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1.
Trends Microbiol ; 2024 Oct 31.
Artigo em Inglês | MEDLINE | ID: mdl-39487079

RESUMO

In this review, we delineate the unique set of characteristics associated with cryosphere environments (namely, ice and permafrost) which present both challenges and opportunities for studying ancient environmental microbiomes (AEMs). In a field currently reliant on several assumptions, we discuss the theoretical and empirical feasibility of recovering microbial nucleic acids (NAs) from ice and permafrost with varying degrees of antiquity. We also summarize contamination control best practices and highlight considerations for the latest approaches, including shotgun metagenomics, and downstream bioinformatic authentication approaches. We review the adoption of existing software and provide an overview of more recently published programs, with reference to their suitability for AEM studies. Finally, we summarize outstanding challenges and likely future directions for AEM research.

2.
Lancet Reg Health Eur ; 44: 101022, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39444701

RESUMO

Background: Co-administration of inactivated influenza vaccine (IIV) and SARS-CoV-2 vaccine may impact SARS-CoV-2 vaccine induced humoral immune responses. We aimed to compare IIV and SARS-CoV-2 vaccine induced cellular and humoral immune responses in those receiving concomitant vaccination to those receiving these vaccines separately. Methods: We conducted a cohort study between 29th September 2021 and 5th August 2022 in healthcare workers who worked at the local NHS trust and in the surrounding area that were vaccinated with a mRNA SARS-CoV-2 booster and cell-based IIV. We measured haemagglutination inhibition assay (HAI) titres, SARS-CoV-2 anti-spike antibody and SARS-CoV-2 ELISpot count pre-vaccination, 1-month and 6-months post-vaccination and evaluated differences by vaccine strategy. Findings: We recruited 420 participants, 234/420 (56%) were vaccinated concomitantly and 186/420 (44%) separately. The 1-month post-vaccination mean fold rise (MFR) in SARS-CoV-2 anti-spike antibodies was lower in those vaccinated concomitantly compared to separately (MFR [95% confidence interval (CI)] 9.7 [8.3, 11.4] vs 12.8 [10.3, 15.9], p = 0.04). After adjustment for age and sex, the adjusted geometric mean ratio (aGMR) remained lower for those vaccinated concomitantly compared to separately (aGMR [95% CI] 0.80 [0.70, 0.92], p = 0.001). At 6-months post-vaccination, we found no statistically significant difference in SARS-CoV-2 anti-spike antibody titres (aGMR [95% CI] 1.09 [0.87, 1.35], p = 0.45). We found no statistically significant correlation between vaccine strategy with SARS-CoV-2 ELISpot count and influenza HAI titres at 1-month and 6-months post-vaccination. Interpretation: Our study found that concomitant vaccination with SARS-CoV-2 and IIV has no statistically significant impacts on long-term immunogenicity. Further research is required to understand the underlying mechanisms and assess the clinical significance of reduced anti-spike antibodies in those vaccinated concomitantly. Funding: Research and Innovation (UKRI) through the COVID-19 National Core Studies Immunity (NCSi) programme (MC_PC_20060).

4.
J Med Virol ; 96(9): e29924, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39295283

RESUMO

We performed a comparative, retrospective analysis (March 2019-April 2023) of children diagnosed with non-polio enterovirus (NPEV) central nervous system (CNS) infections (n = 47 vs. 129 contemporaneous controls without NPEV, all <18 years old), requiring cerebrospinal fluid (CSF) testing upon presentation to hospital. We found that showed that admissions decreased during pandemic restrictions (13% vs. controls 33%, p = 0.003). The median age of children with NPEV was 41 days (IQR: 18-72), most were male (n = 76, 59%) and were less likely to present with symptoms of irritability (11% vs. controls 26%, p = 0.04), but more likely to be febrile (93% vs. controls 73%, p = 0.007), have higher respiratory rates (mean 44 bpm, SD 11, vs. controls 36 bpm, SD 14, p = 0.001), higher heart rates (mean 171 bpm, SD 27 vs. controls 141 bpm, SD 36, p < 0.001), higher CSF protein (median 0.66 g/L, interquartile range [IQR] 0.46-1.01, vs. controls 0.53 mg/mL, IQR 0.28-0.89, p = 0.04), higher CSF white cell count (WCC) (median WCC 9.5×106/L, IQR 1-16 vs. controls 3.15×106/L, IQR 2.7-3.6, p < 0.001), but lower CSF glucose (median 2.8 mmol/L, IQR 2.4-3.1 vs. controls 3.1 mmol/L, IQR 2.7-3.6, p < 0.001). Phylogenetic analysis showed that these NPEVs originated from Europe (EV A71, CV B4, E21, E6, CV B3, CV B5, E7, E11, E18), North America (CV B4, E18), South America (E6), Middle East (CV B5), Africa (CV B5, E18), South Asia (E15), East/Southeast Asia (E25, CV A9, E7, E11, E18), and Australia (CV B5).


