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1.
Nature ; 2021 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-34695836

RESUMO

SARS-CoV-2 is a single-stranded RNA virus that causes coronavirus disease 2019 (COVID-19). Given its acute and often self-limiting course, components of the innate immune system are likely central in controlling virus replication thereby determining clinical outcome. Natural killer (NK) cells are innate lymphocytes with notable activity against a broad range of viruses, including RNA viruses1,2. NK cell function may be altered during COVID-19 despite increased representation of NK cells with an activated and 'adaptive' phenotype3,4. Here we show that viral load decline in COVID-19 correlates with NK cell status and that NK cells can control SARS-CoV-2 replication by recognizing infected target cells. In severe COVID-19, NK cells show remarkable defects in virus control, cytokine production and cell-mediated cytotoxicity despite high expression of cytotoxic effector molecules. Single-cell RNA-sequencing (scRNA-seq) of NK cells along the time course of the entire COVID-19 disease spectrum reveals a unique gene expression signature. Transcriptional networks of interferon-driven NK cell activation are superimposed by a dominant TGFß response signature with reduced expression of genes related to cell-cell adhesion, granule exocytosis and cell-mediated cytotoxicity. In severe COVID-19, serum levels of TGFß peak during the first 2 weeks of infection, and serum obtained from these patients profoundly inhibits NK cell function in a TGFß-dependent manner. Our data reveal that untimely production of TGFß is a hallmark of severe COVID-19 and may inhibit NK cell function and early virus control.

2.
Infect Dis (Lond) ; 53(12): 947-952, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34445926

RESUMO

INTRODUCTION: Most SARS-CoV-2 antigen-detecting rapid diagnostic tests require nasopharyngeal sampling, which is frequently perceived as uncomfortable and requires healthcare professionals, thus limiting scale-up. Nasal sampling could enable self-sampling and increase acceptability. The term nasal sampling is often not used uniformly and sampling protocols differ. METHODS: This manufacturer-independent, prospective diagnostic accuracy study, compared professional anterior nasal and nasal mid-turbinate sampling for a WHO-listed SARS-CoV-2 antigen-detecting rapid diagnostic test. The second group of participants collected a nasal mid-turbinate sample themselves and underwent a professional nasopharyngeal swab for comparison. The reference standard was real-time polymerase chain reaction (RT-PCR) using combined oro-/nasopharyngeal sampling. Individuals with high suspicion of SARS-CoV-2 infection were tested. Sensitivity, specificity, and percent agreement were calculated. Self-sampling was observed without intervention. Feasibility was evaluated by observer and participant questionnaires. RESULTS: Among 132 symptomatic adults, both professional anterior nasal and nasal mid-turbinate sampling yielded a sensitivity of 86.1% (31/36 RT-PCR positives detected; 95%CI: 71.3-93.9) and a specificity of 100.0% (95%CI: 95.7-100). The positive percent agreement was 100% (95%CI: 89.0-100). Among 96 additional adults, self nasal mid-turbinate and professional nasopharyngeal sampling yielded an identical sensitivity of 91.2% (31/34; 95%CI 77.0-97.0). Specificity was 98.4% (95%CI: 91.4-99.9) with nasal mid-turbinate and 100.0% (95%CI: 94.2-100) with nasopharyngeal sampling. The positive percent agreement was 96.8% (95%CI: 83.8-99.8). Most participants (85.3%) considered self-sampling as easy to perform. CONCLUSION: Professional anterior nasal and nasal mid-turbinate sampling are of equivalent accuracy for an antigen-detecting rapid diagnostic test in ambulatory symptomatic adults. Participants were able to reliably perform nasal mid-turbinate sampling themselves, following written and illustrated instructions. Nasal self-sampling will facilitate scaling of SARS-CoV-2 antigen testing.


