Oropharyngeal Microbiome Analysis in Patients with Varying SARS-CoV-2 Infection Severity: A Prospective Cohort Study

Patients with COVID-19 infection have distinct oropharyngeal microbiota composition and diversity metrics according to disease severity. However, these findings are not consistent across the literature. We conducted a multicenter, prospective study in patients with COVID-19 requiring outpatient versus inpatient management to explore the microbial abundance of taxa at the phylum, family, genus, and species level, and we utilized alpha and beta diversity indices to further describe our findings. We collected oropharyngeal washing specimens at the time of study entry, which coincided with the COVID-19 diagnosis, to conduct all analyses. We included 43 patients in the study, of whom 16 were managed as outpatients and 27 required hospitalization. Proteobacteria, Actinobacteria, Bacteroidetes, Saccharibacteria TM7, Fusobacteria, and Spirochaetes were the most abundant phyla among patients, while 61 different families were detected, of which the Streptococcaceae and Staphylococcaceae families were the most predominant. A total of 132 microbial genera were detected, with Streptococcus being the predominant genus in outpatients, in contrast to hospitalized patients, in whom the Staphylococcus genus was predominant. LeFSe analysis identified 57 microbial species in the oropharyngeal washings of study participants that could discriminate the severity of symptoms of COVID-19 infections. Alpha diversity analysis did not reveal a difference in the abundance of bacterial species between the groups, but beta diversity analysis established distinct microbial communities between inpatients and outpatients. Our study provides information on the complex association between the oropharyngeal microbiota and SARS-CoV-2 infection. Although our study cannot establish causation, knowledge of specific taxonomic changes with increasing SARS-CoV-2 infection severity can provide us with novel clues for the prognostic classification of COVID-19 patients.

Investigating ABO Blood Groups and Secretor Status in Relation to SARS-CoV-2 Infection and COVID-19 Severity

The ABO blood groups, Lewis antigens, and secretor systems are important components of transfusion medicine. These interconnected systems have been also shown to be associated with differing susceptibility to bacterial and viral infections, likely as the result of selection over the course of evolution and the constant tug of war between humans and infectious microbes. This comprehensive narrative review aimed to explore the literature and to present the current state of knowledge on reported associations of the ABO, Lewis, and secretor blood groups with SARS-CoV-2 infection and COVID-19 severity. Our main finding was that the A blood group may be associated with increased susceptibility to SARS-CoV-2 infection, and possibly also with increased disease severity and overall mortality. The proposed pathophysiological pathways explaining this potential association include antibody-mediated mechanisms and increased thrombotic risk amongst blood group A individuals, in addition to altered inflammatory cytokine expression profiles. Preliminary evidence does not support the association between ABO blood groups and COVID-19 vaccine response, or the risk of developing long COVID. Even though the emergency state of the pandemic is over, further research is needed especially in this area since tens of millions of people worldwide suffer from lingering COVID-19 symptoms.

Antimicrobial and Diagnostic Stewardship of the Novel β-Lactam/β-Lactamase Inhibitors for Infections Due to Carbapenem-Resistant Enterobacterales Species and Pseudomonas aeruginosa

Carbapenem-resistant Gram-negative bacterial infections are a major public health threat due to the limited therapeutic options available. The introduction of the new β-lactam/β-lactamase inhibitors (BL/BLIs) has, however, altered the treatment options for such pathogens. Thus, four new BL/BLI combinations-namely, ceftazidime/avibactam, meropenem/vaborbactam, imipenem/relebactam, and ceftolozane/tazobactam-have been approved for infections attributed to carbapenem-resistant Enterobacterales species and Pseudomonas aeruginosa. Nevertheless, although these antimicrobials are increasingly being used in place of other drugs such as polymyxins, their optimal clinical use is still challenging. Furthermore, there is evidence that resistance to these agents might be increasing, so urgent measures should be taken to ensure their continued effectiveness. Therefore, clinical laboratories play an important role in the judicious use of these new antimicrobial combinations by detecting and characterizing carbapenem resistance, resolving the presence and type of carbapenemase production, and accurately determining the minimum inhibitor concentrations (MICs) for BL/BLIs. These three targets must be met to ensure optimal BL/BLIs use and prevent unnecessary exposure that could lead to the development of resistance. At the same time, laboratories must ensure that results are interpreted in a timely manner to avoid delays in appropriate treatment that might be detrimental to patient safety. Thus, we herein present an overview of the indications and current applications of the new antimicrobial combinations and explore the diagnostic limitations regarding both carbapenem resistance detection and the interpretation of MIC results. Moreover, we suggest the use of alternative narrower-spectrum antibiotics based on susceptibility testing and present data regarding the effect of synergies between BL/BLIs and other antimicrobials. Finally, in order to address the absence of a standardized approach to using the novel BL/BLIs, we propose a diagnostic and therapeutic algorithm, which can be modified based on local epidemiological criteria. This framework could also be expanded to incorporate other new antimicrobials, such as cefiderocol, or currently unavailable BL/BLIs such as aztreonam/avibactam and cefepime/taniborbactam.

Predominance of Recombinant Norovirus Strains in Greece, 2016-2018

GII.4 noroviruses have caused the overwhelming majority of norovirus-related gastroenteritis cases during the past two decades. However, a trend towards the emergence of new genotypes and novel GII.4 variants provided the impetus to explore further the changing patterns in norovirus epidemiology during the present study. Genotyping of 60 norovirus strains detected during a period of 33 months (January 2016-October 2018) was performed on the basis of the capsid VP1-coding ORF2 gene sequence. All norovirus strains detected were classified into seven genotypes, six of which belonged to genogroup GII. GII.2 was the dominant genotype till February 2017, whereas GII.4 prevailed thereafter. Most of the GII.4 strains were of the Sydney_2012 variant, whereas five strains could not be classified. Further recombination analysis at the ORF1/ORF2 gene junction revealed that 23 out of 24 strains were recombinant, thereby showcasing the significant role of genetic recombination in norovirus evolution and epidemiology. Continuous genomic surveillance and molecular characterization are essential for tracking norovirus evolution, which could contribute to the elucidation of new aspects of virus-host interactions that potentially affect host morbidity and epidemiology.

Adverse events of acute nephrotoxicity reported to EudraVigilance and VAERS after COVID-19 vaccination

OBJECTIVES

The present study aimed to estimate the reporting rates (RRs) of acute kidney injury (AKI) and renal failure (RF) after COVID-19 vaccination in the European Economic Area (EEA) and the United States.

METHODS

We retrieved and analyzed pharmacovigilance data on suspected AKI and RF cases and fatalities post COVID-19 vaccination with licensed vaccines reported to EudraVigilance and VAERS between week 52/2020 and week 52/2022 or week 1/2023, respectively. Reporting rates with 95% confidence intervals were estimated per million administered vaccine doses.