Assuntos
Infecções por Enterovirus , Enterovirus , Epidemiologia Molecular , Humanos , Infecções por Enterovirus/epidemiologia , Infecções por Enterovirus/virologia , Infecções por Enterovirus/líquido cefalorraquidiano , Masculino , Feminino , Estudos Retrospectivos , Lactente , Pré-Escolar , Criança , Enterovirus/genética , Enterovirus/isolamento & purificação , Enterovirus/classificação , Filogenia , Recém-Nascido , Líquido Cefalorraquidiano/virologia , Adolescente
5.
Sci Rep ; 14(1): 20211, 2024 08 30.
Artigo em Inglês | MEDLINE | ID: mdl-39215108

RESUMO

The risk of virus transmission via the touching of contaminated masks has long been assumed by infection control teams. Yet, robust evidence to support this belief has been lacking. This risk was investigated in a laboratory setting by measuring the amount of viable influenza virus successfully transferred from artificially contaminated medical (surgical) mask surfaces to a human finger used to swipe their outer surface under various experimental conditions. Despite being exposed to high levels of virus contamination on the masks, very little or no viable virus was successfully transferred from the mask to the finger in these experiments.


Assuntos
Influenza Humana , Máscaras , Humanos , Máscaras/virologia , Influenza Humana/transmissão , Influenza Humana/prevenção & controle , Influenza Humana/virologia , Tato , Contaminação de Equipamentos , Orthomyxoviridae
6.
Antiviral Res ; 229: 105956, 2024 09.
Artigo em Inglês | MEDLINE | ID: mdl-38969237

RESUMO

Baloxavir marboxil (baloxavir), approved as an anti-influenza drug in Japan in March 2018, can induce reduced therapeutic effectiveness due to PA protein substitutions. We assessed PA substitutions in clinical samples from influenza-infected children and adults pre- and post-baloxavir treatment, examining their impact on fever and symptom duration. During the 2022-2023 influenza season, the predominant circulating influenza subtype detected by cycling-probe RT-PCR was A(H3N2) (n = 234), with a minor circulation of A(H1N1)pdm09 (n = 10). Of the 234 influenza A(H3N2) viruses collected prior to baloxavir treatment, 2 (0.8%) viruses carry PA/I38T substitution. One virus was collected from a toddler and one from an adult, indicating the presence of viruses with reduced susceptibility to baloxavir, without prior exposure to the drug. Of the 54 paired influenza A(H3N2) viruses collected following baloxavir treatment, 8 (14.8%) viruses carried E23 K/G, or I38 M/T substitutions in PA. Variant calling through next-generation sequencing (NGS) showed varying proportions (6-100 %), a polymorphism and a mixture of PA/E23 K/G, and I38 M/T substitutions in the clinical samples. These eight viruses were obtained from children aged 7-14 years, with a median fever duration of 16.7 h and a median symptom duration of 93.7 h, which were similar to those of the wild type. However, the delayed viral clearance associated with the emergence of PA substitutions was observed. No substitutions conferring resistance to neuraminidase inhibitors were detected in 37 paired samples collected before and following oseltamivir treatment. These findings underscore the need for ongoing antiviral surveillance, informing public health strategies and clinical antiviral recommendations for seasonal influenza.


