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1.
Pathogens ; 11(4):462, 2022.
Article in English | ProQuest Central | ID: covidwho-1810061

ABSTRACT

Several professional societies advise against using real-time Reverse-Transcription PCR (rtRT-PCR) cycle threshold (Ct) values to guide clinical decisions. We comparatively assessed the variability of Ct values generated by six diagnostic approaches by testing serial dilutions of well-characterized isolates of 10 clinically most relevant SARS-CoV-2 genomic variants: Alpha, Beta, Gamma, Delta, Eta, Iota, Omicron, A.27, B.1.258.17, and B.1 with D614G mutation. Comparison of three fully automated rtRT-PCR analyzers and a reference manual rtRT-PCR assay using RNA isolated with three different nucleic acid isolation instruments showed substantial inter-variant intra-test and intra-variant inter-test variability. Ct value differences were dependent on both the rtRT-PCR platform and SARS-CoV-2 genomic variant. Differences ranging from 2.0 to 8.4 Ct values were observed when testing equal concentrations of different SARS-CoV-2 variants. Results confirm that Ct values are an unreliable surrogate for viral load and should not be used as a proxy of infectivity and transmissibility, especially when different rtRT-PCR assays are used in parallel and multiple SARS-CoV-2 variants are circulating. A detailed turn-around time (TAT) comparative assessment showed substantially different TATs, but parallel use of different diagnostic approaches was beneficial and complementary, allowing release of results for more than 81% of non-priority samples within 8 h after admission.

2.
Microorganisms ; 10(2)2022 Jan 24.
Article in English | MEDLINE | ID: covidwho-1715558

ABSTRACT

Bats are natural reservoirs of a variety of zoonotic viruses, many of which cause severe human diseases. Characterizing viruses of bats inhabiting different geographical regions is important for understanding their viral diversity and for detecting viral spillovers between animal species. Herein, the diversity of DNA viruses of five arthropodophagous bat species from Argentina was investigated using metagenomics. Fecal samples of 29 individuals from five species (Tadarida brasiliensis, Molossus molossus, Eumops bonariensis, Eumops patagonicus, and Eptesicus diminutus) living at two different geographical locations, were investigated. Enriched viral DNA was sequenced using Illumina MiSeq, and the reads were trimmed and filtered using several bioinformatic approaches. The resulting nucleotide sequences were subjected to viral taxonomic classification. In total, 4,520,370 read pairs were sequestered by sequencing, and 21.1% of them mapped to viral taxa. Circoviridae and Genomoviridae were the most prevalent among vertebrate viral families in all bat species included in this study. Samples from the T. brasiliensis colony exhibited lower viral diversity than samples from other species of New World bats. We characterized 35 complete genome sequences of novel viruses. These findings provide new insights into the global diversity of bat viruses in poorly studied species, contributing to prevention of emerging zoonotic diseases and to conservation policies for endangered species.

3.
J Clin Med ; 11(5)2022 Feb 23.
Article in English | MEDLINE | ID: covidwho-1700709

ABSTRACT

Vaccine breakthrough SARS-CoV-2 infections necessitating hospitalization have emerged as a relevant problem with longer time interval since vaccination and the predominance of the Delta variant. The aim of this study was to evaluate the association between primary vaccination with four SARS-CoV-2 vaccines authorized for use in the European Union-BNT162b2, ChAdOx-1S, mRNA-1273 or Ad.26.COV2.S-and progression to critically severe disease (mechanical ventilation or death) and duration of hospitalization among adult patients with PCR-confirmed acute COVID-19 hospitalized during the Delta variant predominance (October-November 2021) in Slovenia. Among the 529 enrolled patients hospitalized with COVID-19 (median age, 65 years; 58.2% men), 175 (33.1%) were fully vaccinated at the time of symptom onset. Compared with 345 unvaccinated patients, fully vaccinated patients with breakthrough infections were older, more often immunocompromised, and had higher Charlson comorbidity index scores. After adjusting for sex, age, and comorbidities, fully vaccinated patients had lower odds for progressing to critically severe disease and were discharged from the hospital earlier than unvaccinated patients. Vaccination against SARS-CoV-2 remains an extremely effective intervention to alleviate morbidity and mortality in COVID-19 patients.