RESULTS

In total, 4,244 AKI and 1,557 RF suspected cases were notified to EudraVigilance (1,692 AKI/971 RF) and VAERS (2,552 AKI/586 RF) during the study period following the administration of >1.6 billion COVID-19 vaccine doses (EEA: 970,934,453/US: 666,511,603). The overall RRs were 3.03 (95 % CI: 2.94-3.12) for AKI and 1.11 (95 % CI: 1.06-1.17) for RF per million administered vaccine doses. Indices for statistically significant increased risks were found in subjects, especially males, ≥65 years compared to 18-64 years old (AKI: OR = 7.23, 95 % CI: 6.63-7.88, p = 0.000, and RF: OR = 4.74, 95 % CI: 3.99-5.63, p < 0.001). AKI reporting rates were higher in the US, while RF reporting rates were higher in Europe. Both potential side effects were elevated following vectored rather than mRNA vaccines, with the highest reporting rates post AD26.COV2.S vaccination in the US (AKI: RR = 12.24, 95 % CI: 10.66-13.81; RF: RR = 3.17, 95 % CI: 2.36-3.97). There were 1,312 deaths possibly associated with AKI (RR = 0.94, 95 % CI: 0.89-0.99) and 460 deaths possibly associated with RF (RR = 0.33, 95 % CI: 0.30-0.36) per million vaccine doses. Fatalities were lower in Europe than in the US (AKI: OR = 0.25, 95 % CI: 0.22-0.28, p < 0.001; RF: OR = 0.82, 95 % CI: 0.69-0.99, p = 0.036).

CONCLUSIONS

AKI and RF may be observed rarely following vaccination against COVID-19. Further studies are warranted to confirm these findings and uncover the underlying pathophysiological mechanism.

Paired associated SARS-CoV-2 spike variable positions: a network analysis approach to emerging variants

Amino acids in variable positions of proteins may be correlated, with potential structural and functional implications. Here, we apply exact tests of independence in R × C contingency tables to examine noise-free associations between variable positions of the SARS-CoV-2 spike protein, using as a paradigm sequences from Greece deposited in GISAID (N = 6,683/1,078 full length) for the period 29 February 2020 to 26 April 2021 that essentially covers the first three pandemic waves. We examine the fate and complexity of these associations by network analysis, using associated positions (exact P ≤ 0.001 and Average Product Correction ≥ 2) as links and the corresponding positions as nodes. We found a temporal linear increase of positional differences and a gradual expansion of the number of position associations over time, represented by a temporally evolving intricate web, resulting in a non-random complex network of 69 nodes and 252 links. Overconnected nodes corresponded to the most adapted variant positions in the population, suggesting a direct relation between network degree and position functional importance. Modular analysis revealed 25 k-cliques comprising 3 to 11 nodes. At different k-clique resolutions, one to four communities were formed, capturing epistatic associations of circulating variants (Alpha, Beta, B.1.1.318), but also Delta, which dominated the evolutionary landscape later in the pandemic. Cliques of aminoacidic positional associations tended to occur in single sequences, enabling the recognition of epistatic positions in real-world virus populations. Our findings provide a novel way of understanding epistatic relationships in viral proteins with potential applications in the design of virus control procedures. IMPORTANCE Paired positional associations of adapted amino acids in virus proteins may provide new insights for understanding virus evolution and variant formation. We investigated potential intramolecular relationships between variable SARS-CoV-2 spike positions by exact tests of independence in R × C contingency tables, having applied Average Product Correction (APC) to eliminate background noise. Associated positions (exact P ≤ 0.001 and APC ≥ 2) formed a non-random, epistatic network of 25 cliques and 1-4 communities at different clique resolutions, revealing evolutionary ties between variable positions of circulating variants and a predictive potential of previously unknown network positions. Cliques of different sizes represented theoretical combinations of changing residues in sequence space, allowing the identification of significant aminoacidic combinations in single sequences of real-world populations. Our analytic approach that links network structural aspects to mutational aminoacidic combinations in the spike sequence population offers a novel way to understand virus epidemiology and evolution.

SARS-CoV-2 Reinfections and Long COVID in the Post-Omicron Phase of the Pandemic

We are reviewing the current state of knowledge on the virological and immunological correlates of long COVID, focusing on recent evidence for the possible association between the increasing number of SARS-CoV-2 reinfections and the parallel pandemic of long COVID. The severity of reinfections largely depends on the severity of the initial episode; in turn, this is determined both by a combination of genetic factors, particularly related to the innate immune response, and by the pathogenicity of the specific variant, especially its ability to infect and induce syncytia formation at the lower respiratory tract. The cumulative risk of long COVID as well as of various cardiac, pulmonary, or neurological complications increases proportionally to the number of SARS-CoV-2 infections, primarily in the elderly. Therefore, the number of long COVID cases is expected to remain high in the future. Reinfections apparently increase the likelihood of long COVID, but less so if they are mild or asymptomatic as in children and adolescents. Strategies to prevent SARS-CoV-2 reinfections are urgently needed, primarily among older adults who have a higher burden of comorbidities. Follow-up studies using an established case definition and precise diagnostic criteria of long COVID in people with or without reinfection may further elucidate the contribution of SARS-CoV-2 reinfections to the long COVID burden. Although accumulating evidence supports vaccination, both before and after the SARS-CoV-2 infection, as a preventive strategy to reduce the risk of long COVID, more robust comparative observational studies, including randomized trials, are needed to provide conclusive evidence of the effectiveness of vaccination in preventing or mitigating long COVID in all age groups. Thankfully, answers not only on the prevention, but also on treatment options and rates of recovery from long COVID are gradually starting to emerge.

Epidemiological Transition and Strategies for the Control of Hepatitis A in Serbia

Background: Improvements in socioeconomic and hygienic conditions during the past decades led to declining hepatitis A (HA) seroprevalence in many countries. Aiming at informing HA vaccination policy, we assessed current epidemiological trends in Serbia by analyzing surveillance data for 2002–2021. Methods: Data on cases and outbreaks were obtained from the Serbian national surveillance database and descriptively analyzed. HA incidence was calculated in relation to time, patients’ residence, and demographics. Results: Overall, 13,679 HA cases and 419 outbreaks were recorded with the highest incidence in the southeast. Downward HA trends were observed, while infant mortality was halved, and gross domestic product based on purchasing power parity (GDP PP) per capita, tripled. The average incidence dropped from 14.8 (95% CI 14.4–15.2)/100,000) in 2002–2006 to 1 (95% CI 0.9–1.1)/100,000)/100,000 in 2017–2021, while the number of outbreaks decreased (from 174 to 14). Sporadic cases and family clusters living in poor sanitary conditions occurred in recent years. The contact route of transmission was dominant (410/419, 97.9%). The highest average age-specific HA incidence shifted from 5–9 years in 2002–2006 to 10–19 years in 2017–2021.Serbia is transitioning towards very low HA endemicity. Enhanced surveillance and vaccination of high-risk groups are recommended as future public health priorities.

Anaphylactic Reactions to COVID-19 Vaccines: An Updated Assessment Based on Pharmacovigilance Data

This study aimed at producing an updated assessment of the incidence of anaphylaxis associated with COVID-19 vaccines based on pharmacovigilance data. Anaphylactic reaction and anaphylactic shock data post-COVID-19-vaccination reported from week 52, 2020 to week 1 or week 2, 2023 were collected from the VAERS and EudraVigilance databases, respectively, and analyzed comparatively. Incidence rates were calculated using the corresponding administered vaccine doses as denominators for all licensed vaccines and both platform types (mRNA or vectored). The latest data from the present analysis showed lower anaphylaxis incidence associated with COVID-19 vaccination compared to previous estimates from week 52, 2020 to week 39, 2021 (anaphylactic reaction: 8.96 (95% CI 8.80-9.11)/million doses overall (EEA: 14.19 (95% CI 13.92-14.47)/million/US: 3.17 (95% CI 3.03-3.31)/million); anaphylactic shock: 1.46 (95% CI 1.39-1.52)/million doses overall (EEA: 2.47 (95% CI 2.36-2.58)/million/US: 0.33 (95% CI 0.29-0.38)/million)). Incidence rates varied by vaccine and were higher as captured in EudraVigilance compared to the VAERS and for vectored compared to mRNA vaccines. Most reported cases had a favorable outcome. The extremely rare fatalities (overall rates across continents 0.04 (95% CI 0.03-0.06)/million doses for anaphylactic reaction and 0.02 (95% CI 0.01-0.03)/million vaccine doses for anaphylactic shock) were also associated with vector-rather than mRNA-based vaccines. The diminished incidence of anaphylaxis post-vaccination with COVID-19 vaccines offers assurance about their safety, as does the continuous potential adverse events monitoring through specialized pharmacovigilance databases.