Assuntos
COVID-19 , SARS-CoV-2 , Adulto , Humanos , Estudos Prospectivos , Sensibilidade e Especificidade , Conchas Nasais
3.
Infection ; 2021 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-34383260

RESUMO

PURPOSE: Rapid antigen-detecting tests (Ag-RDTs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transform pandemic control. Thus far, sensitivity (≤ 85%) of lateral-flow assays has limited scale-up. Conceivably, microfluidic immunofluorescence Ag-RDTs could increase sensitivity for SARS-CoV-2 detection. METHODS: This multi-centre diagnostic accuracy study investigated performance of the microfluidic immunofluorescence LumiraDx™ assay, enrolling symptomatic and asymptomatic participants with suspected SARS-CoV-2 infection. Participants collected a supervised nasal mid-turbinate (NMT) self-swab for Ag-RDT testing, in addition to a professionally collected nasopharyngeal (NP) swab for routine testing with reverse transcriptase polymerase chain reaction (RT-PCR). Results were compared to calculate sensitivity and specificity. Sub-analyses investigated the results by viral load, symptom presence and duration. An analytical study assessed exclusivity and limit-of-detection (LOD). In addition, we evaluated ease-of-use. RESULTS: The study was conducted between November 2nd 2020 and 4th of December 2020. 761 participants were enrolled, with 486 participants reporting symptoms on testing day. 120 out of 146 RT-PCR positive cases were detected positive by LumiraDx™, resulting in a sensitivity of 82.2% (95% CI 75.2-87.5%). Specificity was 99.3% (CI 98.3-99.7%). Sensitivity was increased in individuals with viral load ≥ 7 log10 SARS-CoV2 RNA copies/ml (93.8%; CI 86.2-97.3%). Testing against common respiratory commensals and pathogens showed no cross-reactivity and LOD was estimated to be 2-56 PFU/mL. The ease-of-use-assessment was favourable for lower throughput settings. CONCLUSION: The LumiraDx™ assay showed excellent analytical sensitivity, exclusivity and clinical specificity with good clinical sensitivity using supervised NMT self-sampling. TRIAL REGISTRATION NUMBER AND REGISTRATION DATE: DRKS00021220 and 01.04.2020.

4.
J Clin Virol ; 141: 104874, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34144452

RESUMO

BACKGROUND: Considering the possibility of nasal self-sampling and the ease of use in performing SARS-CoV-2 antigen-detecting rapid diagnostic tests (Ag-RDTs), self-testing is a feasible option. OBJECTIVE: The goal of this study was a head-to-head comparison of diagnostic accuracy of patient self-testing with professional testing using a SARS-CoV-2 Ag-RDT. STUDY DESIGN: We performed a manufacturer-independent, prospective diagnostic accuracy study of nasal mid-turbinate self-sampling and self-testing with symptomatic adults using a WHO-listed SARS-CoV-2 Ag-RDT. Procedures were observed without intervention. For comparison, Ag-RDTs with nasopharyngeal sampling were professionally performed. Estimates of agreement, sensitivity, and specificity relative to RT-PCR on a combined oro-/nasopharyngeal sample were calculated. Feasibility was evaluated by observer and participant questionnaires. RESULTS: Among 146 symptomatic adults, 40 (27.4%) were RT-PCR-positive for SARS-CoV-2. Sensitivity with self-testing was 82.5% (33/40; 95% CI 68.1-91.3), and 85.0% (34/40; 95% CI 70.9-92.9) with professional testing. At high viral load (≥7.0 log10 SARS-CoV-2 RNA copies/ml), sensitivity was 96.6% (28/29; 95% CI 82.8-99.8) for both self- and professional testing. Deviations in sampling and testing were observed in 25 out of the 40 PCR-positives. Most participants (80.9%) considered the Ag-RDT as easy to perform. CONCLUSION: Laypersons suspected for SARS-CoV-2 infection were able to reliably perform the Ag-RDT and test themselves. Procedural errors might be reduced by refinement of the instructions for use or the product design/procedures. Self-testing allows more wide-spread and frequent testing. Paired with the appropriate information of the public about the benefits and risks, self-testing may have significant impact on the pandemic.


