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1.
Euro Surveill ; 26(27)2021 07.
Article in English | MEDLINE | ID: covidwho-1577032

ABSTRACT

BackgroundInfluenza virus presents a considerable challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid infection diagnosis, rationalising antimicrobial therapy, and supporting infection-control interventions.AimTo evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings.MethodsWe conducted Oxford Nanopore Technologies (Oxford, United Kingdom (UK)) metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic standards (Xpert Xpress Flu/RSV assay; BioFire FilmArray Respiratory Panel 2 assay). We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data.ResultsCompared to standard testing, Nanopore metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses. Of 59 samples with haemagglutinin subtype determined, 40 were H1 and 19 H3. We identified an influenza A(H3N2) genome encoding the oseltamivir resistance S331R mutation in neuraminidase, potentially associated with an emerging distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in a ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant community-circulating strain. We also detected other potentially pathogenic viruses and bacteria from the metagenome.ConclusionNanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Full genome generation can help investigate and manage nosocomial outbreaks.


Subject(s)
Cross Infection , Influenza, Human , Nanopores , Antiviral Agents/therapeutic use , Cross Infection/diagnosis , Cross Infection/drug therapy , Drug Resistance , Drug Resistance, Viral/genetics , Humans , Influenza A Virus, H3N2 Subtype/genetics , Influenza, Human/diagnosis , Influenza, Human/drug therapy , Influenza, Human/epidemiology , Metagenome , Neuraminidase/genetics , Seasons , United Kingdom
2.
Euro Surveill ; 25(42)2020 10.
Article in English | MEDLINE | ID: covidwho-886127

ABSTRACT

SARS-CoV-2 IgG screening of 1,000 antenatal serum samples in the Oxford area, United Kingdom, between 14 April and 15 June 2020, yielded a 5.3% seroprevalence, mirroring contemporaneous regional data. Among the 53 positive samples, 39 showed in vitro neutralisation activity, correlating with IgG titre (Pearson's correlation p<0.0001). While SARS-CoV-2 seroprevalence in pregnancy cohorts could potentially inform population surveillance, clinical correlates of infection and immunity in pregnancy, and antenatal epidemiology evolution over time need further study.


Subject(s)
Antibodies, Neutralizing/blood , Antibodies, Viral/blood , Betacoronavirus/immunology , Coronavirus Infections/epidemiology , Immunoglobulin G/blood , Pandemics , Pneumonia, Viral/epidemiology , Population Surveillance , Pregnancy Complications, Infectious/blood , Pregnancy Trimester, First/blood , Adolescent , Adult , COVID-19 , Cohort Studies , Coronavirus Infections/blood , England/epidemiology , Enzyme-Linked Immunosorbent Assay , Female , Humans , Middle Aged , Pneumonia, Viral/blood , Pregnancy , Prenatal Diagnosis , Prevalence , SARS-CoV-2 , Seroepidemiologic Studies , Single-Blind Method , Young Adult
3.
Elife ; 92020 08 21.
Article in English | MEDLINE | ID: covidwho-727516

ABSTRACT

We conducted voluntary Covid-19 testing programmes for symptomatic and asymptomatic staff at a UK teaching hospital using naso-/oro-pharyngeal PCR testing and immunoassays for IgG antibodies. 1128/10,034 (11.2%) staff had evidence of Covid-19 at some time. Using questionnaire data provided on potential risk-factors, staff with a confirmed household contact were at greatest risk (adjusted odds ratio [aOR] 4.82 [95%CI 3.45-6.72]). Higher rates of Covid-19 were seen in staff working in Covid-19-facing areas (22.6% vs. 8.6% elsewhere) (aOR 2.47 [1.99-3.08]). Controlling for Covid-19-facing status, risks were heterogenous across the hospital, with higher rates in acute medicine (1.52 [1.07-2.16]) and sporadic outbreaks in areas with few or no Covid-19 patients. Covid-19 intensive care unit staff were relatively protected (0.44 [0.28-0.69]), likely by a bundle of PPE-related measures. Positive results were more likely in Black (1.66 [1.25-2.21]) and Asian (1.51 [1.28-1.77]) staff, independent of role or working location, and in porters and cleaners (2.06 [1.34-3.15]).


Subject(s)
Coronavirus Infections/epidemiology , Health Personnel/statistics & numerical data , Pneumonia, Viral/epidemiology , Adolescent , Adult , Age Factors , Aged , Asymptomatic Infections/epidemiology , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/transmission , Coronavirus Infections/virology , Female , Hospitals, Teaching/statistics & numerical data , Humans , Incidence , Infectious Disease Transmission, Patient-to-Professional/statistics & numerical data , Intensive Care Units/statistics & numerical data , Male , Middle Aged , Pandemics , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Risk , SARS-CoV-2 , Surveys and Questionnaires , United Kingdom/epidemiology , Young Adult
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