Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 26
Filter
1.
J Infect Dis ; 2022 Jun 07.
Article in English | MEDLINE | ID: covidwho-1878785

ABSTRACT

BACKGROUND: Longer-term humoral responses to two-dose COVID-19 vaccines remain incompletely characterized in people living with HIV (PLWH), as do initial responses to a third dose. METHODS: We measured antibodies against the SARS-CoV-2 spike protein receptor-binding domain, ACE2 displacement and viral neutralization against wild-type and Omicron strains up to six months following two-dose vaccination, and one month following the third dose, in 99 PLWH receiving suppressive antiretroviral therapy, and 152 controls. RESULTS: Though humoral responses naturally decline following two-dose vaccination, we found no evidence of lower antibody concentrations nor faster rates of antibody decline in PLWH compared to controls after accounting for sociodemographic, health and vaccine-related factors. We also found no evidence of poorer viral neutralization in PLWH after two doses, nor evidence that a low nadir CD4+ T-cell count compromised responses. Post-third-dose humoral responses substantially exceeded post-second-dose levels, though Omicron-specific responses were consistently weaker than against wild-type. Nevertheless, post-third-dose responses in PLWH were comparable to or higher than controls. An mRNA-1273 third dose was the strongest consistent correlate of higher post-third-dose responses. CONCLUSION: PLWH receiving suppressive antiretroviral therapy mount strong antibody responses after two- and three-dose COVID-19 vaccination. Results underscore the immune benefits of third doses in light of Omicron.

2.
Emerg Infect Dis ; 28(6): 1154-1162, 2022 06.
Article in English | MEDLINE | ID: covidwho-1862554

ABSTRACT

We tested swab specimens from pets in households in Ontario, Canada, with human COVID-19 cases by quantitative PCR for SARS-CoV-2 and surveyed pet owners for risk factors associated with infection and seropositivity. We tested serum samples for spike protein IgG and IgM in household pets and also in animals from shelters and low-cost neuter clinics. Among household pets, 2% (1/49) of swab specimens from dogs and 7.7% (5/65) from cats were PCR positive, but 41% of dog serum samples and 52% of cat serum samples were positive for SARS-CoV-2 IgG or IgM. The likelihood of SARS-CoV-2 seropositivity in pet samples was higher for cats but not dogs that slept on owners' beds and for dogs and cats that contracted a new illness. Seropositivity in neuter-clinic samples was 16% (35/221); in shelter samples, 9.3% (7/75). Our findings indicate a high likelihood for pets in households of humans with COVID-19 to seroconvert and become ill.


Subject(s)
COVID-19 , Cat Diseases , Dog Diseases , Animals , COVID-19/epidemiology , COVID-19/veterinary , Cat Diseases/epidemiology , Cats , Dog Diseases/diagnosis , Dog Diseases/epidemiology , Dogs , Immunoglobulin G , Immunoglobulin M , Ontario/epidemiology , Pets , Risk Factors , SARS-CoV-2
3.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-337000

ABSTRACT

ABSTRACT SARS-CoV-2 Omicron infections are common among individuals who are vaccinated or have recovered from prior variant infection, but few reports have documented serial Omicron infections. We characterized SARS-CoV-2 humoral responses in a healthy young person who acquired laboratory-confirmed Omicron BA.1.15 ten weeks after a third dose of BNT162b2, and BA.2 thirteen weeks later. Responses were compared to those of 124 COVID-19 naive vaccinees. One month after the second and third vaccine doses, the participant’s wild-type and BA.1-specific IgG, ACE2 competition and virus neutralization activities were average for a COVID-19 naive triple-vaccinated individual. BA.1 infection boosted the participant’s responses to the cohort ≥95th percentile, but even this strong “hybrid” immunity failed to protect against BA.2. Moreover, reinfection increased BA.1 and BA.2-specific responses only modestly. Results illustrate the risk of Omicron infection in fully vaccinated individuals and highlight the importance of personal and public health measures as vaccine-induced immune responses wane.

