Genomic Surveillance of SARS-CoV-2 in Healthcare Workers: A Critical Sentinel Group for Monitoring the SARS-CoV-2 Variant Shift.
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ABSTRACT:
SUBMITTER: Padilha DA
PROVIDER: S-EPMC10146896 | biostudies-literature | 2023 Apr
REPOSITORIES: biostudies-literature
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Genomic Surveillance of SARS-CoV-2 in Healthcare Workers: A Critical Sentinel Group for Monitoring the SARS-CoV-2 Variant Shift.
Padilha Dayane Azevedo DA Souza Doris Sobral Marques DSM Kawagoe Eric Kazuo EK Filho Vilmar Benetti VB Amorim Ariane Nicaretta AN Barazzetti Fernando Hartmann FH Schörner Marcos André MA Fernandes Sandra Bianchini SB Coelho Bruna Kellet BK Rovaris Darcita Buerger DB Dos Anjos Marlei Pickler Debiase MPD Moser Juliana Righetto JR Melo Fernanda Rosene FR De Souza Bianca Bittencourt BB Bessa Dimitri da Costa DDC Mendes Fernando Henrique de Paula E Silva FHPES Boing Alexandra Crispim AC Boing Antonio Fernando AF Lacerda Josimari Telino de JT Moura Guilherme Valle GV Bastiani Daniela Carolina De DC Moraes Milene Höehr de MH De Oliveira Luiz Felipe Valter LFV Moreira Renato Simões RS Stoco Patricia Hermes PH Bazzo Maria Luiza ML Fongaro Gislaine G Wagner Glauber G
Viruses 20230417 4
SARS-CoV-2 genome surveillance is important for monitoring risk groups and health workers as well as data on new cases and mortality rate due to COVID-19. We characterized the circulation of SARS-CoV-2 variants from May 2021 to April 2022 in the state of Santa Catarina, southern Brazil, and evaluated the similarity between variants present in the population and healthcare workers (HCW). A total of 5291 sequenced genomes demonstrated the circulation of 55 strains and four variants of concern (Alp ...[more]
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Project description:BackgroundTo support the COVID-19 pandemic response, many countries, including Belgium, implemented baseline genomic surveillance (BGS) programs aiming to early detect and characterize new SARS-CoV-2 variants. In parallel, Belgium maintained a sentinel network of six hospitals that samples patients with severe acute respiratory infections (SARI) and integrated SARS-CoV-2 detection within a broader range of respiratory pathogens. We evaluate the ability of the SARI surveillance to monitor general trends and early signals of viral genetic evolution of SARS-CoV-2 and compare it with the BGS as a reference model.MethodsNine-hundred twenty-five SARS-CoV-2 positive samples from patients fulfilling the Belgian SARI definition between January 2020 and December 2022 were sequenced using the ARTIC Network amplicon tiling approach on a MinION platform. Weekly variant of concern (VOC) proportions and types were compared to those that were circulating between 2021 and 2022, using 96,251 sequences of the BGS.ResultsSARI surveillance allowed timely detection of the Omicron (BA.1, BA.2, BA.4, and BA.5) and Delta (B.1.617.2) VOCs, with no to 2 weeks delay according to the start of their epidemic growth in the Belgian population. First detection of VOCs B.1.351 and P.1 took longer, but these remained minor in Belgium. Omicron BA.3 was never detected in SARI surveillance. Timeliness could not be evaluated for B.1.1.7, being already major at the start of the study period.ConclusionsGenomic surveillance of SARS-CoV-2 using SARI sentinel surveillance has proven to accurately reflect VOCs detected in the population and provides a cost-effective solution for long-term genomic monitoring of circulating respiratory viruses.