4.
Prev Med ; 156: 106960, 2022 03.
Article in English | MEDLINE | ID: covidwho-1655254

ABSTRACT

The global confrontation with COVID-19 has not only diverted current healthcare resources to deal with the infection but has also resulted in increased resources in the areas of testing and screening, as well as educating most of the global public of the benefits of vaccination. When the COVID-19 pandemic eventually recedes, the opportunity must not be missed to ensure that these newly created resources are maintained and redeployed for use in testing and immunisation against other vaccine-preventable infectious diseases. A notable example is infection by human papillomavirus (HPV), the commonest sexually transmitted human virus and the leading cause of a variety of cancers in both men and women, such as cervical, head and neck, anal, vaginal, vulvar and penile cancers. The most important is cervical cancer, the objective of the global elimination goals targeting the vaccination of young female and male adolescents, screening all women and treatment of all infected women. As the campaigns to control SARS-CoV-2, the eradication of HPV-induced cancers also relies on effective prevention and control programs. The lessons learned and the technical, logistical and human resources which have been established to combat COVID-19 by vaccination and testing must be applied to the eradication of other infections which affect the global population. This commentary summarizes the opportunities that the COVID-19 pandemic has created for HPV prevention and control, lists the already available tools for HPV control, and emphasizes the potential public health threats amidst the ongoing COVID-19 pandemic.


Subject(s)
Alphapapillomavirus , COVID-19 , Papillomavirus Infections , Papillomavirus Vaccines , Uterine Cervical Neoplasms , Adolescent , COVID-19/prevention & control , Female , Humans , Male , Pandemics/prevention & control , Papillomaviridae , Papillomavirus Infections/epidemiology , Papillomavirus Vaccines/therapeutic use , SARS-CoV-2 , Uterine Cervical Neoplasms/diagnosis , Vaccination
5.
J Mol Diagn ; 23(8): 920-928, 2021 08.
Article in English | MEDLINE | ID: covidwho-1386075

ABSTRACT

The Alinity m (Abbott Molecular, Des Plaines, IL) automated molecular analyzer allows continuous loading of samples and sample-to-result molecular detection of several microorganisms. The detection of SARS-CoV-2 by the Alinity m was compared with that of the cobas 6800 (Roche Molecular Systems, Branchburg, NJ; standard comparator) in a manufacturer-independent clinical evaluation on 2157 consecutive nasopharyngeal swab samples. Valid initial results on Alinity m and cobas 6800 were obtained from 2129 (98.7%) and 2157 (100%) samples, respectively. The overall percent agreement (95% CI) was 98.3% (2092/2129 [97.6%-98.7%]); positive percent agreement, 100% (961/961 [99.6%-100%]); negative percent agreement, 96.8% (1131/1168 [95.7%-97.7%]); and high κ value, 0.965 (0.954-0.976). There were 37 discordant results on Alinity m and, based on discordant analyses, including previous and/or follow-up PCR results, 22 could be considered analytically true positive with high probability. Due to a lack of additional information and an inability to perform repeated/further testing, the status of the remaining 15 discordant results remained unresolved. The throughput of the two analyzers was compared using testing on 564 samples in parallel across two 8-hour shifts in clinical practice. The turnaround times were compared using processing of 94 routine samples in parallel on each working day for 5 consecutive days. The two analyzers showed similar performance, with certain differences that have potential importance in some laboratory settings.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Nasopharynx/virology , RNA, Viral/genetics , SARS-CoV-2/genetics , COVID-19/virology , COVID-19 Nucleic Acid Testing/economics , Humans , RNA, Viral/analysis , Reproducibility of Results , SARS-CoV-2/isolation & purification
6.
Emerg Infect Dis ; 27(9): 2450-2453, 2021 09.
Article in English | MEDLINE | ID: covidwho-1369633

ABSTRACT

We report a case of natural infection with severe acute respiratory syndrome coronavirus 2 transmitted from an owner to a pet ferret in the same household in Slovenia. The ferret had onset of gastroenteritis with severe dehydration. Whole-genome sequencing of the viruses isolated from the owner and ferret revealed a 2-nt difference.