Anaphylaxis rates following mRNA COVID-19 vaccination in children and adolescents: Analysis of data reported to EudraVigilance

AIM

The present study aimed to estimate the anaphylaxis rates following mRNA COVID-19 vaccination in children and adolescents in Europe.

METHODS

We retrieved data on 371 anaphylaxis cases following mRNA COVID-19 vaccination in children ≤ 17 years old notified to EudraVigilance as of October 8, 2022. Overall, 27,120,512 doses of BNT162b2 vaccine and 1,400,300 doses of mRNA-1273 vaccine have been delivered to children during the study period.

RESULTS

The overall mean anaphylaxis rate was 12.81 [95% confidence interval (CI): 11.49-14.12] per 10⁶ mRNA vaccine doses [12.14 (95% CI: 6.37-17.91) per 10⁶ doses for mRNA-1273 and 12.84 (95% CI: 11.49-14.19) per 10⁶ doses for BNT162b2]. Children 12-17 years old accounted for 317 anaphylaxis cases, followed by 48 cases in children 3-11 years old, and 6 cases in children 0-2 years old. Children 10-17 years old had a mean anaphylaxis rate of 13.52 (95% CI: 12.03-15.00) cases per 10⁶ mRNA vaccine doses and children 5-9 years old had a mean anaphylaxis rate of 9.51 (95% CI: 6.82-12.20) cases per 10⁶ mRNA vaccine doses. There were two fatalities, both in the 12-17 years age group. The fatal anaphylaxis rate was 0.07 cases per 10⁶ mRNA vaccine doses.

CONCLUSIONS

Anaphylaxis is a rare adverse event after receiving an mRNA COVID-19 vaccine in children. Continuous surveillance of serious adverse events is needed to guide vaccination policies as we move towards SARS-CoV-2 endemicity. Larger real-world studies on COVID-19 vaccination in children, using clinical case confirmation, are imperative.

Incidence, Risk, and Severity of SARS-CoV-2 Reinfections in Children and Adolescents Between March 2020 and July 2022 in Serbia

IMPORTANCE

During the COVID-19 pandemic, children and adolescents were massively infected worldwide. In 2022, reinfections became a main feature of the endemic phase of SARS-CoV-2, so it is important to understand the epidemiology and clinical impact of reinfections.

OBJECTIVE

To assess the incidence, risk, and severity of pediatric SARS-CoV-2 reinfection.

DESIGN, SETTING, AND PARTICIPANTS

This retrospective cohort study used epidemiologic data of documented SARS-CoV-2 infections from the surveillance database of the Institute for Public Health of Vojvodina. A total of 32 524 children and adolescents from Vojvodina, Serbia, with laboratory-confirmed SARS-CoV-2 infection between March 6, 2020, and April 30, 2022, were followed up for reinfection until July 31, 2022.

MAIN OUTCOMES AND MEASURES

Incidence rates of documented SARS-CoV-2 reinfection per 1000 person-months, estimated risk of documented reinfection 90 days or more after laboratory confirmation of primary infection, reinfection severity, hospitalizations, and deaths.

RESULTS

The study cohort included 32 524 children and adolescents with COVID-19 (mean [SD] age, 11.2 [4.9] years; 15 953 [49.1%] male), including 964 children (3.0%) who experienced documented reinfection. The incidence rate of documented reinfections was 3.2 (95% CI, 3.0-3.4) cases per 1000 person-months and was highest in adolescents aged 12 to 17 years (3.4; 95% CI, 3.2-3.7). Most reinfections (905 [93.9%]) were recorded in 2022. The cumulative reinfection risk was 1.3% at 6 months, 1.9% at 9 months, 4.0% at 12 months, 6.7% at 15 months, 7.2% at 18 months, and 7.9% after 21 months. Pediatric COVID-19 cases were generally mild. The proportion of severe clinical forms decreased from 14 (1.4%) in initial episodes to 3 (0.3%) in reinfections. Reinfected children were approximately 5 times less likely to have severe disease during reinfection compared with initial infection (McNemar odds ratio, 0.2; 95% CI, 0.0-0.8). Pediatric reinfections rarely led to hospitalization (0.5% vs 1.3% during primary infections), and none resulted in death.

CONCLUSIONS AND RELEVANCE

This cohort study found that the SARS-CoV-2 reinfection risk remained substantially lower for children and adolescents compared with adults as of July 2022. Pediatric infections were mild, and reinfections were even milder than primary infections.

Comparative assessment of myocarditis and pericarditis reporting rates related to mRNA COVID-19 vaccines in Europe and the United States

OBJECTIVES

The novel mRNA vaccines proved to be safe and effective in averting severe COVID-19. Vaccine-related complications recorded by pharmacovigilance systems, such as "EudraVigilance" in Europe and "VAERS" in the United States (US), rarely include myocarditis and pericarditis. Given the novelty of the platform and the increasing global-scale vaccine production needs, we assessed their reporting rates comparatively across continents.

METHODS

Data of myocarditis and pericarditis cases post COVID-19 vaccination reported through week 40/2021 were collected for mRNA vaccines from EudraVigilance and VAERS. The corresponding administered vaccine doses were used as denominators to estimate reporting rates for comparison purposes.

RESULTS

Low reporting rates of myocarditis (7.64/million vaccine doses) and pericarditis (5.32/million) was found, with higher rates of both disorders in EudraVigilance compared to VAERS; these differences were more pronounced post mRNA-1273 (~5-fold) than post BNT162b2 vaccination (~1.5-fold). Most myocarditis cases occurred in males <30 years. Pericarditis affected predominantly males <40 and both sexes >40 years. The extremely rare fatalities related to myocarditis (0.102/million) or pericarditis (0.017/million) were also higher in EudraVigilance versus VAERS.

CONCLUSIONS

Understanding the underlying causes of the observed differences could provide guidance for the enhanced quality of mRNA vaccines that would foster vaccine acceptance.

Temporal relationship of myocarditis and pericarditis following COVID-19 vaccination: A pragmatic approach

Background

Complications following COVID-19 vaccination, particularly with mRNA vaccines, rarely include myocarditis and pericarditis. This work principally aimed at defining a realistic temporal relationship between vaccination and myocarditis/pericarditis development.

Methods

All relevant cases reported from week 52/2020 through week 41/2021 in the VAERS database were retrieved and analyzed for licensed vaccines. These included BNT162b2, mRNA-1273, and AD26.COV2·S. Incidence rates were calculated using the corresponding administered vaccine doses as denominators. Additionally, analyzed parameters included demographics, dose series, hospitalization length and outcome.