4.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-336797

ABSTRACT

ABSTRACT Public health emergencies like SARS, MERS, and COVID-19 have prioritized surveillance of zoonotic coronaviruses, resulting in extensive genomic characterization of coronavirus diversity in bats. Sequencing viral genomes directly from animal specimens remains a laboratory challenge, however, and most bat coronaviruses have been characterized solely by PCR amplification of small regions from the best-conserved gene. This has resulted in limited phylogenetic resolution and left viral genetic factors relevant to threat assessment undescribed. In this study, we evaluated whether a technique called hybridization probe capture can achieve more extensive genome recovery from surveillance specimens. Using a custom panel of 20,000 probes, we captured and sequenced coronavirus genomic material in 21 swab specimens collected from bats in the Democratic Republic of the Congo. For 15 of these specimens, probe capture recovered more genome sequence than had been previously generated with standard amplicon sequencing protocols, providing a median 6.1-fold improvement (ranging up to 69.1-fold). Probe capture data also identified five novel alpha- and betacoronaviruses in these specimens, and their full genomes were recovered with additional deep sequencing. Based on these experiences, we discuss how probe capture could be effectively operationalized alongside other sequencing technologies for high-throughput, genomics-based discovery and surveillance of bat coronaviruses.

5.
J Infect Dis ; 2022 May 11.
Article in English | MEDLINE | ID: covidwho-1840054

ABSTRACT

BACKGROUND: Third COVID-19 vaccine doses are broadly recommended, but immunogenicity data remain limited, particularly in older adults. METHODS: We measured circulating antibodies against the SARS-CoV-2 spike protein receptor-binding domain, ACE2 displacement, and virus neutralization against ancestral and Omicron (BA.1) strains from pre-vaccine up to one month following the third dose, in 151 adults aged 24-98 years who received COVID-19 mRNA vaccines. RESULTS: Following two vaccine doses, humoral immunity was weaker, less functional and less durable in older adults, where a higher number of chronic health conditions was a key correlate of weaker responses and poorer durability. One month after the third dose, antibody concentrations and function exceeded post-second-dose levels, and responses in older adults were comparable in magnitude to those in younger adults at this time. Humoral responses against Omicron were universally weaker than against the ancestral strain after both the second and third doses. Nevertheless, after three doses, anti-Omicron responses in older adults reached equivalence to those in younger adults. One month after three vaccine doses, the number of chronic health conditions, but not age, was the strongest consistent correlate of weaker humoral responses. CONCLUSION: Results underscore the immune benefits of third COVID-19 vaccine doses, particularly in older adults.

6.
Can Commun Dis Rep ; 47(12): 543-552, 2021 Dec 09.
Article in English | MEDLINE | ID: covidwho-1836029

ABSTRACT

BACKGROUND: In March 2021, a coronavirus disease 2019 (COVID-19) outbreak was declared at a large long-term care and short stay facility in British Columbia, Canada-well after introduction of the vaccination program in long-term care facilities that resulted in a dramatic decline in the number of outbreaks in this type of setting. The objective of this study is to provide the descriptive epidemiology of this outbreak, in the context of partial immunization of both residents and staff at the facility. METHODS: The cases' information was extracted from a provincial information system (Panorama). Descriptive analysis was performed using Microsoft Excel and SAS. Outbreak management controls included, but were not limited to, asymptomatic testing and efforts to increase vaccination. RESULTS: Twenty-six cases among the 241 resident and three cases among the 418 staff (corresponding to attack rates of 10% and less than 1%, respectively) were identified. The attack rate in residents was considerably lower than the average attack rate for COVID-19 outbreaks in long-term care facilities before the vaccine rollout. Seventeen resident cases were either partially or fully immunized. Four of the eight hospitalized cases and two of the three deceased cases were partially immunized. Seventeen cases were temporary stay residents. The three staff cases were not vaccinated. Ten cases were identified as part of asymptomatic testing. CONCLUSION: Introduction of vaccination at facilities contributed to lower attack rates and higher numbers of asymptomatic cases in this outbreak. Screening asymptomatic individuals identified additional cases among vaccinated residents. Findings underscore the importance of achieving high vaccine coverage, including among temporary stay residents, to prevent virus introduction and subsequent unrecognized transmission opportunities.