Subject(s)
COVID-19 , Ferrets , Animals , Humans , SARS-CoV-2 , Slovenia
7.
Clin Microbiol Infect ; 27(7): 1039.e1-1039.e7, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1202998

ABSTRACT

OBJECTIVES: Seroprevalence surveys provide crucial information on cumulative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure. This Slovenian nationwide population study is the first longitudinal 6-month serosurvey using probability-based samples across all age categories. METHODS: Each participant supplied two blood samples: 1316 samples in April 2020 (first round) and 1211 in October/November 2020 (second round). The first-round sera were tested using Euroimmun Anti-SARS-CoV-2 ELISA IgG (ELISA) and, because of uncertain estimates, were retested using Elecsys Anti-SARS-CoV-2 (Elecsys-N) and Elecsys Anti-SARS-CoV-2 S (Elecsys-S). The second-round sera were concomitantly tested using Elecsys-N/Elecsys-S. RESULTS: The populations of both rounds matched the overall population (n = 3000), with minor settlement type and age differences. The first-round seroprevalence corrected for the ELISA manufacturer's specificity was 2.78% (95% highest density interval [HDI] 1.81%-3.80%), corrected using pooled ELISA specificity calculated from published data 0.93% (95% CI 0.00%-2.65%), and based on Elecsys-N/Elecsys-S results 0.87% (95% HDI 0.40%-1.38%). The second-round unadjusted lower limit of seroprevalence on 11 November 2020 was 4.06% (95% HDI 2.97%-5.16%) and on 3 October 2020, unadjusted upper limit was 4.29% (95% HDI 3.18%-5.47%). CONCLUSIONS: SARS-CoV-2 seroprevalence in Slovenia increased four-fold from late April to October/November 2020, mainly due to a devastating second wave. Significant logistic/methodological challenges accompanied both rounds. The main lessons learned were a need for caution when relying on manufacturer-generated assay evaluation data, the importance of multiple manufacturer-independent assay performance assessments, the need for concomitant use of highly-specific serological assays targeting different SARS-CoV-2 proteins in serosurveys conducted in low-prevalence settings or during epidemic exponential growth and the usefulness of a Bayesian approach for overcoming complex methodological challenges.


Subject(s)
COVID-19 Serological Testing/statistics & numerical data , COVID-19/epidemiology , COVID-19/immunology , Adolescent , Adult , Age Distribution , Aged , Aged, 80 and over , Antibodies, Viral/blood , Bayes Theorem , Child , Child, Preschool , Enzyme-Linked Immunosorbent Assay , Female , Humans , Immunoglobulin G/blood , Infant , Infant, Newborn , Male , Middle Aged , Pandemics , Population Surveillance , Prevalence , Sensitivity and Specificity , Seroepidemiologic Studies , Sex Distribution , Slovenia/epidemiology , Young Adult
8.
J Clin Virol ; 139: 104820, 2021 06.
Article in English | MEDLINE | ID: covidwho-1174355

ABSTRACT

BACKGROUND: Neutralization tests (NT) are the gold standard for detecting and quantifying anti-SARS-CoV-2 neutralizing antibodies (NAb), but their complexity restricts them to research settings or reference laboratories. Antibodies against S protein receptor binding domain (RBD) have been shown to confer a neutralizing activity against SARS-CoV-2. Assays quantitatively measuring anti-S1-RBD-SARS-CoV-2 antibodies could be of great value for NAb screening of potential donors for convalescent-phase plasma therapy, assessing natural or vaccine-induced immunity, stratifying individuals for vaccine receipt, and documenting vaccine response. METHODS: Elecsys Anti-SARS-CoV-2 S (Elecsys-S), a high-throughput automated electrochemiluminescence double-antigen sandwich immunoassay for quantitative measurement of pan-anti-S1-RBD-SARS-CoV-2 antibodies, was evaluated against NT on 357 patients with PCR-confirmed SARS-CoV-2 infection. NT was performed in a BSL-3 laboratory using a Slovenian SARS-CoV-2 isolate; the NT titer ≥1:20 was considered positive. RESULTS: Elecsys-S detected pan-anti-S1-RBD-SARS-CoV-2 antibodies in 352/357 (98.6 %) samples. NAb were identified by NT in 257/357 (72 %) samples. The Elecsys-S/NT agreement was moderate (Cohen's kappa 0.56). High NT titer antibodies (≥1:160) were detected in 106/357 (30 %) samples. Elecsys-S's pan-anti-S1-RBD-SARS-CoV-2 antibody concentrations correlated with individual NT titer categories (the lowest concentrations were identified in NT-negative samples and the highest in samples with NT titer 1:1,280), and the Elecsys-S cutoff value for reasonable prediction of NAb generated after natural infection was established (133 BAU/mL). CONCLUSION: Although NT should remain the gold standard for assessing candidates for convalescent-phase plasma donors, selected commercial anti-SARS-CoV-2 assays with optimized cutoff, like Elecsys-S, could be used for rapid, automated, and large-scale screening of individuals with clinically relevant NAb levels as suitable donors.