Assuntos
COVID-19 , SARS-CoV-2 , Adulto , Antígenos Virais , Estudos de Viabilidade , Humanos , Estudos Prospectivos , RNA Viral , Autoteste , Sensibilidade e Especificidade
5.
Clin Microbiol Infect ; 27(10): 1520.e7-1520.e10, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34139335

RESUMO

OBJECTIVES: Dexamethasone has become the standard of care for severe coronavirus disease 2019 (COVID-19), but its virological impact is poorly understood. The objectives of this work were to characterize the kinetics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) concentration in the upper respiratory tract (URT) and the antibody response in patients with (D+) and without (D-) dexamethasone treatment. METHODS: Data and biosamples from hospitalized patients with severe COVID-19, enrolled between 4th March and 11th December 2020 in a prospective observational study, were analysed. SARS-CoV-2 virus concentration in serial URT samples was measured using RT-PCR. SARS-CoV-2-specific immunoglobulins A and G (IgA and IgG) were measured in serum samples using S1-ELISA. RESULTS: We compared 101 immunocompetent patients who received dexamethasone (according to the inclusion criteria and dosage determined in the RECOVERY trial) to 93 immunocompetent patients with comparable disease severity from the first months of the pandemic, who had not been treated with dexamethasone or other glucocorticoids. We found no inter-group differences in virus concentration kinetics, duration of presence of viral loads >106 viral copies/mL (D+ median 17 days (IQR 13-24), D- 19 days (IQR 13-29)), or time from symptom onset until seroconversion (IgA: D+ median 11.5 days (IQR 11-12), D- 14 days (IQR 11.5-15.75); IgG: D+ 13 days (IQR 12-14.5), D- 12 days (IQR 11-15)). CONCLUSION: Dexamethasone does not appear to lead to a change in virus clearance or a delay in antibody response in immunocompetent patients hospitalized with severe COVID-19.


Assuntos
Anticorpos Antivirais/sangue , COVID-19/tratamento farmacológico , Dexametasona/uso terapêutico , SARS-CoV-2/isolamento & purificação , Anti-Inflamatórios/uso terapêutico , COVID-19/sangue , COVID-19/imunologia , COVID-19/virologia , Hospitalização , Humanos , Imunoglobulina A/sangue , Imunoglobulina G/sangue , Cinética , Estudos Prospectivos , RNA Viral/análise , Sistema Respiratório/virologia , SARS-CoV-2/genética , SARS-CoV-2/imunologia , Soroconversão , Carga Viral
6.
Emerg Infect Dis ; 27(8): 2174-2178, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34102097

RESUMO

We detected delayed and reduced antibody and T-cell responses after BNT162b2 vaccination in 71 elderly persons (median age 81 years) compared with 123 healthcare workers (median age 34 years) in Germany. These data emphasize that nonpharmaceutical interventions for coronavirus disease remain crucial and that additional immunizations for the elderly might become necessary.


Assuntos
COVID-19 , Adulto , Idoso , Idoso de 80 Anos ou mais , Vacinas contra COVID-19 , Alemanha/epidemiologia , Humanos , SARS-CoV-2 , Linfócitos T , Vacinação
7.
Emerg Infect Dis ; 27(8): 2169-2173, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34102098

RESUMO

One week after second vaccinations were administered, an outbreak of B.1.1.7 lineage severe acute respiratory syndrome coronavirus 2 infections occurred in a long-term care facility in Berlin, Germany, affecting 16/20 vaccinated and 4/4 unvaccinated residents. Despite considerable viral loads, vaccinated residents experienced mild symptoms and faster time to negative test results.