| S-EPMC10570899 | biostudies-literature
Project description:BackgroundLittle is known about the cocirculation of influenza and SARS-CoV-2 viruses during the COVID-19 pandemic and the use of respiratory disease sentinel surveillance platforms for monitoring SARS-CoV-2 activity in sub-Saharan Africa.ObjectiveWe aimed to describe influenza and SARS-CoV-2 cocirculation in Kenya and how the SARS-CoV-2 data from influenza sentinel surveillance correlated with that of universal national surveillance.MethodsFrom April 2020 to March 2022, we enrolled 7349 patients with severe acute respiratory illness or influenza-like illness at 8 sentinel influenza surveillance sites in Kenya and collected demographic, clinical, underlying medical condition, vaccination, and exposure information, as well as respiratory specimens, from them. Respiratory specimens were tested for influenza and SARS-CoV-2 by real-time reverse transcription polymerase chain reaction. The universal national-level SARS-CoV-2 data were also obtained from the Kenya Ministry of Health. The universal national-level SARS-CoV-2 data were collected from all health facilities nationally, border entry points, and contact tracing in Kenya. Epidemic curves and Pearson r were used to describe the correlation between SARS-CoV-2 positivity in data from the 8 influenza sentinel sites in Kenya and that of the universal national SARS-CoV-2 surveillance data. A logistic regression model was used to assess the association between influenza and SARS-CoV-2 coinfection with severe clinical illness. We defined severe clinical illness as any of oxygen saturation <90%, in-hospital death, admission to intensive care unit or high dependence unit, mechanical ventilation, or a report of any danger sign (ie, inability to drink or eat, severe vomiting, grunting, stridor, or unconsciousness in children younger than 5 years) among patients with severe acute respiratory illness.ResultsOf the 7349 patients from the influenza sentinel surveillance sites, 76.3% (n=5606) were younger than 5 years. We detected any influenza (A or B) in 8.7% (629/7224), SARS-CoV-2 in 10.7% (768/7199), and coinfection in 0.9% (63/7165) of samples tested. Although the number of samples tested for SARS-CoV-2 from the sentinel surveillance was only 0.2% (60 per week vs 36,000 per week) of the number tested in the universal national surveillance, SARS-CoV-2 positivity in the sentinel surveillance data significantly correlated with that of the universal national surveillance (Pearson r=0.58; P<.001). The adjusted odds ratios (aOR) of clinical severe illness among participants with coinfection were similar to those of patients with influenza only (aOR 0.91, 95% CI 0.47-1.79) and SARS-CoV-2 only (aOR 0.92, 95% CI 0.47-1.82).ConclusionsInfluenza substantially cocirculated with SARS-CoV-2 in Kenya. We found a significant correlation of SARS-CoV-2 positivity in the data from 8 influenza sentinel surveillance sites with that of the universal national SARS-CoV-2 surveillance data. Our findings indicate that the influenza sentinel surveillance system can be used as a sustainable platform for monitoring respiratory pathogens of pandemic potential or public health importance.
| S-EPMC11002741 | biostudies-literature
Project description:BackgroundThe emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning of vaccine-induced immunity over time contributed to increased rates of breakthrough infection specifically among healthcare workers (HCWs). SARS-CoV-2 genomic surveillance is an important tool for timely detection and characterization of circulating variants as well as monitoring the emergence of new strains. Our study is the first national SARS-CoV-2 genomic surveillance among HCWs in Lebanon.MethodsWe collected 250 nasopharyngeal swabs from HCWs across Lebanon between December 2021 and January 2022. Data on the date of positive PCR, vaccination status, specific occupation, and hospitalization status of participants were collected. Extracted viral RNA from nasopharyngeal swabs was converted to cDNA, library prepped using the coronaHIT method, followed by whole genome sequencing on the Illumina NextSeq 500 platform.ResultsA total of 133 (57.1%) samples belonging to the Omicron (BA.1.1) sub-lineage were identified, as well as 44 (18.9%) samples belonging to the BA.1 sub-lineage, 28 (12%) belonging to the BA.2 sub-lineage, and only 15 (6.6%) samples belonging to the Delta variant sub-lineage B.1.617.2. These results show that Lebanon followed the global trend in terms of circulating SARS-CoV-2 variants with Delta rapidly replaced by the Omicron variant.ConclusionThis study underscores the importance of continuous genomic surveillance programs in Lebanon for the timely detection and characterization of circulating variants. The latter is critical to guide public health policy making and to timely implement public health interventions.