Subject(s)
Antibodies, Viral/blood , COVID-19/diagnosis , Immunoassay/methods , Luminescent Measurements/methods , Neutralization Tests , Spike Glycoprotein, Coronavirus/immunology , COVID-19 Serological Testing , High-Throughput Screening Assays , Humans , Spike Glycoprotein, Coronavirus/chemistry
9.
J Clin Virol ; 137: 104784, 2021 04.
Article in English | MEDLINE | ID: covidwho-1122967

ABSTRACT

BACKGROUND: Accurate anti-SARS-CoV-2 assays are needed to inform diagnostic, therapeutic, and public health decisions. The first manufacturer-independent head-to-head comparison of two rapid high-throughput automated electrochemiluminescence double-antigen sandwich immunoassays targeting total anti-SARS-CoV-2 antibodies against two different viral proteins, Elecsys Anti-SARS-CoV-2 (Elecsys-N) and Elecsys Anti-SARS-CoV-2 S (Elecsys-S) (Roche Diagnostics), was performed in a routine setting during the exponential growth phase of the epidemic's second wave. METHODS: The diagnostic specificity of Elecsys-N and Elecsys-S was initially evaluated on a panel of 572 pre-COVID-19 samples, showing 100 % specificity of both assays. Elecsys-N/Elecsys-S head-to-head comparison used 3,416 consecutive blood samples from individuals that were tested for the presence of anti-SARS-CoV-2 within commercial out-of-pocket serologic testing. RESULTS: Elecsys-N/Elecsys-S head-to-head comparison showed overall agreement of 98.68 % (3,371/3,416; 95 % CI, 98.23-99.03 %), positive agreement of 95.16 % (884/929; 95 % CI, 93.52-96.41 %), and a high kappa value of 0.996 (95 % CI, 0.956-0.976). Previous SARS-CoV-2 PCR positivity was identified in 14/24 (58.3 %) Elecsys-N negative/Elecsys-S positive individuals and in 4/21 (19.0 %) Elecsys-N positive/Elecsys-S negative individuals. CONCLUSION: The first Elecsys-N/Elecsys-S head-to-head comparison showed excellent agreement of two highly specific and rapid high-throughput automated anti-SARS-CoV-2 assays. An important question is whether laboratories offering two different antibody assays could benefit from combining the assays; if so, should use be concomitant or sequential-and, in the latter case, in which order? Based on our results, we favor concomitant over sequential Elecsys-N/Elecsys-S use when testing individuals for anti-SARS-CoV-2 antibodies in high-incidence settings; for example, during the exponential or stationary growth phase of the COVID-19 epidemic.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/methods , COVID-19/diagnosis , High-Throughput Screening Assays/methods , Nucleoproteins/immunology , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , COVID-19/blood , Electrochemistry/methods , Humans , Immunoassay/methods , Immunoglobulin G/blood , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
10.
Front Microbiol ; 11: 619498, 2020.
Article in English | MEDLINE | ID: covidwho-1024512
11.
J Perinat Med ; 49(3): 269-273, 2021 Mar 26.
Article in English | MEDLINE | ID: covidwho-890211