Assuntos
COVID-19 , SARS-CoV-2 , Berlim , Surtos de Doenças , Alemanha/epidemiologia , Humanos , Assistência de Longa Duração , Vacinação
8.
Science ; 373(6551)2021 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-34035154

RESUMO

Two elementary parameters for quantifying viral infection and shedding are viral load and whether samples yield a replicating virus isolate in cell culture. We examined 25,381 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Germany, including 6110 from test centers attended by presymptomatic, asymptomatic, and mildly symptomatic (PAMS) subjects, 9519 who were hospitalized, and 1533 B.1.1.7 lineage infections. The viral load of the youngest subjects was lower than that of the older subjects by 0.5 (or fewer) log10 units, and they displayed an estimated ~78% of the peak cell culture replication probability; in part this was due to smaller swab sizes and unlikely to be clinically relevant. Viral loads above 109 copies per swab were found in 8% of subjects, one-third of whom were PAMS, with a mean age of 37.6 years. We estimate 4.3 days from onset of shedding to peak viral load (108.1 RNA copies per swab) and peak cell culture isolation probability (0.75). B.1.1.7 subjects had mean log10 viral load 1.05 higher than that of non-B.1.1.7 subjects, and the estimated cell culture replication probability of B.1.1.7 subjects was higher by a factor of 2.6.


Assuntos
Infecções Assintomáticas , COVID-19/transmissão , COVID-19/virologia , SARS-CoV-2/fisiologia , Adolescente , Adulto , Fatores Etários , Idoso , Idoso de 80 Anos ou mais , COVID-19/diagnóstico , Teste de Ácido Nucleico para COVID-19 , Células CACO-2 , Criança , Pré-Escolar , Feminino , Alemanha , Hospitalização , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Probabilidade , SARS-CoV-2/isolamento & purificação , SARS-CoV-2/patogenicidade , Carga Viral , Replicação Viral , Eliminação de Partículas Virais , Adulto Jovem
9.
Microorganisms ; 9(4)2021 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-33918332

RESUMO

BACKGROUND: International travel is a major driver of the introduction and spread of SARS-CoV-2. AIM: To investigate SARS-CoV-2 genetic diversity in the region of a major transport hub in Germany, we characterized the viral sequence diversity of the SARS-CoV-2 variants circulating in Frankfurt am Main, the city with the largest airport in Germany, from the end of October to the end of December 2020. METHODS: In total, we recovered 136 SARS-CoV-2 genomes from nasopharyngeal swab samples. We isolated 104 isolates that were grown in cell culture and RNA from the recovered viruses and subjected them to full-genome sequence analysis. In addition, 32 nasopharyngeal swab samples were directly sequenced. RESULTS AND CONCLUSION: We found 28 different lineages of SARS-CoV-2 circulating during the study period, including the variant of concern B.1.1.7 (Δ69/70, N501Y). Six of the lineages had not previously been observed in Germany. We detected the spike protein (S) deletion Δ69/Δ70 in 15% of all sequences, a four base pair (bp) deletion (in 2.9% of sequences) and a single bp deletion (in 0.7% of sequences) in ORF3a, leading to ORF3a truncations. In four sequences (2.9%), an amino acid deletion at position 210 in S was identified. In a single sample (0.7%), both a 9 bp deletion in ORF1ab and a 7 bp deletion in ORF7a were identified. One sequence in lineage B.1.1.70 had an N501Y substitution while lacking the Δ69/70 in S. The high diversity of sequences observed over two months in Frankfurt am Main highlights the persisting need for continuous SARS-CoV-2 surveillance using full-genome sequencing, particularly in cities with international airport connections.