Assuntos
Substituição de Aminoácidos , Antivirais , Dibenzotiepinas , Farmacorresistência Viral , Vírus da Influenza A Subtipo H3N2 , Influenza Humana , Morfolinas , Piridonas , Triazinas , Proteínas Virais , Humanos , Dibenzotiepinas/uso terapêutico , Dibenzotiepinas/farmacologia , Influenza Humana/tratamento farmacológico , Influenza Humana/virologia , Vírus da Influenza A Subtipo H3N2/genética , Vírus da Influenza A Subtipo H3N2/efeitos dos fármacos , Vírus da Influenza A Subtipo H3N2/enzimologia , Triazinas/uso terapêutico , Triazinas/farmacologia , Japão , Antivirais/farmacologia , Antivirais/uso terapêutico , Morfolinas/uso terapêutico , Farmacorresistência Viral/genética , Criança , Adulto , Pré-Escolar , Adolescente , Proteínas Virais/genética , RNA Polimerase Dependente de RNA/genética , Feminino , Masculino , Tiepinas/uso terapêutico , Tiepinas/farmacologia , Lactente , Pessoa de Meia-Idade , Estações do Ano , Piridinas/uso terapêutico , Piridinas/farmacologia , Adulto Jovem , Vírus da Influenza A Subtipo H1N1/genética , Vírus da Influenza A Subtipo H1N1/efeitos dos fármacos , Idoso
9.
J Med Virol ; 96(2): e29326, 2024 02.
Artigo em Inglês | MEDLINE | ID: mdl-38345166

RESUMO

The recurrent multiwave nature of coronavirus disease 2019 (COVID-19) necessitates updating its symptomatology. We characterize the effect of variants on symptom presentation, identify the symptoms predictive and protective of death, and quantify the effect of vaccination on symptom development. With the COVID-19 cases reported up to August 25, 2022 in Hong Kong, an iterative multitier text-matching algorithm was developed to identify symptoms from free text. Multivariate regression was used to measure associations between variants, symptom development, death, and vaccination status. A least absolute shrinkage and selection operator technique was used to identify a parsimonious set of symptoms jointly associated with death. Overall, 70.9% (54 450/76 762) of cases were symptomatic with 102 symptoms identified. Intrinsically, the wild-type and delta variant caused similar symptoms among unvaccinated symptomatic cases, whereas the wild-type and omicron BA.2 subvariant had heterogeneous patterns, with seven symptoms (fatigue, fever, chest pain, runny nose, sputum production, nausea/vomiting, and sore throat) more frequent in the BA.2 cohort. With ≥2 vaccine doses, BA.2 was more likely than delta to cause fever among symptomatic cases. Fever, blocked nose, pneumonia, and shortness of breath remained jointly predictive of death among unvaccinated symptomatic elderly in the wild-type-to-omicron transition. Number of vaccine doses required for reducing occurrence varied by symptoms. We substantiate that omicron has a different clinical presentation compared to previous variants. Syndromic surveillance can be bettered with reduced reliance on symptom-based case identification, increased weighing on symptoms predictive of death in outcome prediction, individual-based risk assessment in care homes, and incorporating free-text symptom reporting.


Assuntos
COVID-19 , Vacinas , Idoso , Humanos , SARS-CoV-2/genética , COVID-19/epidemiologia , Hong Kong/epidemiologia , Febre
12.
Viruses ; 15(10)2023 09 30.
Artigo em Inglês | MEDLINE | ID: mdl-37896810

RESUMO

Influenza is a highly contagious respiratory illness that commonly causes outbreaks among human communities. Details about the exact nature of the droplets produced by human respiratory activities such as breathing, and their potential to carry and transmit influenza A and B viruses is still not fully understood. The objective of our study was to characterize and quantify influenza viral shedding in exhaled aerosols from natural patient breath, and to determine their viral infectivity among participants in a university cohort in tropical Singapore. Using the Gesundheit-II exhaled breath sampling apparatus, samples of exhaled breath of two aerosol size fractions ("coarse" > 5 µm and "fine" ≤ 5 µm) were collected and analyzed from 31 study participants, i.e., 24 with influenza A (including H1N1 and H3N2 subtypes) and 7 with influenza B (including Victoria and Yamagata lineages). Influenza viral copy number was quantified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Infectivity of influenza virus in the fine particle fraction was determined by culturing in Madin-Darby canine kidney cells. Exhaled influenza virus RNA generation rates ranged from 9 to 1.67 × 105 and 10 to 1.24 × 104 influenza virus RNA copies per minute for the fine and coarse aerosol fractions, respectively. Compared to the coarse aerosol fractions, influenza A and B viruses were detected more frequently in the fine aerosol fractions that harbored 12-fold higher viral loads. Culturable virus was recovered from the fine aerosol fractions from 9 of the 31 subjects (29%). These findings constitute additional evidence to reiterate the important role of fine aerosols in influenza transmission and provide a baseline range of influenza virus RNA generation rates.