Results

Overall, 2016 myocarditis and 1380 pericarditis cases, (4.96/10⁶ and 3.40/10⁶ administered vaccine doses, respectively), were recorded. Most myocarditis cases occurred following BNT162b2 (5.60/10⁶ doses) in males <30 years. Pericarditis affected predominantly males <40, both sexes >40 years, and was most common post AD26.COV2·S (4.78/10⁶ doses). Hospitalization was required for 40.3% and 27.2% of myocarditis and pericarditis cases, respectively. A bimodal pattern was found for both myocarditis and pericarditis, with two peaks that coincided temporally, but were reversed in intensity. The first peak was recorded 1–3 days post-vaccination and was more pronounced in myocarditis, while the second was recorded 15–30 days post-vaccination and was more intense in pericarditis.

Conclusions

Myocarditis/pericarditis after COVID-19 vaccination is rare and depicts a bimodal pattern.

The Role of Oral Antivirals for COVID-19 Treatment in Shaping the Pandemic Landscape

Several vaccines against coronavirus disease 2019 (COVID-19) were developed and made available in a record time, just over a year after the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [...].

Anaphylaxis rates associated with COVID-19 vaccines are comparable to those of other vaccines

We retrieved data on 8940 anaphylaxis cases post-COVID-19 vaccination from the US Vaccine Adverse Event Reporting System and the European EudraVigilance from week 52/2020 through week 31/2021 and compared them with those of other vaccines. Overall, 837,830,000 COVID-19 vaccine doses were delivered in the US and Europe during the study period, for which the vaccine name was known. The mean anaphylaxis rate was estimated at 10.67 cases per 10⁶ doses of COVID-19 vaccines (range: 7.99-19.39 cases per 10⁶ doses depending on the vaccine). COVID-19 vaccines ranked fifth in reported anaphylaxis rates, behind rabies, tick-borne encephalitis, measles-mumps-rubella-varicella, and human papillomavirus vaccines (70.77, 20, 19.8, and 13.65 cases per 10⁶ vaccine doses, respectively). COVID-19 vaccines are within the range of anaphylaxis rates reported across several common vaccines in these two passive reporting systems. These data should be communicated to reassure the general population about the safety profile of COVID-19 vaccines.

A study of the evolution of the third COVID-19 pandemic wave in the Athens metropolitan area, Greece, through two cross-sectional seroepidemiological surveys: March, June 2021

We studied the third coronavirus disease 2019 (COVID‐19) pandemic wave in Athens metropolitan area (3 738 901 inhabitants) through two seroepidemiological surveys. Persons presenting in 12 healthcare facilities across Athens in March and June 2021 were studied (764 and 901, respectively). Immunoglobulin G antibodies against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) spike protein were measured by a chemiluminescent microparticle immunoassay. In March the seroprevalence rate was 11.6%, meaning that 435 208 residents of Athens had evidence of immunity. The respective values in June were 55.7% and 2 082 568 residents. The highest seroprevalence rates attributed to SARS‐CoV‐2 infection were recorded in persons <18 years (16.3% in March and 31.6% in June), while immunity was mainly vaccine‐induced in persons 18–64 years and >65 years. Infection‐attributed immunity also increased in older‐age groups. Wide ranges in seroprevalence rates were noted across areas in March and June. The highest seroprevalence rates were recorded in Piraeus (47.2%) and West Attica (37.5%). However, the highest increase (>5 times) occurred in Piraeus and the South Section of Athens, which are among the most densely populated areas in Athens. In both study periods, history of COVID‐19 or febrile episode, and having a cohabitant with COVID‐19 were associated with increased risk for seropositivity among unvaccinated persons (p values <0.001 for all). Residing in Piraeus, the South Section or West Attica was associated with increased risk for seropositivity in June (p values <0.001). Wide heterogeneity in seroprevalence rates was found across areas in Athens, which is mainly attributed to population density. The impact of population mobility and socioeconomic status should be explored.

Environmental testing for SARS-CoV-2 in three tertiary-care hospitals during the peak of the third COVID-19 wave

Contamination of surfaces has been implicated in transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We tested by real-time PCR for SARS-CoV-2 contamination environmental samples from three hospitals during the peak of the third pandemic wave. Overall, 19 of 463 (4.1%) samples tested positive: 12 of 173 (6.9%) samples from a COVID-19 hospital, 3 of 177 (1.7%) samples from a non-COVID-19 hospital, and 4 of 113 (3.5%) samples from a pediatric hospital with dedicated COVID-19 clinics. Most positive samples originated from emergency departments (EDs) (47.3%) and the intensive care units (ICUs) (26.3%) of the COVID-19 hospital. Positive samples belonged almost exclusively (18/19) to the highly transmissible B.1.1.7 cluster, that might explain environmental contamination at this stage of the pandemic. The frequency and efficiency of disinfection in high-risk patient areas, such as EDs and ICUs, should be reinforced, especially during this period where highly transmissible variants of concern are widespread.

A case series of acute pericarditis following COVID-19 vaccination in the context of recent reports from Europe and the United States

Background

COVID-19 vaccines were efficacious and safe in clinical trials. We report nine events of acute pericarditis (AP) in eight patients following COVID-19 vaccination with BNT162b2 (6/9), AZD1222 (2/9) and mRNA-1273 (1/9).

Methods

All patients were referred for AP temporally linked with COVID-19 vaccination. Chest pain was the most common clinical manifestation. Alternative etiologies were excluded upon thorough diagnostic work up. AP diagnosis was established according to ESC guidelines.

Findings

Five events occurred after the first vaccine dose and four after the second. The mean age in this cohort was 65.8 ± 10.2 years and the men/women ratio 3/5. All events resolved without sequelae; two events were complicated by cardiac tamponade requiring emergent pericardial decompression. Hospitalization was required in four cases.

Interpretation

Although causality cannot be firmly established, AP has emerged as a possible complication following COVID-19 vaccination. Further investigation is indispensable to fully characterize this new entity.

Molecular Epidemiology of SARS-CoV-2 in Greece Reveals Low Rates of Onward Virus Transmission after Lifting of Travel Restrictions Based on Risk Assessment during Summer 2020

The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread rapidly during the first months of 2020 and continues to expand in multiple areas across the globe. Molecular epidemiology has provided an added value to traditional public health tools by identifying SARS-CoV-2 clusters or providing evidence that clusters based on virus sequences and contact tracing are highly concordant. Our aim was to infer the levels of virus importation and to estimate the impact of public health measures related to travel restrictions to local transmission in Greece. Our phylogenetic and phylogeographic analyses included 389 full-genome SARS-CoV-2 sequences collected during the first 7 months of the pandemic in Greece and a random collection in five replicates of 3,000 sequences sampled globally, as well as the best hits to our data set identified by BLAST. Phylogenetic trees were reconstructed by the maximum likelihood method, and the putative source of SARS-CoV-2 infections was inferred by phylogeographic analysis. Phylogenetic analyses revealed the presence of 89 genetically distinct viruses identified as independent introductions into Greece. The proportion of imported strains was 41%, 11.5%, and 8.8% during the three periods of sampling, namely, March (no travel restrictions), April to June (strict travel restrictions), and July to September (lifting of travel restrictions based on thorough risk assessment), respectively. The results of phylogeographic analysis were confirmed by a Bayesian approach. Our findings reveal low levels of onward transmission from imported cases during summer and underscore the importance of targeted public health measures that can increase the safety of international travel during a pandemic. IMPORTANCE Our study based on current state-of-the-art molecular epidemiology methods suggests that virus screening and public health measures after the lifting of travel restrictions prevented SARS-CoV-2 onward transmission from imported cases during summer 2020 in Greece. These findings provide important data on the efficacy of targeted public health measures and have important implications regarding the safety of international travel during a pandemic. Our results can provide a roadmap about prevention policy in the future regarding the reopening of borders in the presence of differences in vaccination coverage, the circulation of the virus, and the presence of newly emergent variants across the globe.

