza Vaccine Effectiveness. New Challenges in Analysis and Reporting"

A special issue of International Journal of Environmental Research and Public Health (ISSN 1660-4601). This special issue belongs to the section "Infectious Disease Epidemiology".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 24008

Special Issue Editors

Dr. Joan Puig-Barberà
E-Mail Website
Guest Editor
Vaccines Research Area FISABIO, 46020 Valencia, Spain
Interests: hospitalization; influenza; human, vaccination; community-acquired infections; epidemiology; immunology, virology; prevention & control; respiratory syncytial viruses; population surveillance; reverse transcriptase polymerase chain reaction
Special Issues, Collections and Topics in MDPI journals
Dr. George Kassianos
E-Mail Website
Guest Editor
1. President British Global & Travel Health Association, London, UK
2. Board Member European Scientific Working Group on Influenza (ESWI), London, UK
3. National Immunisation Lead Royal College of General Practitioners, London, UK
Interests: immunisations; cardiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the coming years, we will face challenges in applying new methods to estimate and report acute respiratory viruses epidemiology and vaccine effectiveness to provide robust estimates that better answer the information needs of policymakers, public health authorities, clinicians, patients and the general public, the pharma industry, and regulatory bodies.

We aim to improve the understanding of new approaches in research management, the gathering of clinic-epidemiological data, integration of molecular information, and reporting of results.

The scope of this Special Issue will cover the analysis and reporting of coronavirus (SARS-CoV-2) and influenza epidemiology, and vaccine efficacy and effectiveness in the next years of the first half of the twenty-first century.

We look for manuscripts that explore the challenges posed by the use of new data sources, big data, and real-world data analysis; the leadership of independent institutions, the private sector and public-private partnerships in promoting, directing, and publishing new knowledge and insights on influenza epidemiology and vaccine effectiveness; the role of molecular epidemiology and, finally, causal inference coming from observational data by counterfactual analysis.

Dr. Joan Puig-Barberà
Dr. George Kassianos
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Environmental Research and Public Health is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2500 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • COVID-19
  • betacoronavirus
  • severe acute respiratory syndrome coronavirus 2
  • comorbidity
  • prevalence
  • epidemiology
  • immunology
  • epidemics
  • pandemics
  • host-pathogen interactions
  • antiviral agents/therapeutic use
  • clinical laboratory techniques/methods
  • diagnosis, prevention, control, and therapy
  • viral vaccines
  • causality clinical trials as topic/methods* confounding factors, epidemiologic
  • effect modifier, epidemiologic* egg adaptation
  • epidemiologic research design*: epidemiology
  • influenza
  • pragmatic trials
  • propensity score analysis
  • relative vaccine effectiveness
  • repeat vaccination
  • research design
  • sequencing
  • serologic assays
  • surveillance
  • test-negative design
  • vaccination
  • vaccine effectiveness
  • vaccine response
  • virus interference

Published Papers (10 papers)