10.
Infection ; 49(4): 703-714, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-33890243

RESUMO

PURPOSE: Adequate patient allocation is pivotal for optimal resource management in strained healthcare systems, and requires detailed knowledge of clinical and virological disease trajectories. The purpose of this work was to identify risk factors associated with need for invasive mechanical ventilation (IMV), to analyse viral kinetics in patients with and without IMV and to provide a comprehensive description of clinical course. METHODS: A cohort of 168 hospitalised adult COVID-19 patients enrolled in a prospective observational study at a large European tertiary care centre was analysed. RESULTS: Forty-four per cent (71/161) of patients required invasive mechanical ventilation (IMV). Shorter duration of symptoms before admission (aOR 1.22 per day less, 95% CI 1.10-1.37, p < 0.01) and history of hypertension (aOR 5.55, 95% CI 2.00-16.82, p < 0.01) were associated with need for IMV. Patients on IMV had higher maximal concentrations, slower decline rates, and longer shedding of SARS-CoV-2 than non-IMV patients (33 days, IQR 26-46.75, vs 18 days, IQR 16-46.75, respectively, p < 0.01). Median duration of hospitalisation was 9 days (IQR 6-15.5) for non-IMV and 49.5 days (IQR 36.8-82.5) for IMV patients. CONCLUSIONS: Our results indicate a short duration of symptoms before admission as a risk factor for severe disease that merits further investigation and different viral load kinetics in severely affected patients. Median duration of hospitalisation of IMV patients was longer than described for acute respiratory distress syndrome unrelated to COVID-19.


Assuntos
COVID-19/epidemiologia , COVID-19/virologia , SARS-CoV-2/fisiologia , COVID-19/terapia , Estudos de Coortes , Alemanha/epidemiologia , Hospitalização , Humanos , Hipertensão/complicações , Cinética , Estudos Prospectivos , Respiração Artificial , Fatores de Risco , Centros de Atenção Terciária , Fatores de Tempo , Carga Viral , Eliminação de Partículas Virais
12.
Biomarkers ; 26(3): 213-220, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33455451

RESUMO

BACKGROUND: In the emergency department (ED) setting, rapid testing for SARS-CoV-2 is likely associated with advantages to patients and healthcare workers, for example, enabling early but rationale use of limited isolation resources. Most recently, several SARS-CoV-2 rapid point-of-care antigen tests (AGTEST) became available. There is a growing need for data regarding their clinical utility and performance in the diagnosis of SARS-CoV-2 infection in the real life setting EDs. METHODS: We implemented AGTEST (here: Roche/SD Biosensor) in all four adult and the one paediatric EDs at Charité - Universitätsmedizin Berlin in our diagnostic testing strategy. Test indication was limited to symptomatic suspected COVID-19 patients. Detailed written instructions on who to test were distributed and testing personnel were trained in proper specimen collection and handling. In each suspected COVID-19 patient, two sequential deep oro-nasopharyngeal swabs were obtained for viral tests. The first swab was collected for nucleic acid testing through SARS-CoV-2 real-time reverse transcriptase (rt)-PCR diagnostic panel (PCRTEST) in the central laboratory. The second swab was collected to perform the AGTEST. Analysis of routine data was prospectively planned and data were retrieved from the medical records after the inclusion period in the adult or paediatric ED. Diagnostic performance was calculated using the PCRTEST as reference standard. False negative and false positive AGTEST results were analysed individually and compared with viral concentrations derived from the calibrated PCRTEST. RESULTS: We included n = 483 patients including n = 202 from the paediatric ED. N = 10 patients had to be excluded due to missing data and finally n = 473 patients were analysed. In the adult cohort, the sensitivity of the AGTEST was 75.3 (95%CI: 65.8/83.4)% and the specificity was 100 (95%CI: 98.4/100)% with a SARS-CoV-2 prevalence of 32.8%; the positive predictive value was 100 (95%CI: 95.7/100)% and the negative predictive value 89.2 (95%CI: 84.5/93.9)%. In the paediatric cohort, the sensitivity was 72.0 (95%CI: 53.3/86.7)%, the specificity was 99.4 (95%CI:97.3/99.9)% with a prevalence of 12.4%; the positive predictive value was 94.7 (95%CI: 78.3/99.7)% and the negative predictive value was 96.2 (95%CI:92.7/98.3)%. Thus, n = 22 adult and n = 7 paediatric patients showed false negative AGTEST results and only one false positive AGTEST occurred, in the paediatric cohort. Calculated viral concentrations from the rt-PCR lay between 3.16 and 9.51 log10 RNA copies/mL buffer. All false negative patients in the adult ED cohort, who had confirmed symptom onset at least seven days earlier had less than 5 × 105 RNA copies/mL buffer. CONCLUSIONS: We conclude that the use of AGTEST among symptomatic patients in the emergency setting is useful for the early identification of COVID-19, but patients who test negative require confirmation by PCRTEST and must stay isolated until this result becomes available. Adult patients with a false negative AGTEST and symptom onset at least one week earlier have typically a low SARS-CoV-2 RNA concentration and are likely no longer infectious.