Glimpses into evolutionary trajectories of SARS-CoV-2: emerging variants and potential immune evasion routes

Tweetable abstract An opinion on the coronaviruses' evolution paradoxes, the continuing adaptation of the SARS-CoV-2 in humans following the zoonotic transmission, and clues into escape routes from host immune responses.

Pixel-Based Machine Learning and Image Reconstitution for Dot-ELISA Pathogen Diagnosis in Biological Samples

Serological methods serve as a direct or indirect means of pathogen infection diagnosis in plant and animal species, including humans. Dot-ELISA (DE) is an inexpensive and sensitive, solid-state version of the microplate enzyme-linked immunosorbent assay, with a broad range of applications in epidemiology. Yet, its applicability is limited by uncertainties in the qualitative output of the assay due to overlapping dot colorations of positive and negative samples, stemming mainly from the inherent color discrimination thresholds of the human eye. Here, we report a novel approach for unambiguous DE output evaluation by applying machine learning-based pattern recognition of image pixels of the blot using an impartial predictive model rather than human judgment. Supervised machine learning was used to train a classifier algorithm through a built multivariate logistic regression model based on the RGB ("Red," "Green," "Blue") pixel attributes of a scanned DE output of samples of known infection status to a model pathogen (Lettuce big-vein associated virus). Based on the trained and cross-validated algorithm, pixel probabilities of unknown samples could be predicted in scanned DE output images, which would then be reconstituted by pixels having probabilities above a cutoff. The cutoff may be selected at will to yield desirable false positive and false negative rates depending on the question at hand, thus allowing for proper dot classification of positive and negative samples and, hence, accurate diagnosis. Potential improvements and diagnostic applications of the proposed versatile method that translates unique pathogen antigens to the universal basic color language are discussed.

Lessons from the devastating impact of the first COVID-19 wave in Italy

Herein, we are critically examining the chain of events and discussing previously unrecognized factors that led to the 'perfect COVID-19 storm' in northern Italy during the first epidemic wave in spring 2020. SARS-CoV-2 was circulating uncontrollably at least for five weeks before the adoption of containment measures, and the role of exponential growth in the spread of the virus, conveyed by a high R₀, was likely underestimated. An understanding of this failure's causes and contexts will help us to control the strong second wave of the pandemic we are now facing in Europe, and to be better prepared for future outbreaks.

A bulletin from Greece: a health system under the pressure of the second COVID-19 wave

In this article, we analyze the cascade of events since the beginning of the coronavirus disease 2019 (COVID-19) pandemic in Greece, with emphasis on the crisis' management so as to preserve the functionality of the national health system, which remains vulnerable due to the financial recession of the previous decade and chronic shortcomings . We compare and contrast the situation during the first and second epidemic wave. Understanding what possibly went wrong and when, is crucial . Such knowledge provides valuable guidance for the confrontation of the strong second wave that we are currently facing in Europe and other regions around the globe, as well as for the future waves that may follow.

Tracing day-zero and forecasting the COVID-19 outbreak in Lombardy, Italy: A compartmental modelling and numerical optimization approach

INTRODUCTION

Italy became the second epicenter of the novel coronavirus disease 2019 (COVID-19) pandemic after China, surpassing by far China's death toll. The disease swept through Lombardy, which remained in lockdown for about two months, starting from the 8th of March. As of that day, the isolation measures taken in Lombardy were extended to the entire country. Here, assuming that effectively there was one case "zero" that introduced the virus to the region, we provide estimates for: (a) the day-zero of the outbreak in Lombardy, Italy; (b) the actual number of asymptomatic infected cases in the total population until March 8; (c) the basic (R0)and the effective reproduction number (Re) based on the estimation of the actual number of infected cases. To demonstrate the efficiency of the model and approach, we also provide a tentative forecast two months ahead of time, i.e. until May 4, the date on which relaxation of the measures commenced, on the basis of the COVID-19 Community Mobility Reports released by Google on March 29.

METHODS

To deal with the uncertainty in the number of the actual asymptomatic infected cases in the total population Volpert et al. (2020), we address a modified compartmental Susceptible/ Exposed/ Infectious Asymptomatic/ Infected Symptomatic/ Recovered/ Dead (SEIIRD) model with two compartments of infectious persons: one modelling the cases in the population that are asymptomatic or experience very mild symptoms and another modelling the infected cases with mild to severe symptoms. The parameters of the model corresponding to the recovery period, the time from the onset of symptoms to death and the time from exposure to the time that an individual starts to be infectious, have been set as reported from clinical studies on COVID-19. For the estimation of the day-zero of the outbreak in Lombardy, as well as of the "effective" per-day transmission rate for which no clinical data are available, we have used the proposed SEIIRD simulator to fit the numbers of new daily cases from February 21 to the 8th of March. This was accomplished by solving a mixed-integer optimization problem. Based on the computed parameters, we also provide an estimation of the basic reproduction number R0 and the evolution of the effective reproduction number Re. To examine the efficiency of the model and approach, we ran the simulator to "forecast" the epidemic two months ahead of time, i.e. from March 8 to May 4. For this purpose, we considered the reduction in mobility in Lombardy as released on March 29 by Google COVID-19 Community Mobility Reports, and the effects of social distancing and of the very strict measures taken by the government on March 20 and March 21, 2020.

RESULTS

Based on the proposed methodological procedure, we estimated that the expected day-zero was January 14 (min-max rage: January 5 to January 23, interquartile range: January 11 to January 18). The actual cumulative number of asymptomatic infected cases in the total population in Lombardy on March 8 was of the order of 15 times the confirmed cumulative number of infected cases, while the expected value of the basic reproduction number R0 was found to be 4.53 (min-max range: 4.40- 4.65). On May 4, the date on which relaxation of the measures commenced the effective reproduction number was found to be 0.987 (interquartiles: 0.857, 1.133). The model approximated adequately two months ahead of time the evolution of reported cases of infected until May 4, the day on which the phase I of the relaxation of measures was implemented over all of Italy. Furthermore the model predicted that until May 4, around 20% of the population in Lombardy has recovered (interquartile range: ∼10% to ∼30%).

Human genetic factors associated with susceptibility to SARS-CoV-2 infection and COVID-19 disease severity

BACKGROUND

The emergence of the novel coronavirus in Wuhan, Hubei Province, China, in December 2019 marked the synchronization of the world to a peculiar clock that is counting infected cases and deaths instead of hours and minutes. The pandemic, highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has indeed caused considerable morbidity and mortality and drastically changed our everyday lives. As we continue to become acquainted with the seventh coronavirus known to infect our species, a number of its characteristics keep surprising us. Among those is the wide spectrum of clinical manifestations of the resulting coronavirus disease 2019 (COVID-19), which ranges from asymptomatic or mildly symptomatic infections to severe pneumonia, respiratory failure, and death.