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Research

Article
Using Social Network Analysis to Identify Spatiotemporal Spread Patterns of COVID-19 around the World: Online Dashboard Development
Int. J. Environ. Res. Public Health 2021, 18(5), 2461; https://doi.org/10.3390/ijerph18052461 - 03 Mar 2021
Cited by 10 | Viewed by 1619
Abstract
The COVID-19 pandemic has spread widely around the world. Many mathematical models have been proposed to investigate the inflection point (IP) and the spread pattern of COVID-19. However, no researchers have applied social network analysis (SNA) to cluster their characteristics. We aimed to [...] Read more.
The COVID-19 pandemic has spread widely around the world. Many mathematical models have been proposed to investigate the inflection point (IP) and the spread pattern of COVID-19. However, no researchers have applied social network analysis (SNA) to cluster their characteristics. We aimed to illustrate the use of SNA to identify the spread clusters of COVID-19. Cumulative numbers of infected cases (CNICs) in countries/regions were downloaded from GitHub. The CNIC patterns were extracted from SNA based on CNICs between countries/regions. The item response model (IRT) was applied to create a general predictive model for each country/region. The IP days were obtained from the IRT model. The location parameters in continents, China, and the United States were compared. The results showed that (1) three clusters (255, n = 51, 130, and 74 in patterns from Eastern Asia and Europe to America) were separated using SNA, (2) China had a shorter mean IP and smaller mean location parameter than other counterparts, and (3) an online dashboard was used to display the clusters along with IP days for each country/region. Spatiotemporal spread patterns can be clustered using SNA and correlation coefficients (CCs). A dashboard with spread clusters and IP days is recommended to epidemiologists and researchers and is not limited to the COVID-19 pandemic. Full article
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Article
Seroprevalence Study and Cross-Sectional Survey on COVID-19 for a Plan to Reopen the University of Alicante (Spain)
Int. J. Environ. Res. Public Health 2021, 18(4), 1908; https://doi.org/10.3390/ijerph18041908 - 16 Feb 2021
Cited by 12 | Viewed by 1991
Abstract
The implementation of strategies to mitigate possible cases of COVID-19 were addressed at the University of Alicante for the safe reopening of the 2020/2021 academic year. To discover the prevalence of immunity against SARS-CoV-2, a study was designed using a rapid immunoassay test [...] Read more.
The implementation of strategies to mitigate possible cases of COVID-19 were addressed at the University of Alicante for the safe reopening of the 2020/2021 academic year. To discover the prevalence of immunity against SARS-CoV-2, a study was designed using a rapid immunoassay test (carried out between 6 and 22 July 2020), and in addition a cross-sectional survey was conducted on risk factors, symptoms, predisposition for becoming vaccinated, and sources of information about COVID-19. A random sample, stratified by students, faculty, and administrative staff, was selected. The seroprevalence found was 2.64% (39/1479; 95% CI 1.8–3.4), and the adjusted seroprevalence was 2.89% (95% CI 2.1–3.7). The average age of the students was 23.2 years old, and 47.6 years old for staff. In relation to COVID-19, the following was found: 17.7% pauci-symptomatic, 1.3% symptomatic, 5.5% contact with cases, 4.9% confined, and 0.3% PCR positive. More than 90% complied with preventive measures. The proportion willing to receive the COVID-19 vaccine was 91%. Their sources of information were the Internet (74%) and television (70.1%). They requested that the university offer information (45.1%), training (27%), and provide Personal Protective Equipment (PPE) (26.3%). Lastly, 87.9% would repeat the test. A plan was established that included the follow-up of cases and contacts, random sample testing, training courses, bimodal teaching, a specific website, and the distribution of PPE. Full article
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Article
Influenza Vaccine Effectiveness and Waning Effect in Hospitalized Older Adults. Valencia Region, Spain, 2018/2019 Season
Int. J. Environ. Res. Public Health 2021, 18(3), 1129; https://doi.org/10.3390/ijerph18031129 - 27 Jan 2021
Cited by 2 | Viewed by 1730
Abstract
Influenza vaccination is annually recommended for specific populations at risk, such as older adults. We estimated the 2018/2019 influenza vaccine effectiveness (IVE) overall, by influenza subtype, type of vaccine, and by time elapsed since vaccination among subjects 65 years old or over in [...] Read more.
Influenza vaccination is annually recommended for specific populations at risk, such as older adults. We estimated the 2018/2019 influenza vaccine effectiveness (IVE) overall, by influenza subtype, type of vaccine, and by time elapsed since vaccination among subjects 65 years old or over in a multicenter prospective study in the Valencia Hospital Surveillance Network for the Study of Influenza and other Respiratory Viruses (VAHNSI, Spain). Information about potential confounders was obtained from clinical registries and/or by interviewing patients and vaccination details were only ascertained by registries. A test-negative design was performed in order to estimate IVE. As a result, IVE was estimated at 46% (95% confidence interval (CI): (16%, 66%)), 41% (95% CI: (−34%, 74%)), and 45% (95% CI: (7%, 67%)) against overall influenza, A(H1N1)pdm09 and A(H3N2), respectively. An intra-seasonal not relevant waning effect was detected. The IVE for the adjuvanted vaccine in ≥75 years old was 45% (2%, 69%) and for the non-adjuvanted vaccine in 65–74 years old was 59% (−16%, 86%). Thus, our data revealed moderate vaccine effectiveness against influenza A(H3N2) and not significant against A(H1N1)pdm09. Significant protection was conferred by the adjuvanted vaccine to patients ≥75 years old. Moreover, an intra-seasonal not relevant waning effect was detected, and a not significant IVE decreasing trend was observed over time. Full article