7.
Clin Infect Dis ; 2022 Apr 19.
Article in English | MEDLINE | ID: covidwho-1795352

ABSTRACT

BACKGROUND: The Canadian COVID-19 immunization strategy deferred second doses and allowed mixed schedules. We compared two-dose vaccine effectiveness (VE) by vaccine type (mRNA and/or ChAdOx1), interval between doses, and time since second dose in two of Canada's larger provinces. METHODS: Two-dose VE against SARS-CoV-2 infection or hospitalization among adults ≥18-years-old, including due to Alpha, Gamma and Delta variants of concern (VOC), was assessed at ≥14 days post-vaccination by test-negative design studies separately conducted in British Columbia and Quebec, Canada between May 30 and November 27 (epi-weeks 22-47), 2021. RESULTS: In both provinces, all homologous or heterologous mRNA and/or ChAdOx1 two-dose schedules were associated with ≥90% reduction in SARS-CoV-2 hospitalization risk for at least 7 months. With slight decline from a peak of >90%, VE against infection was ≥80% for at least 6 months following homologous mRNA vaccination, lower by ∼10% when both doses were ChAdOx1 but comparably-high following heterologous ChAdOx1 + mRNA receipt. Findings were similar by age group, sex and VOC. VE was significantly higher with longer 7-8-week vs. manufacturer-specified 3-4-week interval between mRNA doses. CONCLUSIONS: Two doses of any mRNA and/or ChAdOx1 combination gave substantial and sustained protection against SARS-CoV-2 hospitalization, spanning Delta-dominant circulation. ChAdOx1 VE against infection was improved by heterologous mRNA series completion. A 7-8-week interval between first and second doses improved mRNA VE and may be the optimal schedule outside periods of intense epidemic surge. Findings support interchangeability and extended intervals between SARS-CoV-2 vaccine doses, with potential global implications for low-coverage areas and, going forward, for children.

8.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-330919

ABSTRACT

Background: Longer-term humoral responses to two-dose COVID-19 vaccines remain incompletely characterized in people living with HIV (PLWH), as do initial responses to a third dose. Methods: We measured antibodies against the SARS-CoV-2 spike protein receptor-binding domain, ACE2 displacement and viral neutralization against wild-type and Omicron strains up to six months following two-dose vaccination, and one month following the third dose, in 99 PLWH receiving suppressive antiretroviral therapy, and 152 controls. Results: Though humoral responses naturally decline following two-dose vaccination, we found no evidence of lower antibody concentrations nor faster rates of antibody decline in PLWH compared to controls after accounting for sociodemographic, health and vaccine-related factors. We also found no evidence of poorer viral neutralization in PLWH after two doses, nor evidence that a low nadir CD4+ T-cell count compromised responses. Post-third-dose humoral responses substantially exceeded post-second-dose levels, though anti-Omicron responses were consistently weaker than against wild-type. Nevertheless, post-third-dose responses in PLWH were comparable to or higher than controls. An mRNA-1273 third dose was the strongest consistent correlate of higher post-third-dose responses. Conclusion: PLWH receiving suppressive antiretroviral therapy mount strong antibody responses after two- and three-dose COVID-19 vaccination. Results underscore the immune benefits of third doses in light of Omicron.