ABSTRACT

OBJECTIVES: Information on the usefulness of screen-and-test strategies of pregnant women for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is lacking. METHODS: We retrospectively reviewed the Ljubljana Maternity Hospital database and searched for pregnant women, who were admitted to the hospital between March 15 and May 16, 2020, for a planned procedure or hospitalization. Their medical records were examined and SARS-CoV-2 test results were retrieved. RESULTS: During the two-month period analyzed, there were a total of 265 scheduled admissions of pregnant women to our hospital. Two hundred two (76.2%) were tested for SARS-CoV-2 1 day prior to admission. All tested negative for SARS-CoV-2 RNA, regardless of having coronavirus disease 2019 (COVID-19)-compatible signs or symptoms (n=28) or not (n=174). CONCLUSIONS: In a population with a low SARS-CoV-2 burden, usefulness of universal testing of pregnant women before admission to the hospital is limited. We recommend that obstetric units in regions with low SARS-CoV-2 burden enforce rational use of personal protective equipment and diligent screening protocols using targeted questionnaires, whereas SARS-CoV-2 laboratory testing should be performed only in screen-positives: those with high clinical suspicion of COVID-19 and/or suspected epidemiological history.


Subject(s)
COVID-19 Serological Testing/methods , COVID-19/diagnosis , Mass Screening/methods , Practice Patterns, Physicians'/statistics & numerical data , Pregnancy Complications, Infectious/diagnosis , Prenatal Care/methods , Adult , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Serological Testing/statistics & numerical data , Cost of Illness , Female , Hospitalization , Humans , Infection Control/methods , Infection Control/standards , Mass Screening/standards , Mass Screening/statistics & numerical data , Practice Patterns, Physicians'/standards , Pregnancy , Pregnancy Complications, Infectious/epidemiology , Pregnancy Complications, Infectious/prevention & control , Prenatal Care/standards , Prenatal Care/statistics & numerical data , Quality Improvement , Retrospective Studies , Slovenia/epidemiology
12.
Viruses ; 12(8)2020 08 14.
Article in English | MEDLINE | ID: covidwho-831474

ABSTRACT

To date, the microbiome, as well as the virome of the Croatian populations of bats, was unknown. Here, we present the results of the first viral metagenomic analysis of guano, feces and saliva (oral swabs) of seven bat species (Myotis myotis, Miniopterus schreibersii, Rhinolophus ferrumequinum, Eptesicus serotinus, Myotis blythii, Myotis nattereri and Myotis emarginatus) conducted in Mediterranean and continental Croatia. Viral nucleic acids were extracted from sample pools, and analyzed using Illumina sequencing. The presence of 63 different viral families representing all seven Baltimore groups were confirmed, most commonly insect viruses likely reflecting the diet of insectivorous bats. Virome compositions of our samples were largely impacted by the sample type: invertebrate-infecting viruses were most frequently found in feces, bacterial viruses in guano, whereas vertebrate-infecting viruses were most common in swabs. Most vertebrate-infecting virus sequences were assigned to retroviruses, parvoviruses, iridoviruses, and poxviruses. We further report the complete genome sequence of a novel adeno-associated virus, densovirus and a near complete length genome sequence of a novel iflavirus. Additionally, one of the most interesting findings in this study was the difference in viromes between two contrasting habitats, the continental and Mediterranean Croatia.


Subject(s)
Chiroptera/virology , Disease Reservoirs/veterinary , Ecosystem , Metagenome , Virome/genetics , Virus Diseases/veterinary , Animals , Croatia , Disease Reservoirs/virology , Feces/virology , High-Throughput Nucleotide Sequencing , Insect Viruses/classification , Metagenomics , Phylogeny , Saliva/virology , Sequence Analysis, DNA , Viruses/classification , Viruses/isolation & purification , Zoonoses/virology
14.
Int J Cancer ; 148(2): 277-284, 2021 01 15.
Article in English | MEDLINE | ID: covidwho-635339