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Article
Challenges and Adaptation of a European Influenza Vaccine Effectiveness Study Platform in Response to the COVID-19 Emergence: Experience from the DRIVE Project
Int. J. Environ. Res. Public Health 2021, 18(3), 1058; https://doi.org/10.3390/ijerph18031058 - 25 Jan 2021
Cited by 2 | Viewed by 1789
Abstract
The Development of Robust and Innovative Vaccine Effectiveness (DRIVE) project is a public–private partnership aiming to build capacity in Europe for yearly estimation of brand-specific influenza vaccine effectiveness (IVE). DRIVE is a five-year project funded by IMI (Innovative Medicines Initiative). It was initiated [...] Read more.
The Development of Robust and Innovative Vaccine Effectiveness (DRIVE) project is a public–private partnership aiming to build capacity in Europe for yearly estimation of brand-specific influenza vaccine effectiveness (IVE). DRIVE is a five-year project funded by IMI (Innovative Medicines Initiative). It was initiated as a response to the guidance on influenza vaccines by EMA (European Medicines Agency), which advised vaccine manufacturers to work with public health institutes to set up a joint IVE study platform. The COVID-19 pandemic reached Europe in February 2020 and overlapped with the 2019/2020 influenza season only in the last weeks. However, several elements of the DRIVE study network were impacted. The pandemic specifically affected the study sites’ routines and the subsequent assessment of the 2019/20 influenza season. Moreover, the current social distancing measures and lockdown policies across Europe are expected to also limit the circulation of influenza for the 2020/21 season, and therefore the impact of COVID-19 will be higher than in the season 2019/20. Consequently, DRIVE has planned to adapt its study platform to the COVID-19 challenge, encompassing several COVID-19 particularities in the study procedures, data collection and IVE analysis for the 2020/21 season. DRIVE will study the feasibility of implementing these COVID-19 components and establish the foundations of future COVID-19 vaccine effectiveness studies. Full article
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Article
No Evidence of SARS-CoV-2 Circulation in Rome (Italy) during the Pre-Pandemic Period: Results of a Retrospective Surveillance
Int. J. Environ. Res. Public Health 2020, 17(22), 8461; https://doi.org/10.3390/ijerph17228461 - 16 Nov 2020
Cited by 10 | Viewed by 4393
Abstract
In March 2020, the World Health Organization (WHO) declared that the COVID-19 outbreak recorded over the previous months could be characterized as a pandemic. The first known Italian SARS-CoV-2 positive case was reported on 21 February. In some countries, cases of suspected “COVID-19-like [...] Read more.
In March 2020, the World Health Organization (WHO) declared that the COVID-19 outbreak recorded over the previous months could be characterized as a pandemic. The first known Italian SARS-CoV-2 positive case was reported on 21 February. In some countries, cases of suspected “COVID-19-like pneumonia” had been reported earlier than those officially accepted by health authorities. This has led many investigators to check preserved biological or environmental samples to see whether the virus was detectable on dates prior to those officially stated. With regard to Italy, the results of a microbiological screening in sewage samples collected between the end of February and the beginning of April 2020 from wastewaters in Milan (Northern Italy) and Rome (Central Italy) showed presence of SARS-CoV-2. In the present study, we evaluated, by means of a standardized diagnostic method, the SARS-CoV-2 infection prevalence amongst patients affected by severe acute respiratory syndrome (SARI) in an academic hospital located in Central Italy during the period of 1 November 2019–1 March 2020. Overall, the number of emergency room (ER) visits during the investigated period was 13,843. Of these, 1208 had an influenza-like syndrome, but only 166 matched the definition of SARI as stated in the study protocol. A total of 52 SARI cases were laboratory confirmed as influenza: 26 as a type B virus, 25 as a type A, and 1 as both viruses. Although about 17% of the total sample had laboratory or radiological data compatible with COVID-19, all the nasopharyngeal swabs stored underwent SARS-CoV-2 RT-PCR and tested negative. Based on our result, it is confirmed that the COVID-19 pandemic spread did not start prior to the “official” onset in central Italy. Routine monitoring of SARI causative agents at the local level is critical for reporting epidemiologic and etiologic trends that may differ from one country to another and also among different influenza seasons. This has a practical impact on prevention and control strategies. Full article