| S-EPMC9880935 | biostudies-literature
Project description:The novel coronavirus 2019 (COVID-19) global pandemic has drastically affected the world economy, raised public anxiety, and placed a substantial psychological burden on the governments and healthcare professionals by affecting over 4.7 million people worldwide. As a preventive measure to minimise the risk of community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in India, a nationwide lockdown was imposed initially for 21 days to limit the movement of 1.3 billion people. These restrictions continue in most areas, with a conditional relaxation occurring in a few Indian states. In an attempt to assess the emerging mutants of SARS-CoV-2 and determine their spread in India, we analysed 112 complete genomes of SARS-CoV-2 in a time-lapse manner. We found 72 distinct SARS-CoV-2 haplotypes, defined by 143 polymorphic sites and high haplotype diversity, suggesting that this virus possesses a high evolutionary potential. We also demonstrated that early introduction of SARS-CoV-2 into India was from China, Italy and Iran and observed signs of community spread of the virus following its rapid demographic expansion since its first outbreak in the country. Additionally, we identified 18 mutations in the SARS-CoV-2 spike glycoprotein and a few selected mutations showed to increase stability, binding affinity, and molecular flexibility in the overall tertiary structure of the protein that may facilitate interaction between the receptor binding domain (RBD) of spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptor. The study provides a pragmatic view of haplotype-dependent spread of SARS-CoV-2 in India which could be important in tailoring the pharmacologic treatments to be more effective for those infected with the most common haplotypes. The findings based on the time-lapse sentinel surveillance of SARS-CoV-2 will aid in the development of a real-time practical framework to tackle the ongoing, fast-evolving epidemic challenges in the country.
| S-EPMC7580942 | biostudies-literature
Project description:BackgroundAsymptomatic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections are well documented. Healthcare workers (HCW) are at increased risk of infection due to occupational exposure to infected patients. We aim to determine the prevalence of SARS-CoV-2 antibodies among HCW who did not come to medical attention.MethodsWe prospectively recruited 400 HCW from the National Public Health Laboratory and two COVID-19 designated public hospitals in Klang Valley, Malaysia between 13/4/2020 and 12/5/2020. Quota sampling was used to ensure representativeness of HCW involved in direct and indirect patient care. All participants answered a self-administered questionnaire and blood samples were taken to test for SARS-CoV-2 antibodies by surrogate virus neutralization test.FindingsThe study population comprised 154 (38.5%) nurses, 103 (25.8%) medical doctors, 47 (11.8%) laboratory technologists and others (23.9%). A majority (68.9%) reported exposure to SARS-CoV-2 in the past month within their respective workplaces. Adherence to personal protection equipment (PPE) guidelines and hand hygiene were good, ranging from 91-100% compliance. None (95% CI: 0, 0.0095) of the participants had SARS-CoV-2 antibodies detected, despite 182 (45.5%) reporting some symptoms one month prior to study recruitment. One hundred and fifteen (29%) of participants claimed to have had contact with known COVID-19 persons outside of their workplace.InterpretationZero seroprevalence among HCW suggests a low incidence of undiagnosed COVID-19 infection in our healthcare setting during the first local wave of SARS-CoV-2 infection. The occupational risk of SARS-CoV-2 transmission within healthcare facilities can be prevented by adherence to infection control measures and appropriate use of PPE.