MAIN BODY

Data, now from patient populations, are beginning to accumulate on human genetic factors that may contribute to the observed diversified disease severity. Therefore, we deemed it prudent to review the associations between specific human genetic variants and clinical disease severity or susceptibility to infection that have been reported in the literature to date (at the time of writing this article in early August 2020 with updates in mid-September). With this work, we hope (i) to assist the fast-paced biomedical research efforts to combat the virus by critically summarizing current knowledge on the potential role of host genetics, and (ii) to help guide current genetics and genomics research towards candidate gene variants that warrant further investigation in larger studies. We found that determinants of differing severity of COVID-19 predominantly include components of the immune response to the virus, while determinants of differing susceptibility to SARS-CoV-2 mostly entail genes related to the initial stages of infection (i.e., binding of the cell surface receptor and entry).

CONCLUSION

Elucidating the genetic determinants of COVID-19 severity and susceptibility to SARS-CoV-2 infection would allow for the stratification of individuals according to risk so that those at high risk would be prioritized for immunization, for example, if or when safe and effective vaccines are developed. Our enhanced understanding of the underlying biological mechanisms could also guide personalized therapeutics. Such knowledge is already beginning to provide clues that help explain, at least in part, current epidemiologic observations regarding the typically more severe or benign disease course in older males and children, respectively.

SARS-CoV-2 transmission, the ambiguous role of children and considerations for the reopening of schools in the fall

Tweetable abstract The reopening of schools in the fall entails risks given the controversies in pediatric COVID-19 pathogenesis and the ambiguous role of children in transmission.

Data-based analysis, modelling and forecasting of the COVID-19 outbreak

Since the first suspected case of coronavirus disease-2019 (COVID-19) on December 1st, 2019, in Wuhan, Hubei Province, China, a total of 40,235 confirmed cases and 909 deaths have been reported in China up to February 10, 2020, evoking fear locally and internationally. Here, based on the publicly available epidemiological data for Hubei, China from January 11 to February 10, 2020, we provide estimates of the main epidemiological parameters. In particular, we provide an estimation of the case fatality and case recovery ratios, along with their 90% confidence intervals as the outbreak evolves. On the basis of a Susceptible-Infectious-Recovered-Dead (SIDR) model, we provide estimations of the basic reproduction number (R0), and the per day infection mortality and recovery rates. By calibrating the parameters of the SIRD model to the reported data, we also attempt to forecast the evolution of the outbreak at the epicenter three weeks ahead, i.e. until February 29. As the number of infected individuals, especially of those with asymptomatic or mild courses, is suspected to be much higher than the official numbers, which can be considered only as a subset of the actual numbers of infected and recovered cases in the total population, we have repeated the calculations under a second scenario that considers twenty times the number of confirmed infected cases and forty times the number of recovered, leaving the number of deaths unchanged. Based on the reported data, the expected value of R0 as computed considering the period from the 11th of January until the 18th of January, using the official counts of confirmed cases was found to be ∼4.6, while the one computed under the second scenario was found to be ∼3.2. Thus, based on the SIRD simulations, the estimated average value of R0 was found to be ∼2.6 based on confirmed cases and ∼2 based on the second scenario. Our forecasting flashes a note of caution for the presently unfolding outbreak in China. Based on the official counts for confirmed cases, the simulations suggest that the cumulative number of infected could reach 180,000 (with a lower bound of 45,000) by February 29. Regarding the number of deaths, simulations forecast that on the basis of the up to the 10th of February reported data, the death toll might exceed 2,700 (as a lower bound) by February 29. Our analysis further reveals a significant decline of the case fatality ratio from January 26 to which various factors may have contributed, such as the severe control measures taken in Hubei, China (e.g. quarantine and hospitalization of infected individuals), but mainly because of the fact that the actual cumulative numbers of infected and recovered cases in the population most likely are much higher than the reported ones. Thus, in a scenario where we have taken twenty times the confirmed number of infected and forty times the confirmed number of recovered cases, the case fatality ratio is around ∼0.15% in the total population. Importantly, based on this scenario, simulations suggest a slow down of the outbreak in Hubei at the end of February.

Data-based analysis, modelling and forecasting of the COVID-19 outbreak

Since the first suspected case of coronavirus disease-2019 (COVID-19) on December 1st, 2019, in Wuhan, Hubei Province, China, a total of 40,235 confirmed cases and 909 deaths have been reported in China up to February 10, 2020, evoking fear locally and internationally. Here, based on the publicly available epidemiological data for Hubei, China from January 11 to February 10, 2020, we provide estimates of the main epidemiological parameters. In particular, we provide an estimation of the case fatality and case recovery ratios, along with their 90% confidence intervals as the outbreak evolves. On the basis of a Susceptible-Infectious-Recovered-Dead (SIDR) model, we provide estimations of the basic reproduction number (R0), and the per day infection mortality and recovery rates. By calibrating the parameters of the SIRD model to the reported data, we also attempt to forecast the evolution of the outbreak at the epicenter three weeks ahead, i.e. until February 29. As the number of infected individuals, especially of those with asymptomatic or mild courses, is suspected to be much higher than the official numbers, which can be considered only as a subset of the actual numbers of infected and recovered cases in the total population, we have repeated the calculations under a second scenario that considers twenty times the number of confirmed infected cases and forty times the number of recovered, leaving the number of deaths unchanged. Based on the reported data, the expected value of R0 as computed considering the period from the 11th of January until the 18th of January, using the official counts of confirmed cases was found to be ∼4.6, while the one computed under the second scenario was found to be ∼3.2. Thus, based on the SIRD simulations, the estimated average value of R0 was found to be ∼2.6 based on confirmed cases and ∼2 based on the second scenario. Our forecasting flashes a note of caution for the presently unfolding outbreak in China. Based on the official counts for confirmed cases, the simulations suggest that the cumulative number of infected could reach 180,000 (with a lower bound of 45,000) by February 29. Regarding the number of deaths, simulations forecast that on the basis of the up to the 10th of February reported data, the death toll might exceed 2,700 (as a lower bound) by February 29. Our analysis further reveals a significant decline of the case fatality ratio from January 26 to which various factors may have contributed, such as the severe control measures taken in Hubei, China (e.g. quarantine and hospitalization of infected individuals), but mainly because of the fact that the actual cumulative numbers of infected and recovered cases in the population most likely are much higher than the reported ones. Thus, in a scenario where we have taken twenty times the confirmed number of infected and forty times the confirmed number of recovered cases, the case fatality ratio is around ∼0.15% in the total population. Importantly, based on this scenario, simulations suggest a slow down of the outbreak in Hubei at the end of February.

Declining seroprevalence of hepatitis A in Vojvodina, Serbia

To assess the current hepatitis A virus (HAV) endemicity in the Autonomous Province of Vojvodina, Serbia, we examined the seroprevalence and susceptibility profiles of the general population. A serum bank of 3466 residual samples, collected in 2015-16 as per the specifications of the European Sero-Epidemiology Network 2 project (ESEN2), was tested for anti-HAV antibodies with an enzyme immunoassay. Relationships between anti-HAV positivity and demographic features of respondents were examined by univariable and multivariable analyses. Present-day HAV seroprevalence was compared with that obtained in 1978-79. Surveillance data for hepatitis A recorded between 2008 and 2017 were also analyzed. Age was the only demographic variable found to be independently associated with a HAV seropositive status. Seropositivity (17% overall vs. 79% in 1978-79) increased with age to a maximum of 90% in the elderly ≥60 years. Only 5% of subjects <30 years were seropositive, unlike the 44% of seropositives ≥30 years. The estimated age at midpoint of population immunity (AMPI) increased markedly from 14 years in the late 70s to 55 years in 2015-16. Meanwhile, disease incidence decreased noticeably in recent years (from 11 in 2008 to 2 per 100,000 population in 2017). In the ongoing pre-vaccine era, natural infection provides immunity for merely a third (31%) and two thirds (57%) of people in their 40s and 50s, respectively. Hence, the majority of people ≤40 years (94%) and middle-aged adults 40-49 years (69%) are susceptible to HAV. Older susceptible individuals, particularly those ≥50 years (24%), are prone to severe symptoms. Taken together, these changes reflect the epidemiological transition of Vojvodina and Serbia from high to very low HAV endemicity, thereby supporting the current national policy of immunization of only high-risk groups.