Assuntos
Herpesvirus Cercopitecino 1 , Vírus da Influenza A Subtipo H1N1 , Influenza Humana , Humanos , Animais , Cães , Vírus da Influenza A Subtipo H1N1/genética , Vírus da Influenza A Subtipo H3N2/genética , Singapura , Aerossóis e Gotículas Respiratórios , RNA Viral/genética
13.
Clin Med (Lond) ; 23(5): 527-530, 2023 09.
Artigo em Inglês | MEDLINE | ID: mdl-37775161

RESUMO

In June 2023, the UK began official hearings for its independent investigation into pandemic preparedness. Thus far, the inquiry has been told that planning has been wholly inadequate and that a future outbreak is inevitable. We present here four key problems that contributed to significant morbidity and mortality during the Coronavirus 2019 (COVID-19) pandemic over the past 3 years in the UK - and which will contribute to excess morbidity and mortality in the next outbreak. First, there was misunderstanding about what procedures were deemed as aerosol generating. Aerosol transmission has always been a component of respiratory viruses; however, no specific aerosol-generating procedures are required to transmit any respiratory pathogens over long distances. Second, policy-makers were too binary in their answers to the public in terms of questions about severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). This meant that, as evidence evolved and different conclusions were drawn, the public lost faith in both the UK Government and science. Third, public health guidance did not take into account that certain groups would be impacted differentially by public health guidelines and instead used a one-size-fits-all approach to non-pharmaceutical interventions. Finally, there was worsening of existing inequalities, especially in ethnic minority groups, that resulted in excessive numbers within certain cohorts becoming infected.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , Pandemias/prevenção & controle , Etnicidade , Grupos Minoritários , Aerossóis e Gotículas Respiratórios
15.
CMAJ ; 195(22): E800-E801, 2023 06 05.
Artigo em Francês | MEDLINE | ID: mdl-37277129
17.
Viruses ; 15(4)2023 04 10.
Artigo em Inglês | MEDLINE | ID: mdl-37112923

RESUMO

The COVID-19 pandemic caused by SARS-CoV-2 is associated with a lower fatality rate than its SARS and MERS counterparts. However, the rapid evolution of SARS-CoV-2 has given rise to multiple variants with varying pathogenicity and transmissibility, such as the Delta and Omicron variants. Individuals with advanced age or underlying comorbidities, including hypertension, diabetes and cardiovascular diseases, are at a higher risk of increased disease severity. Hence, this has resulted in an urgent need for the development of better therapeutic and preventive approaches. This review describes the origin and evolution of human coronaviruses, particularly SARS-CoV-2 and its variants as well as sub-variants. Risk factors that contribute to disease severity and the implications of co-infections are also considered. In addition, various antiviral strategies against COVID-19, including novel and repurposed antiviral drugs targeting viral and host proteins, as well as immunotherapeutic strategies, are discussed. We critically evaluate strategies of current and emerging vaccines against SARS-CoV-2 and their efficacy, including immune evasion by new variants and sub-variants. The impact of SARS-CoV-2 evolution on COVID-19 diagnostic testing is also examined. Collectively, global research and public health authorities, along with all sectors of society, need to better prepare against upcoming variants and future coronavirus outbreaks.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , COVID-19/diagnóstico , COVID-19/prevenção & controle , Teste para COVID-19 , Vacinas contra COVID-19 , Pandemias/prevenção & controle , Vacinação , Antivirais/uso terapêutico
19.
Curr Opin Pulm Med ; 29(3): 191-196, 2023 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-36866737

RESUMO

PURPOSE OF REVIEW: The coronavirus disease 2019 pandemic has had a wide-ranging and profound impact on how we think about the transmission of respiratory viruses This review outlines the basis on which we should consider all respiratory viruses as aerosol-transmissible infections, in order to improve our control of these pathogens in both healthcare and community settings. RECENT FINDINGS: We present recent studies to support the aerosol transmission of severe acute respiratory syndrome coronavirus 2, and some older studies to demonstrate the aerosol transmissibility of other, more familiar seasonal respiratory viruses. SUMMARY: Current knowledge on how these respiratory viruses are transmitted, and the way we control their spread, is changing. We need to embrace these changes to improve the care of patients in hospitals and care homes including others who are vulnerable to severe disease in community settings.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , Aerossóis e Gotículas Respiratórios , Pandemias/prevenção & controle
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