Assuntos
Antígenos Virais/sangue , COVID-19/diagnóstico , Serviço Hospitalar de Emergência , Imunoensaio/métodos , SARS-CoV-2/imunologia , COVID-19/virologia , Humanos , SARS-CoV-2/isolamento & purificação
14.
Science ; 369(6502)2020 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-32703849

RESUMO

Smallpox, one of the most devastating human diseases, killed between 300 million and 500 million people in the 20th century alone. We recovered viral sequences from 13 northern European individuals, including 11 dated to ~600-1050 CE, overlapping the Viking Age, and reconstructed near-complete variola virus genomes for four of them. The samples predate the earliest confirmed smallpox cases by ~1000 years, and the sequences reveal a now-extinct sister clade of the modern variola viruses that were in circulation before the eradication of smallpox. We date the most recent common ancestor of variola virus to ~1700 years ago. Distinct patterns of gene inactivation in the four near-complete sequences show that different evolutionary paths of genotypic host adaptation resulted in variola viruses that circulated widely among humans.


Assuntos
Varíola , Vírus da Varíola , Evolução Biológica , Europa (Continente) , Genoma Viral , História Medieval , Humanos , Varíola/história , Varíola/virologia , Vírus da Varíola/genética
15.
Proc Natl Acad Sci U S A ; 117(30): 17977-17983, 2020 07 28.
Artigo em Inglês | MEDLINE | ID: mdl-32651267

RESUMO

Hepatitis delta virus (HDV) is a human hepatitis-causing RNA virus, unrelated to any other taxonomic group of RNA viruses. Its occurrence as a satellite virus of hepatitis B virus (HBV) is a singular case in animal virology for which no consensus evolutionary explanation exists. Here we present a mammalian deltavirus that does not occur in humans, identified in the neotropical rodent species Proechimys semispinosus The rodent deltavirus is highly distinct, showing a common ancestor with a recently described deltavirus in snakes. Reverse genetics based on a tandem minus-strand complementary DNA genome copy under the control of a cytomegalovirus (CMV) promoter confirms autonomous genome replication in transfected cells, with initiation of replication from the upstream genome copy. In contrast to HDV, a large delta antigen is not expressed and the farnesylation motif critical for HBV interaction is absent from a genome region that might correspond to a hypothetical rodent large delta antigen. Correspondingly, there is no evidence for coinfection with an HBV-related hepadnavirus based on virus detection and serology in any deltavirus-positive animal. No other coinfecting viruses were detected by RNA sequencing studies of 120 wild-caught animals that could serve as a potential helper virus. The presence of virus in blood and pronounced detection in reproductively active males suggest horizontal transmission linked to competitive behavior. Our study establishes a nonhuman, mammalian deltavirus that occurs as a horizontally transmitted infection, is potentially cleared by immune response, is not focused in the liver, and possibly does not require helper virus coinfection.