| S-EPMC7982055 | biostudies-literature
Project description:BackgroundHealthcare workers (HCWs) are at risk of SARS-CoV-2 infections due to occupational exposure. The use of airborne personal protective equipment (PPE) significantly reduces this risk. In June 2021, an epidemic of the Delta variant began in New South Wales (NSW), Australia. Concurrent PPE guidelines, set by the Clinical Excellence Commission (CEC), restricted the use of respirators.ObjectiveTo understand the relationship of PPE guidelines with workplace-acquired HCW SARS-CoV-2 infections in different clinical settings and to examine the relationship between rates of community transmission and workplace-acquired HCW infections during the Delta outbreak in NSW.MethodsTotal SARS-CoV-2 HCW infections between 13 June and 30 October 2021 (first four months of the Delta wave) were estimated from the government COVID-19 surveillance reports and compared with the surveillance reports of community transmission. In the absence of a detailed reporting of HCW infections, open-source data including news articles, media releases, and epidemiological surveillance reports were also collected. Data were extracted on HCW cases of SARS-CoV-2 from four hospitals, including the number of HCW cases (per NSW Health definition), clinical setting, PPE guidelines, and evidence of increasing local transmission.ResultsSARS-CoV-2 infections in HCW identified as workplace-acquired infections (n = 177) and those without a known transmission source (n = 532) increased during the period of increasing community transmission (n = 75,014) in NSW. Four hospital COVID-19 clusters affecting 20 HCWs were identified between June and October 2021. HCW clusters occurred in general wards where staff were recommended to wear surgical masks. No workplace-acquired HCW infections were reported in these hospitals from critical care wards, where respirators were recommended during the same outbreak weeks.ConclusionsDifferences in PPE policy across different wards may leave healthcare staff at risk of SARS-CoV-2 infection. During periods of high community transmission, respirators should be provided to protect hospital staff. Formal reporting of HCW infections should occur.
| S-EPMC10513866 | biostudies-literature
Project description:BackgroundData on breakthrough SARS-CoV-2 Delta variant infections in vaccinated individuals are limited.MethodsWe studied breakthrough infections among Oxford-AstraZeneca vaccinated healthcare workers in an infectious diseases hospital in Vietnam. We collected demographic and clinical data alongside serial PCR testing, measurement of SARS-CoV-2 antibodies, and viral whole-genome sequencing.FindingsBetween 11th-25th June 2021 (7-8 weeks after the second dose), 69 staff tested positive for SARS-CoV-2. 62 participated in the study. Most were asymptomatic or mildly symptomatic and all recovered. Twenty-two complete-genome sequences were obtained; all were Delta variant and were phylogenetically distinct from contemporary viruses obtained from the community or from hospital patients admitted prior to the outbreak. Viral loads inferred from Ct values were 251 times higher than in cases infected with the original strain in March/April 2020. Median time from diagnosis to negative PCR was 21 days (range 8-33). Neutralizing antibodies (expressed as percentage of inhibition) measured after the second vaccine dose, or at diagnosis, were lower in cases than in uninfected, fully vaccinated controls (median (IQR): 69.4 (50.7-89.1) vs. 91.3 (79.6-94.9), p=0.005 and 59.4 (32.5-73.1) vs. 91.1 (77.3-94.2), p=0.002). There was no correlation between vaccine-induced neutralizing antibody levels and peak viral loads or the development of symptoms.InterpretationBreakthrough Delta variant infections following Oxford-AstraZeneca vaccination may cause asymptomatic or mild disease, but are associated with high viral loads, prolonged PCR positivity and low levels of vaccine-induced neutralizing antibodies. Epidemiological and sequence data suggested ongoing transmission had occurred between fully vaccinated individuals.FundingWellcome and NIH/NIAID.
| S-EPMC8481205 | biostudies-literature
Project description:In late November 2021, a new SARS-CoV-2 Variant of Concern (VOC) named Omicron (initially named B.1.1.529) was first detected in South Africa. The rapid spread of the SARS-CoV-2 Omicron variant became globally dominant, and the currently available COVID-19 vaccines showed less protection against this variant. This study aimed to investigate healthcare workers' (HCWs) knowledge and perceptions about the novel SARS-CoV-2 Omicron variant. A cross-sectional anonymous electronic survey concerning the SARS-CoV-2 Omicron variant was conducted among HCWs during the second week of January 2022. The survey instrument was distributed through social media among HCWs to explore awareness (2 items), knowledge (10 items), source of information (1 item), and perceptions (10 items). Respondents who answered ≥80% of the items correctly were considered as having good knowledge and perception. A total of 940 of the 1054 HCW participants completed the survey (response rate: 89.1%); they had a mean age of 31.2 ± 11.2 years, most were doctors (45.7%), and most were from Asia (64.3%). All the participants were aware of the SARS-CoV-2 Omicron variant (100%). Only 36.3% attended lectures/discussions about Omicron and used news media to obtain information. Only a quarter of the HCWs demonstrated good knowledge (24.3%, n = 228) and perception (20.6%) about Omicron. However, while significant differences were observed in the knowledge and perception among HCWs, only a small proportion of doctors exhibited good knowledge (13%) and perception (10%) about the Omicron variant. HCWs who had participated in training/discussion related to the Omicron variant were more likely to have higher knowledge and perception scores (odds ratio: 1.80; 95% confidence interval: 1.04-3.11). As the SARS-CoV-2 Omicron variant spreads rapidly across the globe, ongoing educational interventions are warranted to improve knowledge and perceptions of HCWs.
