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1.
Math Biosci Eng ; 19(10): 9853-9876, 2022 07 11.
Article in English | MEDLINE | ID: covidwho-1964172

ABSTRACT

Epidemic spread models are useful tools to study the spread and the effectiveness of the interventions at a population level, to an epidemic. The workhorse of spatially homogeneous class models is the SIR-type ones comprising ordinary differential equations for the unknown state variables. The transition between different states is expressed through rate functions. Inspired by -but not restricted to- features of the COVID-19 pandemic, a new framework for modeling a disease spread is proposed. The main concept refers to the assignment of properties to each individual person as regards his response to the disease. A multidimensional distribution of these properties represents the whole population. The temporal evolution of this distribution is the only dependent variable of the problem. All other variables can be extracted by post-processing of this distribution. It is noteworthy that the new concept allows an improved consideration of vaccination modeling because it recognizes vaccination as a modifier of individuals response to the disease and not as a means for individuals to totally defeat the disease. At the heart of the new approach is an infection age model engaging a sharp cut-off. This model is analyzed in detail, and it is shown to admit self-similar solutions. A hierarchy of models based on the new approach, from a generalized one to a specific one with three dominant properties, is derived. The latter is implemented as an example and indicative results are presented and discussed. It appears that the new framework is general and versatile enough to simulate disease spread processes and to predict the evolution of several variables of the population during this spread.


Subject(s)
COVID-19 , Humans , Pandemics
2.
Acta Trop ; 230: 106391, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1803335

ABSTRACT

Since 2010 when West Nile virus (WNV) emerged in Greece, it causes seasonal outbreaks of human infections almost every year. During May-October of 2019-2021 a total number of 51,504 Culex pipiens mosquitoes were trapped in all seven regional units of Central Macedonia in northern Greece. They were grouped into 1099 pools and tested for WNV. The virus was detected in 5% of the mosquito pools (1.5%, 3.6% and 9.6% pools in 2019, 2020, and 2021, respectively), with significant rate differences among the regional units and years. The highest maximum likelihood estimation for WNV infection rates calculated per 1000 mosquitoes for 2019 and 2020 were 1.89 and 3.84 in Serres, and 7.08 for 2021 in Pella regional unit. Sixteen whole genome sequences were taken by applying a recently described PCR-based next generation sequencing protocol. Phylogenetic analysis showed that the sequences belonged to the Central European clade of WNV lineage 2, and that a virus strain introduced in Greece in 2019 continued to circulate and spread further during 2020-2021. The data are useful for public health and mosquito control programs' operational scheduling, while the whole genome sequences are an added value for molecular epidemiology and evolutionary studies.


Subject(s)
Culex , West Nile Fever , West Nile virus , Animals , Greece/epidemiology , Humans , Phylogeny , West Nile Fever/epidemiology , West Nile virus/genetics
3.
J Med Virol ; 94(7): 3453-3456, 2022 07.
Article in English | MEDLINE | ID: covidwho-1702621

ABSTRACT

Respiratory syncytial virus (RSV) is the most common viral pathogen causing respiratory disease in the pediatric population. An unexpected sudden upsurge of RSV infections among children was observed in September 2021 in Greece. Forty-one rhinopharyngeal samples from children under the age of 2 years with confirmed RSV bronchiolitis were tested to identify the genotype(s) of the RSV strain(s). The children were hospitalized during September-November 2021 in three tertiary hospitals in northern Greece. A one-step RT-PCR which amplifies a fragment of the second hypervariable region of the G protein gene was applied. PCR products were sequenced, and phylogenetic analysis was performed. Most (80.5%) RSV cases were typed as RSV-A, with RSV-B accounting for 19.5% of cases. RSV-A and RSV-B sequences clustered within the ON1 and BA genotypes, respectively. As the same genotypes were detected in cases observed during 2016-2018 in northern Greece, it was suggested that the early upsurge of infections was not related to the emergence of novel strain(s), but it was the result of the absence of immunity among children and their mothers due to the restriction measures taken during the COVID-19 pandemic in the previous RSV season. Awareness is needed to diagnose even the out-of-season RSV infections, while molecular epidemiology plays a key role in monitoring the efficacy of currently available therapeutics and for those under development.


Subject(s)
COVID-19 , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Child , Child, Preschool , Genotype , Greece/epidemiology , Humans , Infant , Pandemics , Phylogeny , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus, Human/genetics , Seasons
4.
Hygiene ; 1(3):80-98, 2021.
Article in English | MDPI | ID: covidwho-1444175

ABSTRACT

The recent COVID-19 pandemic and coronaviruses have been thrust into the lives of humans around the globe. Several concerns of the scientific community, authorities and common people have been aroused concerning the prophylaxis measures that need to be taken in order to safeguard public health. Among others, the possibility of a faecal—oral route, and consequent waterborne or foodborne transmission, have been given little attention. Ground zero was the seafood market of Huanan in Wuhan, China;therefore, it was quite logical at the time to assume a certain degree of relationship between water, seafood and SARS–CoV–2. In this manuscript, a critical review of the current literature concerning these routes of transmission is made. The main questions discussed are whether (i) SARS–CoV–2 can infect food animals, (ii) it can be detected in water, retaining its infectivity for the necessary amount of time, (iii) there is a possibility of contamination of food by SARS–CoV–2 through its various production processes and (iv) there is evidence of foodborne or waterborne transmission.