Assuntos
Coinfecção , Infecções por Hepadnaviridae/veterinária , Hepadnaviridae/fisiologia , Hepatite D/veterinária , Vírus Delta da Hepatite/fisiologia , Doenças dos Roedores/virologia , Roedores/virologia , Animais , Linhagem Celular Tumoral , Genoma Viral , Genômica/métodos , Hepadnaviridae/classificação , Vírus Delta da Hepatite/classificação , Humanos , Filogenia
16.
Vaccine ; 38(33): 5077-5081, 2020 07 14.
Artigo em Inglês | MEDLINE | ID: mdl-32417140

RESUMO

Smallpox eradication, coordinated by the WHO and certified 40 years ago, led to the cessation of routine smallpox vaccination in most countries. It is estimated that over 70% of the world's population is no longer protected against smallpox, and through cross-immunity, to closely related orthopox viruses such as monkeypox. Monkeypox is now a re-emerging disease. Monkeypox is endemic in as yet unconfirmed animal reservoirs in sub-Saharan Africa, while its human epidemiology appears to be changing. Monkeypox in small animals imported from Ghana as exotic pets was at the origin of an outbreak of human monkeypox in the USA in 2003. Travellers infected in Nigeria were at the origin of monkeypox cases in the UK in 2018 and 2019, Israel in 2018 and Singapore in2019. Together with sporadic reports of human infections with other orthopox viruses, these facts invite speculation that emergent or re-emergent human monkeypox might fill the epidemiological niche vacated by smallpox. An ad-hoc and unofficial group of interested experts met to consider these issues at Chatham House, London in June 2019, in order to review available data and identify monkeypox-related research gaps. Gaps identified by the experts included:The experts further agreed on the need for a better understanding of the genomic evolution and changing epidemiology of orthopox viruses, the usefulness of in-field genomic diagnostics, and the best disease control strategies, including the possibility of vaccination with new generation non-replicating smallpox vaccines and treatment with recently developed antivirals.


Assuntos
Monkeypox , Vacina Antivariólica , Varíola , Animais , Gana , Humanos , Israel , Londres , Monkeypox/epidemiologia , Monkeypox/prevenção & controle , Vírus da Varíola dos Macacos , Nigéria , Singapura , Varíola/epidemiologia , Varíola/prevenção & controle , Vacina Antivariólica/efeitos adversos
17.
Nature ; 581(7809): 465-469, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32235945

RESUMO

Coronavirus disease 2019 (COVID-19) is an acute infection of the respiratory tract that emerged in late 20191,2. Initial outbreaks in China involved 13.8% of cases with severe courses, and 6.1% of cases with critical courses3. This severe presentation may result from the virus using a virus receptor that is expressed predominantly in the lung2,4; the same receptor tropism is thought to have determined the pathogenicity-but also aided in the control-of severe acute respiratory syndrome (SARS) in 20035. However, there are reports of cases of COVID-19 in which the patient shows mild upper respiratory tract symptoms, which suggests the potential for pre- or oligosymptomatic transmission6-8. There is an urgent need for information on virus replication, immunity and infectivity in specific sites of the body. Here we report a detailed virological analysis of nine cases of COVID-19 that provides proof of active virus replication in tissues of the upper respiratory tract. Pharyngeal virus shedding was very high during the first week of symptoms, with a peak at 7.11 × 108 RNA copies per throat swab on day 4. Infectious virus was readily isolated from samples derived from the throat or lung, but not from stool samples-in spite of high concentrations of virus RNA. Blood and urine samples never yielded virus. Active replication in the throat was confirmed by the presence of viral replicative RNA intermediates in the throat samples. We consistently detected sequence-distinct virus populations in throat and lung samples from one patient, proving independent replication. The shedding of viral RNA from sputum outlasted the end of symptoms. Seroconversion occurred after 7 days in 50% of patients (and by day 14 in all patients), but was not followed by a rapid decline in viral load. COVID-19 can present as a mild illness of the upper respiratory tract. The confirmation of active virus replication in the upper respiratory tract has implications for the containment of COVID-19.