| S-EPMC8951382 | biostudies-literature
Project description:IntroductionSARS-CoV-2 seroprevalence studies are currently being recommended and implemented in many countries. Forming part of the COVID-19 monitoring and evaluation plan of the Catalan Government Health Department, our network aims to initiate a primary healthcare sentinel monitoring system as a surrogate of SARS-CoV-2 exposure in the Barcelona Metropolitan Area.Methods and analysisThe seroCAP is a serial cross-sectional study, which will be performed in the Barcelona Metropolitan Area to estimate antibodies against SARS-CoV-2. From February 2021 to March 2022, the detection of serum IgG antibodies against SARS-CoV-2 trimeric spike protein will be performed on a monthly basis in blood samples collected for diverse clinical purposes in three reference hospitals from the three Barcelona healthcare areas (BCN areas). The samples (n=2588/month) will be from patients attended by 30 primary healthcare teams at 30 basic healthcare areas (BHA). A lab software algorithm will systematically select the samples by age and sex. Seroprevalence will be estimated and monitored by age, sex, BCN area and BHA. Descriptive and cluster analysis of the characteristics and distribution of SARS-CoV-2 infections will be performed. Sociodemographic, socioeconomic and morbidity-associated factors will be determined using logistic regression. We will explore the association between seroprevalence, SARS-CoV-2 confirmed cases and the implemented measures using interrupted time series analysis.Ethics and disseminationEthical approval was obtained from the University Institute Foundation for Primary Health Care Research Jordi Gol i Gurina ethics committee. An informed consent is not required regarding the approval of the secondary use of biological samples within the framework of the COVID-19 pandemic. A report will be generated quarterly. The final analysis, conclusions and recommendations will be shared with the stakeholders and communicated to the general public. Manuscripts resulting from the network will be submitted for publication in peer-reviewed journals.
| S-EPMC8829838 | biostudies-literature
Project description:Since its first identification in the United Kingdom in late 2020, the highly transmissible B.1.1.7 variant of SARS-CoV-2 has become dominant in several countries raising great concern. We developed a duplex real-time RT-qPCR assay to detect, discriminate, and quantitate SARS-CoV-2 variants containing one of its mutation signatures, the ΔHV69/70 deletion, and used it to trace the community circulation of the B.1.1.7 variant in Spain through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19). The B.1.1.7 variant was detected earlier than clinical epidemiological reporting by the local authorities, first in the southern city of Málaga (Andalucía) in week 20_52 (year_week), and multiple introductions during Christmas holidays were inferred in different parts of the country. Wastewater-based B.1.1.7 tracking showed a good correlation with clinical data and provided information at the local level. Data from wastewater treatment plants, which reached B.1.1.7 prevalences higher than 90% for ≥2 consecutive weeks showed that 8.1 ± 2.0 weeks were required for B.1.1.7 to become dominant. The study highlights the applicability of RT-qPCR-based strategies to track specific mutations of variants of concern as soon as they are identified by clinical sequencing and their integration into existing wastewater surveillance programs, as a cost-effective approach to complement clinical testing during the COVID-19 pandemic.
| S-EPMC8404293 | biostudies-literature