Varicella zoster virus transmission dynamics in Vojvodina, Serbia

This study aimed at establishing baseline key epidemiological parameters for varicella zoster virus (VZV) infection in Vojvodina, Serbia, with the ultimate goal to quantify the VZV transmission potential in the population. Seroprevalence data generated during the first large cross-sectional VZV serosurvey were modelled, using a two-tiered modelling approach to calculate age-specific forces of infection (FOI), the basic reproduction number (R₀) and herd immunity threshold (H). Seroprevalence and modelling data were compared with corresponding pre-vaccination epidemiological parameters from 11 countries participating in the European Sero-Epidemiology Network 2 (ESEN2) project. Serbia fits into the general dynamic VZV transmission patterns in Europe in the pre-vaccine era, with estimated R₀ = 4.12, (95% CI: 2.69–7.07) and H = 0.76 (95% CI: 0.63–0.86). The highest VZV transmission occurs among preschool children, as evidenced by the estimation of the highest FOI (0.22, 95% CI: 0.11–0.34) in the 0.5–4 age group, with a peak FOI of 0.25 at 2.23 years. Seroprevalence was consistently lower in 5–14 year-olds, resulting in considerable shares of VZV-susceptible adolescents (7.3%), and young adults (6%), resembling the situation in a minority of European countries. The obtained key epidemiological parameters showed most intense VZV transmission in preschool children aged <4 years, justifying the consideration of universal childhood immunization in the future. National immunization strategy should consider programs for VZV serologic screening and immunization of susceptible groups, including adolescents and women of reproductive age. This work is an important milestone towards the evaluation of varicella immunization policy options in Serbia.

Forecasting and control policy assessment for the Ebola virus disease (EVD) epidemic in Sierra Leone using small-world networked model simulations

OBJECTIVES

As the Ebola virus disease is still sustained in Sierra Leone, we analysed the epidemic for a recent period (21 December 2014 to 17 April 2015) using a small-world networked model and forecasted its evolution. Policy-control scenarios for the containment of the epidemic were also examined.

METHODS

We developed an agent-based model with 6 million individuals (the population of Sierra Leone) interacting through a small-world social network. The model incorporates the main epidemiological factors, including the effect of burial practices to virus transmission. The effective reproductive number (Re) was evaluated directly from the agent-based simulations. Estimates of the epidemiological variables were computed on the basis of the official cases as reported by the Centers for Disease Control and Prevention (CDC).

RESULTS

From 21 December 2014 to 18 February 2015 the epidemic was in recession compared with previous months, as indicated by the estimated Re of ∼ 0.77 (95% CI 0.72 to 0.82). From 18 February to 17 April 2015, the Re rose above criticality (∼ 1.98, 95% CI 1.33 to 2.22), flashing a note of caution for the situation. By projecting in time, we predicted that the epidemic would continue through July 2015. Our predictions were close to the cases reported by CDC by the end of June, verifying the criticality of the situation. In light of these developments, while revising our manuscript, we expanded our analysis to include the most recent data (until 15 August 2015). By mid-August, Re had fallen below criticality and the epidemic was expected to fade out by early December 2015.

CONCLUSIONS

Our results call for the continuation of drastic control measures, which in the absence of an effective vaccine or therapy at present can only translate to isolation of the infected section of the population, to contain the epidemic.

Modeling the 2014 Ebola Virus Epidemic - Agent-Based Simulations, Temporal Analysis and Future Predictions for Liberia and Sierra Leone

We developed an agent-based model to investigate the epidemic dynamics of Ebola virus disease (EVD) in Liberia and Sierra Leone from May 27 to December 21, 2014. The dynamics of the agent-based simulator evolve on small-world transmission networks of sizes equal to the population of each country, with adjustable densities to account for the effects of public health intervention policies and individual behavioral responses to the evolving epidemic. Based on time series of the official case counts from the World Health Organization (WHO), we provide estimates for key epidemiological variables by employing the so-called Equation-Free approach. The underlying transmission networks were characterized by rather random structures in the two countries with densities decreasing by ~19% from the early (May 27-early August) to the last period (mid October-December 21). Our estimates for the values of key epidemiological variables, such as the mean time to death, recovery and the case fatality rate, are very close to the ones reported by the WHO Ebola response team during the early period of the epidemic (until September 14) that were calculated based on clinical data. Specifically, regarding the effective reproductive number Re, our analysis suggests that until mid October, Re was above 2.3 in both countries; from mid October to December 21, Re dropped well below unity in Liberia, indicating a saturation of the epidemic, while in Sierra Leone it was around 1.9, indicating an ongoing epidemic. Accordingly, a ten-week projection from December 21 estimated that the epidemic will fade out in Liberia in early March; in contrast, our results flashed a note of caution for Sierra Leone since the cumulative number of cases could reach as high as 18,000, and the number of deaths might exceed 5,000, by early March 2015. However, by processing the reported data of the very last period (December 21, 2014-January 18, 2015), we obtained more optimistic estimates indicative of a remission of the epidemic in Sierra Leone, as reflected by the derived Re (~0.82, 95% CI: 0.81-0.83).

The European Sero-Epidemiology Network 2: standardization of assay results for hepatitis B virus

The aim of the European Sero-Epidemiology Network 2 was to coordinate and standardize the serological surveillance of vaccine-preventable diseases in Europe. In this study, the standardization of hepatitis B virus (HBV) results is described. The 15 participating national laboratories tested a unique panel of 172 sera established by the Greek reference centre for HBV surface antigen (HBsAg), antibodies to HBsAg (anti-HBs) and/or to the HBV core antigen (anti-HBc) by assay methods of their choice. Country-specific quantitative measurements for anti-HBs and anti-HBc were transformed into common units using standardization equations derived by regressing each country's panel results against the reference centre's results, thus adjusting for interassay and interlaboratory variability. For HBsAg, a qualitative analysis (positive/negative) showed at least 99% agreement with the reference laboratory for all countries. By combining these standardized and qualitative results for the markers mentioned earlier, it was possible to achieve comparable estimates of the proportion of the population susceptible to HBV, vaccinated against HBV, with a past HBV infection, and with a current infection or chronic carrier state. Standardization is a very important tool that allows for international serological comparisons to assess the current vaccination policies and the progress of HBV control in Europe.

European seroepidemiology network 2: Standardisation of assays for seroepidemiology of varicella zoster virus

BACKGROUND

The aim of the European Sero-Epidemiology Network (ESEN2) is to harmonise the serological surveillance of vaccine-preventable diseases in Europe.

OBJECTIVE

To allow comparison of antibody prevalence in different countries by standardising results into common units.