5.
Virusdisease ; 32(4): 766-769, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1437340

ABSTRACT

The increased demand for SARS-CoV-2 molecular testing during the COVID-19 pandemic resulted in shortage of reagents and consumables. Pooling of specimens could be an alternative strategy to overcome these problems. Initial evaluation of the pooling strategy was performed using known positive specimens, previously tested individually, and their respective pools of plus four (5X), five (6X) and nine (10X) known negative specimens. Subsequently, 35 positive 5X and 35 positive 6X pools containing only one positive specimen per pool were analyzed prospectively regarding the difference in Ct values in pooled versus individual specimens. When the number of samples in the pool were five or six, the average deviation of Ct differences was < 1; therefore, this strategy was followed in the prospective study. Significant difference in Ct values was observed in positive specimens when tested individually and in 5X pools (p = 0.006), while the difference was not significant when positive specimens were tested individually and in 6X pools (p = 0.07). The difference in Ct values was not significant between the 5X and 6X pools. Testing in pools of five or six specimens is a reliable option for SARS-CoV-2 RNA detection when mass testing is needed.

6.
Environ Sci Pollut Res Int ; 29(8): 11304-11319, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1427397

ABSTRACT

Accounting for SARS-CoV-2 adsorption on solids suspended in wastewater is a necessary step towards the reliable estimation of virus shedding rate in a sewerage system, based on measurements performed at a terminal collection station, i.e., at the entrance of a wastewater treatment plant. This concept is extended herein to include several measurement stations across a city to enable the estimation of spatial distribution of virus shedding rate. This study presents a pioneer general model describing the most relevant physicochemical phenomena with a special effort to reduce the complicated algebra. This is performed both in the topology regime, introducing a discrete-continuous approach, and in the domain of independent variables, introducing a monodisperse moment method to reduce the dimensionality of the resulting population balance equations. The resulting simplified model consists of a large system of ordinary differential equations. A sensitivity analysis is performed with respect to some key parameters for a single pipe topology. Specific numerical techniques are employed for the integration of the model. Finally, a parametric case study for an indicative-yet realistic-sewerage piping system is performed to show how the model is applied to SARS-CoV-2 adsorption on wastewater solids in the presence of other competing species. This is the first model of this kind appearing in scientific literature and a first step towards setting up an inverse problem to assess the spatial distribution of virus shedding rate based on its concentration in wastewater.


Subject(s)
COVID-19 , SARS-CoV-2 , Adsorption , Humans , Models, Theoretical , Waste Water
7.
J Med Virol ; 93(3): 1414-1420, 2021 03.
Article in English | MEDLINE | ID: covidwho-1196438

ABSTRACT

There is limited information on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection clustering within families with children. We aimed to study the transmission dynamics of SARS-CoV-2 within families with children in Greece. We studied 23 family clusters of coronavirus disease 2019 (COVID-19). Infection was diagnosed by reverse-transcriptase polymerase chain reaction in respiratory specimens. The level of viral load was categorized as high, moderate, or low based on the cycle threshold values. There were 109 household members (66 adults and 43 children). The median attack rate per cluster was 60% (range: 33.4%-100%). An adult member with COVID-19 was the first case in 21 (91.3%) clusters. Transmission of infection occurred from an adult to a child in 19 clusters and/or from an adult to another adult in 12 clusters. There was no evidence of child-to-adult or child-to-child transmission. In total 68 household members (62.4%) tested positive. Children were more likely to have an asymptomatic SARS-CoV-2 infection compared to adults (40% vs 10.5%; P = .021). In contrast, adults were more likely to develop a severe clinical course compared with children (8.8% vs 0%; P = .021). In addition, infected children were significantly more likely to have a low viral load while adults were more likely to have a moderate viral load (40.7% and 18.6% vs 13.8% and 51.7%, respectively; P = .016). In conclusion, while children become infected by SARS-CoV-2, they do not appear to transmit infection to others. Furthermore, children more frequently have an asymptomatic or mild course compared to adults. Further studies are needed to elucidate the role of viral load on these findings.


Subject(s)
COVID-19/transmission , Disease Hotspot , Adolescent , Adult , Aged , Aged, 80 and over , Asymptomatic Infections , COVID-19/epidemiology , COVID-19/physiopathology , COVID-19/virology , Child , Child, Preschool , Family Health , Female , Greece/epidemiology , Humans , Infant , Male , Middle Aged , SARS-CoV-2/physiology , Severity of Illness Index , Viral Load , Young Adult
10.
J Infect Dis ; 223(7): 1132-1138, 2021 04 08.
Article in English | MEDLINE | ID: covidwho-1003585