ABSTRACT

The age-standardised incidence of cervical cancer in Europe varies widely by country (between 3 and 25/100000 women-years) in 2018. Human papillomavirus (HPV) vaccine coverage is low in countries with the highest incidence and screening performance is heterogeneous among European countries. A broad group of delegates of scientific professional societies and cancer organisations endorse the principles of the WHO call to eliminate cervical cancer as a public health problem, also in Europe. All European nations should, by 2030, reach at least 90% HPV vaccine coverage among girls by the age of 15 years and also boys, if cost-effective; they should introduce organised population-based HPV-based screening and achieve 70% of screening coverage in the target age group, providing also HPV testing on self-samples for nonscreened or underscreened women; and to manage 90% of screen-positive women. To guide member states, a group of scientific professional societies and cancer organisations engage to assist in the rollout of a series of concerted evidence-based actions. European health authorities are requested to mandate a group of experts to develop the third edition of European Guidelines for Quality Assurance of Cervical Cancer prevention based on integrated HPV vaccination and screening and to monitor the progress towards the elimination goal. The occurrence of the COVID-19 pandemic, having interrupted prevention activities temporarily, should not deviate stakeholders from this ambition. In the immediate postepidemic phase, health professionals should focus on high-risk women and adhere to cost-effective policies including self-sampling.


Subject(s)
Alphapapillomavirus/immunology , Papillomavirus Infections/immunology , Papillomavirus Vaccines/immunology , Public Health/methods , Uterine Cervical Neoplasms/prevention & control , Adolescent , Adult , Alphapapillomavirus/physiology , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , Early Detection of Cancer , Europe , Female , Humans , Male , Middle Aged , Pandemics , Papillomavirus Infections/prevention & control , Papillomavirus Infections/virology , Papillomavirus Vaccines/administration & dosage , Public Health/standards , Public Health/statistics & numerical data , SARS-CoV-2/physiology , Uterine Cervical Neoplasms/diagnosis , Uterine Cervical Neoplasms/immunology , Vaccination/methods , World Health Organization , Young Adult
16.
J Clin Microbiol ; 58(6)2020 05 26.
Article in English | MEDLINE | ID: covidwho-46769

ABSTRACT

Laboratories are currently witnessing extraordinary demand globally for sampling devices, reagents, consumables, and diagnostic instruments needed for timely diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. To meet diagnostic needs as the pandemic grows, the U.S. Food and Drug Administration (FDA) recently granted several commercial SARS-CoV-2 tests Emergency Use Authorization (EUA), but manufacturer-independent evaluation data are scarce. We performed the first manufacturer-independent evaluation of the fully automated sample-to-result two-target test cobas 6800 SARS-CoV-2 (cobas) (Roche Molecular Systems, Branchburg, NJ), which received U.S. FDA EUA on 12 March 2020. The comparator was a standardized 3-h SARS-CoV-2 protocol, consisting of RNA extraction using an automated portable instrument, followed by a two-target reverse transcription real-time PCR (RT-PCR), which our laboratory has routinely used since January 2020 [V. M. Corman, O. Landt, M. Kaiser, R. Molenkamp, et al., Euro Surveill 25(3):pii=2000045, 2020, https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045]. cobas and the comparator showed overall agreement of 98.1% and a kappa value of 0.95 on an in-house validation panel consisting of 217 well-characterized retrospective samples. Immediate prospective head-to-head comparative evaluation followed on 502 samples, and the diagnostic approaches showed overall agreement of 99.6% and a kappa value of 0.98. A good correlation (r 2 = 0.96) between cycle threshold values for SARS-CoV-2-specific targets obtained by cobas and the comparator was observed. Our results showed that cobas is a reliable assay for qualitative detection of SARS-CoV-2 in nasopharyngeal swab samples collected in the Universal Transport Medium System (UTM-RT) (Copan, Brescia, Italy). Under the extraordinary circumstances that laboratories are facing worldwide, a safe diagnostic platform switch is feasible in only 48 h and in the midst of the COVID-19 pandemic if carefully planned and executed.


Subject(s)
Betacoronavirus , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Betacoronavirus/genetics , COVID-19 , COVID-19 Testing , COVID-19 Vaccines , Humans , Pandemics , SARS-CoV-2 , Time Factors
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