9.
J Infect Dis ; 2022 Jan 27.
Article in English | MEDLINE | ID: covidwho-1746883

ABSTRACT

INTRODUCTION: In British Columbia, Canada, most adults 50-69 years old became SARS-CoV-2 vaccine-eligible in April 2021, with ChAdOx1 restricted to ≥55-year-olds and second doses deferred ≥6 weeks to optimize single-dose coverage. METHODS: Among adults 50-69-years-old, single-dose mRNA and ChAdOx1 VE against SARS-CoV-2 infection and hospitalization, including variant-specific, was assessed by test-negative design between April 4-October 2, 2021. RESULTS: Single-dose VE included 11,861 cases and 99,544 controls. Median (interquartile range) of post-vaccination follow-up was 32 (15-52) days. Alpha, Gamma and Delta variants comprised 23%, 18% and 56% of genetically-characterized viruses. At 21-55 days post-vaccination, single-dose mRNA and ChAdOx1 VE was 74% (95%CI: 71-76) and 59% (95%CI:53-65) against any infection and 86% (95%CI:80-90) and 94% (95%CI:85-97) against hospitalization, respectively. VE was similar against Alpha and Gamma infections for mRNA (80%;95%CI:76-84 and 80%;95%CI:75-84) and ChAdOx1 (69%;95%CI:60-76 and 66%;95%CI:56-73). mRNA VE was lower at 63% (95%CI:56-69) against Delta but 85% (95%CI:71-92) against Delta-associated hospitalization [non-estimable, ChAdOx1]. CONCLUSIONS: A single mRNA or ChAdOx1 vaccine dose gave important protection against SARS-CoV-2, including early variants-of-concern. ChAdOx1 VE was lower against infection but one dose of either vaccine reduced the hospitalization risk by >85% to at least 8 weeks post-vaccination. Findings inform program options, including longer dosing intervals.

10.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-330325

ABSTRACT

Background: The COVID-19 pandemic remains a global public health concern. Advances in rapid sequencing has led to an unprecedented level of SARS-CoV-2 whole genome sequence (WGS) data and sharing of sequences through global repositories that has enabled almost real-time genomic analysis of the pathogen. WGS data has been used previously to group genetically similar viral pathogens to reveal evidence of transmission, including methods that identify distinct clusters on a phylogenetic tree. Identifying clusters of linked cases can aid in the regional surveillance and management of the disease. In this study, we present a novel method for producing stable genomic clusters of SARS-CoV-2 cases, cov2clusters, and compare the sensitivity and stability of our approach to previous methods used for phylogenetic clustering using real-world SARS-CoV-2 sequence data obtained from British Columbia, Canada, Results: We found that cov2clusters produced more stable clusters than previously used phylogenetic clustering methods when adding sequence data through time, mimicking an increase in sequence data through the pandemic. Our method also showed high sensitivity when compared to epidemiologically informed clusters. These clusters often contained a high number of cases that were identical or near identical genetically. Conclusions: This new approach presented here allows for the identification of stable clusters of SARS-CoV-2 from WGS data. Producing high-resolution SARS-CoV-2 clusters from sequence data alone can a challenge and, where possible, both genomic and epidemiological data should be used in combination.

11.
Can Commun Dis Rep ; 48(1): 22-26, 2022 Jan 26.
Article in English | MEDLINE | ID: covidwho-1726968

ABSTRACT

Background: The Kappa variant is designated as a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of interest (VOI). We identified 195 Kappa variant cases in a region of British Columbia, Canada-the largest published cluster in North America. Objectives: To describe the epidemiology of the Kappa variant in relation to other circulating SARS-CoV-2 variants of concern (VOC) in the region to determine if the epidemiology of the Kappa variant supports a VOI or VOC status. Methods: Clinical specimens testing positive for SARS-CoV-2 collected between March 10 and May 2, 2021, were screened for the detection of known circulating VOCs; approximately 50% of specimens were subsequently selected for whole genome sequencing (WGS). Epidemiological analysis was performed comparing the characteristics of Kappa cases to the main circulating variants in the region (Alpha and Gamma) and to non-VOC/VOI cases. Results: A total of 2,079 coronavirus disease 2019 (COVID-19) cases were reported in the region during the study period, of which 54% were selected for WGS. The 1,131 sequenced cases were categorized into Kappa, Alpha, Gamma and non-VOC/VOI. While Alpha and Gamma cases were found to have a significantly higher attack rate among household contacts compared to non-VOI/VOC cases, Kappa was not. Conclusion: Epidemiological analysis supports the designation of Kappa as a VOI and not a VOC. The Alpha and Gamma variants were found to be more transmissible, explaining their subsequent dominance in the region and the rapid disappearance of the Kappa variant. Variant surveillance strategies should focus on both detection of established VOCs and detection of potential new VOCs.