ABSTRACT

BACKGROUND: There is limited information on the association between upper respiratory tract (URT) viral loads, host factors, and disease severity in SARS-CoV-2-infected patients. METHODS: We studied 1122 patients (mean age, 46 years) diagnosed by polymerase chain reaction (PCR). URT viral load, measured by PCR cycle threshold, was categorized as high, moderate, or low. RESULTS: There were 336 (29.9%) patients with comorbidities; 309 patients (27.5%) had high, 316 (28.2%) moderate, and 497 (44.3%) low viral load. In univariate analyses, compared to patients with moderate or low viral load, patients with high viral load were older, more often had comorbidities, developed Symptomatic disease (COVID-19), were intubated, and died. Patients with high viral load had longer stay in intensive care unit and longer intubation compared to patients with low viral load (P values < .05 for all comparisons). Patients with chronic cardiovascular disease, hypertension, chronic pulmonary disease, immunosuppression, obesity, and chronic neurological disease more often had high viral load (P value < .05 for all comparisons). In multivariate analysis high viral load was associated with COVID-19. Level of viral load was not associated with any other outcome. CONCLUSIONS: URT viral load could be used to identify patients at higher risk for morbidity or severe outcome.


Subject(s)
COVID-19/diagnosis , SARS-CoV-2/isolation & purification , Severity of Illness Index , Viral Load/statistics & numerical data , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/mortality , COVID-19/therapy , COVID-19/virology , COVID-19 Nucleic Acid Testing/statistics & numerical data , Child , Child, Preschool , Comorbidity , Female , Humans , Infant , Infant, Newborn , Intensive Care Units/statistics & numerical data , Intubation, Intratracheal/statistics & numerical data , Length of Stay/statistics & numerical data , Male , Middle Aged , Nasopharynx/virology , Oropharynx/virology , Prospective Studies , Respiration, Artificial/statistics & numerical data , Young Adult
11.
Pediatr Infect Dis J ; 39(12): e388-e392, 2020 12.
Article in English | MEDLINE | ID: covidwho-975365

ABSTRACT

BACKGROUND: There is limited information on severe acute respiratory syndrome virus 2 (SARS-CoV-2) infection in children. METHODS: We retrieved data from the national database on SARS-CoV-2 infections. We studied in-family transmission. The level of viral load was categorized as high, moderate, or low based on the cycle threshold values. RESULTS: We studied 203 SARS-CoV-2-infected children (median age: 11 years; range: 6 days to 18.4 years); 111 (54.7%) had an asymptomatic infection. Among the 92 children (45.3%) with coronavirus disease 2019 (COVID-19), 24 (26.1%) were hospitalized. Infants <1 year were more likely to develop COVID-19 (19.5% of all COVID-19 cases) (P-value = 0.001). There was no significant difference between viral load and age, sex, underlying condition, fever and hospitalization, as well as between type of SARS-CoV-2 infection and age, sex, underlying condition and viral load. Transmission from a household member accounted for 132 of 178 (74.2%) children for whom the source of infection was identified. An adult member with COVID-19 was the first case in 125 (66.8%) family clusters. Child-to-adult transmission was found in one occasion only. CONCLUSIONS: SARS-CoV-2 infection is mainly asymptomatic or mild during childhood. Adults appear to play a key role in spread of the virus in families. Most children have moderate or high viral loads regardless of age, symptoms or severity of infection. Further studies are needed to elucidate the role of children in the ongoing pandemic and particularly in light of schools reopening and the need to prioritize groups for vaccination, when COVID-19 vaccines will be available.


Subject(s)
COVID-19/epidemiology , Adolescent , Asymptomatic Infections/epidemiology , COVID-19/pathology , COVID-19/transmission , COVID-19/virology , Child , Child, Preschool , Contact Tracing , Female , Greece/epidemiology , Hospitalization , Humans , Infant , Infant, Newborn , Male , SARS-CoV-2 , Viral Load
12.
Emerg Infect Dis ; 26(8): 1944-1946, 2020 08.
Article in English | MEDLINE | ID: covidwho-326416
13.
Euro Surveill ; 25(6)2020 02.
Article in English | MEDLINE | ID: covidwho-664

ABSTRACT

Timely detection of novel coronavirus (2019-nCoV) infection cases is crucial to interrupt the spread of this virus. We assessed the required expertise and capacity for molecular detection of 2019-nCoV in specialised laboratories in 30 European Union/European Economic Area (EU/EEA) countries. Thirty-eight laboratories in 24 EU/EEA countries had diagnostic tests available by 29 January 2020. A coverage of all EU/EEA countries was expected by mid-February. Availability of primers/probes, positive controls and personnel were main implementation barriers.


Subject(s)
Betacoronavirus , Clinical Laboratory Techniques/standards , Coronavirus Infections/diagnosis , Coronavirus/genetics , Coronavirus/isolation & purification , Laboratories/standards , Pneumonia, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction/methods , COVID-19 , Clinical Laboratory Techniques/methods , Coronavirus/classification , Coronavirus Infections/genetics , Coronavirus Infections/virology , Disease Outbreaks , European Union , Humans , RNA, Viral/genetics , Reference Standards , SARS-CoV-2 , Sensitivity and Specificity , Sentinel Surveillance , Sequence Analysis
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