Assuntos
Betacoronavirus/imunologia , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/imunologia , Infecções por Coronavirus/virologia , Hospitalização , Pneumonia Viral/imunologia , Pneumonia Viral/virologia , Soroconversão , Replicação Viral , Anticorpos Antivirais/análise , Anticorpos Antivirais/imunologia , Sequência de Bases , Betacoronavirus/genética , Betacoronavirus/patogenicidade , Sangue/virologia , COVID-19 , Teste para COVID-19 , Técnicas de Laboratório Clínico , Proteínas do Envelope de Coronavírus , Infecções por Coronavirus/diagnóstico , Fezes/química , Fezes/virologia , Humanos , Imunoglobulina G/análise , Imunoglobulina G/imunologia , Imunoglobulina M/análise , Imunoglobulina M/imunologia , Pulmão/virologia , Pandemias , Faringe/virologia , Pneumonia Viral/diagnóstico , Polimorfismo de Nucleotídeo Único/genética , RNA Viral/análise , SARS-CoV-2 , Escarro/virologia , Urina/virologia , Proteínas do Envelope Viral/genética , Carga Viral/imunologia , Eliminação de Partículas Virais
18.
PLoS Pathog ; 15(12): e1008224, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31830128

RESUMO

The spectrum of viruses in insects is important for subjects as diverse as public health, veterinary medicine, food production, and biodiversity conservation. The traditional interest in vector-borne diseases of humans and livestock has drawn the attention of virus studies to hematophagous insect species. However, these represent only a tiny fraction of the broad diversity of Hexapoda, the most speciose group of animals. Here, we systematically probed the diversity of negative strand RNA viruses in the largest and most representative collection of insect transcriptomes from samples representing all 34 extant orders of Hexapoda and 3 orders of Entognatha, as well as outgroups, altogether representing 1243 species. Based on profile hidden Markov models we detected 488 viral RNA-directed RNA polymerase (RdRp) sequences with similarity to negative strand RNA viruses. These were identified in members of 324 arthropod species. Selection for length, quality, and uniqueness left 234 sequences for analyses, showing similarity to genomes of viruses classified in Bunyavirales (n = 86), Articulavirales (n = 54), and several orders within Haploviricotina (n = 94). Coding-complete genomes or nearly-complete subgenomic assemblies were obtained in 61 cases. Based on phylogenetic topology and the availability of coding-complete genomes we estimate that at least 20 novel viral genera in seven families need to be defined, only two of them monospecific. Seven additional viral clades emerge when adding sequences from the present study to formerly monospecific lineages, potentially requiring up to seven additional genera. One long sequence may indicate a novel family. For segmented viruses, cophylogenies between genome segments were generally improved by the inclusion of viruses from the present study, suggesting that in silico misassembly of segmented genomes is rare or absent. Contrary to previous assessments, significant virus-host codivergence was identified in major phylogenetic lineages based on two different approaches of codivergence analysis in a hypotheses testing framework. In spite of these additions to the known spectrum of viruses in insects, we caution that basing taxonomic decisions on genome information alone is challenging due to technical uncertainties, such as the inability to prove integrity of complete genome assemblies of segmented viruses.


Assuntos
Insetos/virologia , Infecções por Vírus de RNA/virologia , Vírus de RNA , Animais
19.
J Clin Microbiol ; 57(8)2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31167846

RESUMO

Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-)emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An artificial, simulated in silico data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results.


Assuntos
Biologia Computacional/métodos , Simulação por Computador , Sequenciamento de Nucleotídeos em Larga Escala/normas , Ensaio de Proficiência Laboratorial/estatística & dados numéricos , Análise de Sequência de DNA/normas , Vírus/genética , Análise de Dados , Europa (Continente) , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Colaboração Intersetorial , Ensaio de Proficiência Laboratorial/organização & administração , Reprodutibilidade dos Testes , Análise de Sequência de DNA/estatística & dados numéricos , Vírus/patogenicidade
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