12.
Clin Infect Dis ; 74(7): 1158-1165, 2022 Apr 09.
Article in English | MEDLINE | ID: covidwho-1700948

ABSTRACT

BACKGROUND: Randomized-controlled trials of messenger RNA (mRNA) vaccine protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) included relatively few elderly participants. We assess single-dose mRNA vaccine effectiveness (VE) in adults ≥ 70 years old in British Columbia, Canada, where second doses were deferred by up to 16 weeks and where a spring 2021 wave uniquely included codominant circulation of Alpha (B.1.1.7) and Gamma (P.1) variants of concern (VOC). METHODS: Analyses included community-dwelling adults ≥ 70 years old with specimen collection between 4 April (epidemiological week 14) and 1 May (week 17) 2021. Adjusted VE was estimated by test-negative design. Cases were reverse-transcription polymerase chain reaction (RT-PCR) test-positive for SARS-CoV-2, and controls were test-negative. Vaccine status was defined by receipt of a single-dose ≥ 21 days before specimen collection, but a range of intervals was assessed. Variant-specific VE was estimated against viruses genetically characterized as Alpha, Gamma or non-VOC lineages. RESULTS: VE analyses included 16 993 specimens: 1226 (7%) test-positive cases and 15 767 test-negative controls. Of 1131 (92%) genetically characterized viruses, 509 (45%), 314 (28%), and 276 (24%) were Alpha, Gamma, and non-VOC lineages, respectively. At 0-13 days postvaccination, VE was negligible at 14% (95% confidence interval [CI], 0-26) but increased from 43% (95% CI, 30-53) at 14-20 days to 75% (95% CI, 63-83) at 35-41 days postvaccination. VE at ≥ 21 days postvaccination was 65% (95% CI, 58-71) overall: 72% (95% CI, 58-81), 67% (95% CI, 57-75), and 61% (95% CI, 45-72) for non-VOC, Alpha, and Gamma variants, respectively. CONCLUSIONS: A single dose of mRNA vaccine reduced the risk of SARS-CoV-2 by about two-thirds in adults ≥ 70 years old, with protection only minimally reduced against Alpha and Gamma variants.


Subject(s)
COVID-19 Vaccines , COVID-19 , SARS-CoV-2 , Aged , British Columbia/epidemiology , COVID-19/epidemiology , COVID-19/prevention & control , Humans , RNA, Messenger , SARS-CoV-2/genetics , Vaccines, Synthetic
13.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-327499

ABSTRACT

ABSTRACT The ongoing COVID-19 pandemic necessitates cost-effective, high-throughput, and timely genomic sequencing of SARS-CoV-2 viruses for outbreak investigations, identifying variants of concern (VoC), characterizing vaccine breakthrough infections, and public health surveillance. Additionally, the enormous demand of genomic sequencing on supply chains and the resulting shortages of laboratory supplies necessitate the use of low-reagent and low-consumable methods. Here, we report an optimized library preparation method where the same protocol can be used in a STAT scenario, from sample to sequencer in as little as eight hours, and a high-throughput scenario, where one technologist can perform 576 library preparations over the course of one 8-hour shift. This new method uses Freed et al.’s 1200 bp primer sets (Biol Methods Protoc 5:bpaa014, 2020, https://doi.org/10.1093/biomethods/bpaa014 ) and a modified and truncated Illumina DNA Prep workflow (Illumina, CA, USA). Compared to the original, application of this new method in hundreds of clinical specimens demonstrated equivalent results to the full-length DNA Prep workflow at 45% the cost, 15% of consumables required (such as pipet tips), 25% of manual hands-on time, and 15% of on-instrument time if performing on a liquid handler, with no compromise in sequence quality. Results suggest that this new method is a rapid, simple, cost-effective, and high-quality SARS-CoV-2 whole genome sequencing protocol.