Communication
The Association between Influenza Vaccination and the Risk of SARS-CoV-2 Infection, Severe Illness, and Death: A Systematic Review of the Literature
Int. J. Environ. Res. Public Health 2020, 17(21), 7870; https://doi.org/10.3390/ijerph17217870 - 27 Oct 2020
Cited by 22 | Viewed by 3434
Abstract
We reviewed the association between seasonal influenza vaccination and the risk of SARS-CoV-2 infection or complicated illness or poor outcome (e.g., severe disease, need for hospitalization or ventilatory support, or death) among COVID-19 patients. None of the studies that were reviewed (n [...] Read more.
We reviewed the association between seasonal influenza vaccination and the risk of SARS-CoV-2 infection or complicated illness or poor outcome (e.g., severe disease, need for hospitalization or ventilatory support, or death) among COVID-19 patients. None of the studies that were reviewed (n = 12) found a significant increase in the risk of infection or in the illness severity or lethality, and some reported significantly inverse associations. Our findings support measures aimed at raising influenza vaccination coverage in the coming months. Full article
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Article
Retrospective Assessment of the Antigenic Similarity of Egg-Propagated and Cell Culture-Propagated Reference Influenza Viruses as Compared with Circulating Viruses across Influenza Seasons 2002–2003 to 2017–2018
Int. J. Environ. Res. Public Health 2020, 17(15), 5423; https://doi.org/10.3390/ijerph17155423 - 28 Jul 2020
Cited by 7 | Viewed by 1055
Abstract
Suboptimal vaccine effectiveness against seasonal influenza is a significant public health concern, partly explained by antigenic differences between vaccine viruses and viruses circulating in the environment. Haemagglutinin mutations within vaccine viruses acquired during serial passage in eggs have been identified as a source [...] Read more.
Suboptimal vaccine effectiveness against seasonal influenza is a significant public health concern, partly explained by antigenic differences between vaccine viruses and viruses circulating in the environment. Haemagglutinin mutations within vaccine viruses acquired during serial passage in eggs have been identified as a source of antigenic variation between vaccine and circulating viruses. This study retrospectively compared the antigenic similarity of circulating influenza isolates with egg- and cell-propagated reference viruses to assess any observable trends over a 16-year period. Using annual and interim reports published by the Worldwide Influenza Centre, London, for the 2002–2003 to 2017–2018 influenza seasons, we assessed the proportions of circulating viruses which showed antigenic similarity to reference viruses by season. Egg-propagated reference viruses were well matched against circulating viruses for A/H1N1 and B/Yamagata. However, A/H3N2 and B/Victoria cell-propagated reference viruses appeared to be more antigenically similar to circulating A/H3N2 and B/Victoria viruses than egg-propagated reference viruses. These data support the possibility that A/H3N2 and B/Victoria viruses are relatively more prone to egg-adaptive mutation. Cell-propagated A/H3N2 and B/Victoria reference viruses were more antigenically similar to circulating A/H3N2 and B/Victoria viruses over a 16-year period than were egg-propagated reference viruses. Full article
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Article
Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study
Int. J. Environ. Res. Public Health 2020, 17(15), 5313; https://doi.org/10.3390/ijerph17155313 - 23 Jul 2020
Cited by 9 | Viewed by 2689
Abstract
Background: Coronavirus Disease 2019 (COVID-19) has rapidly spread worldwide, becoming an unprecedented public health emergency. Rapid detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) suspected cases is crucial to control the spread of infection. We aimed to evaluate the time length [...] Read more.
Background: Coronavirus Disease 2019 (COVID-19) has rapidly spread worldwide, becoming an unprecedented public health emergency. Rapid detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) suspected cases is crucial to control the spread of infection. We aimed to evaluate the time length of negativization from the onset of symptoms in healthcare workers (HCWs) with COVID-19, and to evaluate significant variations in cycle threshold (CT) values and gene positivity (E, RdRP, and N genes) among positive individuals who returned to work. Methods: We retrospectively analyzed a consecutive cohort of 182 SARS-CoV-2-positive HCWs in Milan, from 16 March to 30 April 2020. Nasopharyngeal swabs were tested by RT-PCR. Results: Asymptomatic HCWs were 17.6% (32/182), and 58 healed at 30 April 2020. The median time length of negativization was 4 weeks (35% of symptomatic versus 40% of asymptomatic HCWs). Four HCWs, healed at 30 April, turned positive within three weeks during controls set up in the work unit. Three-gene positivity had the greatest variability, and increasing CT values from single- to three-gene positivity among all age groups were observed. Conclusions: Self-isolation longer than two weeks and prolonged follow-up periods for the staff returning to work after COVID-19 could be the most suitable choices to counter the SARS-CoV-2 spread. Further studies are needed to investigate infectiousness profiles among positive individuals. Full article
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Article