STUDY DESIGN

For varicella zoster virus (VZV), a reference laboratory established a panel of 148 samples, characterised by indirect enzyme-immunoassay (ELISA), indirect immunofluorescence, and complement fixation test. Fifty-seven samples were also studied by the fluorescence antibody to membrane antigen test. The geometric mean of the antibody activity (GMAA) obtained from four ELISA determinations was used to characterise each sample of the panel as positive (GMAA: >100 mIU/ml), equivocal (GMAA: 50-100 mIU/ml) or negative (GMAA: <50 mIU/ml) for antibody to VZV (anti-VZV). Thirteen laboratories, using five different ELISA tests, tested the panel.

RESULTS

Agreement with the reference laboratory was above 85% in all cases, and the R(2) values obtained from regression analysis of the quantitative results were always higher than 0.87. Finally, the regression equations could be used to convert national values into a common unitage.

CONCLUSION

This study confirmed that results for anti-VZV obtained by different ELISA methods can be converted into common units, enabling the comparison of the seroprevalence profiles obtained in the participant countries.

Quantitation of human immunodeficiency virus type 1 DNA forms with the second template switch in peripheral blood cells predicts disease progression independently of plasma RNA load

There are several forms of human immunodeficiency virus type 1 (HIV-1) DNA in peripheral blood T cells and lymph nodes in untreated HIV-1-infected individuals and in patients whose plasma HIV-1 RNA levels are suppressed by long-term combination antiretroviral therapy. However, it remains to be established whether the concentration of HIV-1 DNA in cells predicts the clinical outcome of HIV-1 infection. In this report, we measured the concentration of HIV-1 DNA forms which has undergone the second template switch (STS DNA) and 2-long-terminal-repeat DNA circles in peripheral blood mononuclear cell (PBMC) samples. To do this, we used molecular-beacon-based real-time PCR assays and studied 130 patients with hemophilia in the Multicenter Hemophilia Cohort Study. We assessed the influence of baseline HIV-1 STS DNA levels on the progression of HIV-1 disease in the absence of combination antiretroviral therapy by Kaplan-Meier and Cox regression analysis. Among the patients who progressed to AIDS, the median levels (interquartile ranges) of STS HIV-1 DNA in PBMC were significantly higher than those of patients who remained AIDS free during the 16 years of follow-up (1,017 [235 to 6,059] and 286 [31 to 732] copies per 10(6) PBMC, respectively; P < 0.0001). Rates of progression to death and development of AIDS varied significantly (log rank P < 0.001) by quartile distribution of HIV-1 STS DNA levels. After adjustment for age at seroconversion, baseline CD4(+) T-cell counts, plasma viral load, and T-cell-receptor excision circles, the relative hazards (RH) of death and AIDS were significantly increased with higher HIV-1 STS DNA levels (adjusted RH, 1.84 [95% confidence interval (CI), 1.30 to 2.59] and 2.62 [95% CI, 1.75 to 3.93] per 10-fold increase per 10(6) PBMC, respectively). HIV-1 STS DNA levels in each individual remained steady in longitudinal PBMC samples during 16 years of follow-up. Our findings show that the concentration of HIV-1 STS DNA in PBMC complements the HIV-1 RNA load in plasma in predicting the clinical outcome of HIV-1 disease. This parameter may have important implications for understanding the virological response to combination antiretroviral therapy.

Low-dose IFN-alpha monotherapy in treatment-naive individuals with HIV-1 infection: evidence of potent suppression of viral replication

To evaluate the safety and antiviral action of interferon-alpha (IFN-alpha) in HIV-1 infection, we undertook a proof of concept study in 27 treatment-naive patients. Eligible patients comprised two groups: the IFN-alphaT group (n = 17), which received 5 MIU IFN-alpha s.c. daily for 32 consecutive days, and the IFN-alphaNT group (n = 10), which did not receive IFN-alpha prior to highly active antiretroviral therapy (HAART), which was commenced on day 28 in both groups. IFN-alphaTreatment was well tolerated in 14 of the 17 patients of the IFN-alphaT group who completed the study. The mean HIV RNA reduction in the IFN-alphaT group on day 14 was 1.1 log(10). Viral load suppression was inversely associated with baseline viral load (p = 0.031). Four weeks after initiation of HAART, IFN-alphaT and IFN-alphaNT group patients had 2.40 and 1.82 log(10) HIV RNA reduction from baseline, respectively (p < 0.001). There was no evidence of cross-resistance with existing antiretrovirals in patients with HIV-RNA rebound after initial plasma viral load decline > or = 1 log(10) during IFN-alpha monotherapy. Thus, low daily IFN-alpha exhibits potent anti-HIV-1 activity in vivo without serious adverse effects. These properties render IFN-alpha an attractive candidate for further assessment as a constituent of HAART.

Molecular characterization of a complex, recombinant human immunodeficiency virus type 1 (HIV-1) isolate (A/G/J/K/?): evidence to support the existence of a novel HIV-1 subtype

Recombination is one of several factors that contribute to the great genetic diversity of human immunodeficiency virus type 1 (HIV-1). In the current study, analysis of the full-length genome of a novel complex mosaic HIV-1 isolate (99GR303) from a Greek sailor who was possibly infected in Sierra Leone, Africa is presented. The 99GR303 isolate was found to comprise genomic regions belonging to subtypes A, G, J and K as well as of regions of a subtype that remains unclassified. For a partial region of env as well as vpr, no apparent similarity to the known HIV-1 subtypes or to any of the circulating recombinant forms was found. In fact, in the partial env gene, including the C2-V3 region, the 99GR303 isolate formed a new clade, suggesting the existence of an additional HIV-1 subtype. Thus, novel recombinants embody partial genomic regions which may have originated either from subtypes that existed in the past and became extinct or from contemporary subtypes that are extremely rare.

Effect of recent thymic emigrants on progression of HIV-1 disease

BACKGROUND

The concentration of T-cell receptor-rearrangement excision DNA circles (TREC) in peripheral-blood T cells is a marker of recent thymic emigrant alphabeta T cells. We studied the predictive ability of measurements of TREC for clinical outcome in HIV-1-infected individuals.

METHODS

We measured TREC in peripheral-blood mononuclear cells with a real-time PCR assay. We studied 131 Greek participants in the Multicenter Hemophilia Cohort Study who had known HIV-1 seroconversion dates. The prognostic value of baseline TREC, CD4 T-cell count, and HIV-1 RNA concentration was assessed by Kaplan-Meier and Cox's regression analysis.

FINDINGS

Four participants had progressed to AIDS by first blood sampling. Among the remaining 127 individuals, the median value of TREC per 10(6) cells was 6900 (IQR 2370-15604). Baseline TREC values were lower in the 53 who progressed to AIDS than in those who did not (geometric mean 2843 [95% CI 1468-5504] vs 6560 [4723-9113] per 10(6) cells; p=0.017). The relative hazard of AIDS, adjusted for plasma viral load, CD4 T-cell count, and age at seroconversion was 1.44 (95% CI 1.04-2.01; p=0.031) per ten-fold increase in TREC; that for death was 1.52 (1.12-2.06; p=0.007). The adjusted relative hazards of death were 2.91 (1.91-4.44; p<0.001) per ten-fold increase in plasma HIV-1 RNA load and 1.20 (1.04-1.38; p=0.014) per 100-cell decrease in CD4 T-cell count.

INTERPRETATION

The concentration of TREC in the peripheral T-cell pool complements HIV-1 RNA load and CD4 T-cell count in predicting the rate of HIV-1 disease progression. Recent thymic emigrants have a role in the pathogenesis of HIV-1 disease.