Moving Average Based Index for Judging the Peak of the COVID-19 Epidemic
Int. J. Environ. Res. Public Health 2020, 17(15), 5288; https://doi.org/10.3390/ijerph17155288 - 22 Jul 2020
Cited by 3 | Viewed by 1544
Abstract
A pneumonia outbreak caused by a novel coronavirus (COVID-19) has spread around the world. A total of 2,314,621 laboratory-confirmed cases, including 157,847 deaths (6.8%) were reported globally by 20 April 2020. Common symptoms of COVID-19 pneumonia include fever, fatigue, and dry cough. Faced [...] Read more.
A pneumonia outbreak caused by a novel coronavirus (COVID-19) has spread around the world. A total of 2,314,621 laboratory-confirmed cases, including 157,847 deaths (6.8%) were reported globally by 20 April 2020. Common symptoms of COVID-19 pneumonia include fever, fatigue, and dry cough. Faced with such a sudden outbreak of emerging infectious disease, traditional models for predicting the peak of the epidemic often show inconsistent results. With the aim to timely judge the epidemic peak and provide support for decisions for resuming production and returning to normal life based on publicly reported data, we used a seven-day moving average of log-transformed daily new cases (LMA) to establish a new index named the “epidemic evaluation index” (EEI). We used SARS epidemic data from Hong Kong to verify the practicability of the new index, and then applied it to the COVID-19 epidemic analysis. The results showed that the epidemic peaked, respectively, on 9 February and 5 February 2020, in Hubei Province and other provinces in China. The proposed index can be applied for judging the epidemic peak. While the global COVID-19 epidemic reached its peak in the middle of April, the epidemic peaks in some countries have not yet appeared. Global and united efforts are still needed to eventually eliminate the epidemic. Full article
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Article
Prevalence of Sars-Cov-2 Infection in Health Workers (HWs) and Diagnostic Test Performance: The Experience of a Teaching Hospital in Central Italy
Int. J. Environ. Res. Public Health 2020, 17(12), 4417; https://doi.org/10.3390/ijerph17124417 - 19 Jun 2020
Cited by 67 | Viewed by 3006
Abstract
(1) Background: Health workers (HWs) are at high risk of acquiring SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) infections. Therefore, health authorities further recommend screening strategies for SARS-CoV-2 infection in exposed or high-risk HWs. Nevertheless, to date, the best/optimal method to screen HWs [...] Read more.
(1) Background: Health workers (HWs) are at high risk of acquiring SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) infections. Therefore, health authorities further recommend screening strategies for SARS-CoV-2 infection in exposed or high-risk HWs. Nevertheless, to date, the best/optimal method to screen HWs for SARS-CoV-2 infection is still under debate, and data on the prevalence of SARS-CoV-2 infection in HWs are still scarce. The present study aims to assess the SARS-CoV-2 infection rate amongst HWs in a teaching hospital in Central Italy and the diagnostic performance of SARS-CoV-2 serology (index test) in comparison with the SARS-CoV-2 RNA PCR assay (reference standard). (2) Methods: A cross-sectional study on the retrospective data of HWs tested for SARS-CoV-2 by RNA-RT-PCR on nasopharyngeal swabs and by an IgM/IgG serology assay on venous blood samples, irrespective of exposure and/or symptoms, was carried out. (3) Results: A total of 2057 HWs (median age 46, 19–69 years, females 60.2%) were assessed by the RNA RT-PCR assay and 58 (2.7%) tested positive for SARS-CoV-2 infection. Compared with negative HWs, SARS-CoV-2-positives were younger (mean age 41.7 versus 45.2, p < 0.01; 50% versus 31% under or equal to 40 years old, p < 0.002) and had a shorter duration of employment (64 versus 125 months, p = 0.02). Exposure to SARS-CoV-2 was more frequent in positive HWs than in negatives (55.2% versus 27.5%, p < 0.0001). In 44.8% of positive HWs, no exposure was traced. None of the positive HWs had a fatal outcome, none of them had acute respiratory distress syndrome, and only one required hospitalization for mild/moderate pneumonia. In 1084 (51.2%) HWs, nasopharyngeal swabs and an IgM/IgG serology assay were performed. With regard to IgM serology, sensitivity was 0% at a specificity of 98.99% (positive predictive value, PPV 0%, negative predictive value, NPV 99.2%). Concerning IgG serology and irrespective of the time interval between nasopharyngeal swab and serology, sensitivity was 50% at a specificity of 99.1% (PPV 28.6%, NPV 99.6%). IgG serology showed a higher diagnostic performance when performed at least two weeks after testing SARS-CoV-2-positive at the RNA RT-PCR assay by a nasopharyngeal swab. (4) Conclusions: Our experience in Central Italy demonstrated a low prevalence of SARS-CoV-2 infection amongst HWs, but higher than in the general population. Nearly half of the positive HWs reported no previous exposure to SARS-CoV-2-infected subjects and were diagnosed thanks to the proactive screening strategy implemented. IgG serology seems useful when performed at least two weeks after an RNA RT-PCR assay. IgM serology does not seem to be a useful test for the diagnosis of active SARS-CoV-2 infection. High awareness of SARS-CoV-2 infection is mandatory for all people, but especially for HWs, irrespective of symptoms, to safeguard their health and that of patients. Full article
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