14.
J Clin Virol ; 146: 105050, 2022 01.
Article in English | MEDLINE | ID: covidwho-1616567

ABSTRACT

BACKGROUND: Multiplex immunoassays capture a comprehensive profile of the humoral response against SARS-CoV-2 and human endemic coronaviruses. We validated a multiplex panel (V-PLEX Panel 2) from Meso Scale Diagnostics targeting antibodies against nine coronavirus antigens. Performance was compared against alternative single- and multi-antigen immunoassays. METHODS: Sera collected for clinical or public health testing from 2018 to 2020 (n = 135) were used to compare all tested platforms, and inter-test agreement was assessed by Cohen's kappa coefficient. Sample category (positive/negative) was assigned based on collection date relative to the index case in Canada, and SARS-CoV-2 PCR and serology results. 117 out of the 135 samples (31 positive, 86 negative) were assigned a category and were used to calculate sensitivity and specificity, with MSD's test results based upon manufacturer-set cut-offs. RESULTS: We observed SARS-CoV-2 target sensitivities of 100% and specificities >94% for all antigens (RBD, Nucleocapsid, Spike) in V-PLEX Panel 2. When targets were combined, we found a SARS-CoV-2 sensitivity of 100% and specificity of 98.8% with no difference in performance compared to clinical assays, and Cohen's kappa ranging from 0.798 to 0.945 compared to surface plasmon resonance imaging (SPRi). Quantitative measurements of antibodies against the Spike protein of endemic human coronaviruses were concordant with SPRi. CONCLUSION: Meso Scale Diagnostics' V-PLEX Coronavirus Panel 2 allows for highly sensitive and specific detection of anti-coronavirus IgG, and is concordant with other serological assays for detection of antibodies against SARS-CoV-2 and the endemic human coronaviruses, making it a good tool for humoral response characterization after both infection and vaccination.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , Antibodies, Viral , Humans , Immunoassay , Immunoglobulin G , SARS-CoV-2 , Sensitivity and Specificity
15.
J Clin Virol ; 144: 104996, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1505745

ABSTRACT

BACKGROUND: High-throughput assays for the detection of SARS-CoV-2 variants of concern (VOC) and interest (VOI) are a diagnostic alternative when whole genome sequencing (WGS) is unavailable or limited. OBJECTIVE: This study evaluated the clinical and analytical performance of the Seegene Allplex™ SARS-CoV-2 Variants I assay, which detects the HV69/70 deletion, N501Y and E484K mutations of the S gene. METHODS: Genotyping was evaluated on -871 SARS-CoV-2 RNA positive specimens, 408 nasopharyngeal (NP) swabs and 463 saline gargle (SG) specimens, with WGS used as the reference standard. Analytical performance was assessed including stability, reproducibility, limit of detection (LOD), cross-reactivity and interference with various respiratory microorganisms. RESULTS: The clinical study revealed sensitivity of 100% (95% CI 99.27%-100%) and specificity of 100% (95% CI 98.99%-100%) for HV69/70 deletion, sensitivity of 100% (95% CI 99.55%-100%) and specificity of 100% (95% CI 93.73% - 100%) for N501Y, and sensitivity of 100% (95% CI 98.94% - 100%) and specificity of 98.10% (95% CI 96.53% - 99.08%) for E484K mutation. The E484Q mutation was detected in 10 specimens of the Kappa variant (B.1.627.1). Analytical performance demonstrated stability and reproducibility over 7 days, and LOD was calculated at 698 cp/mL for NP swab specimens, and 968 cp/mL for SG specimens. No interference or cross-reactivity with other microorganisms was noted. CONCLUSION: The Allplex™ SARS-CoV-2 Variants I assay is acceptable for clinical use for the detection of variant of concern and variant of interest.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , RNA, Viral , Reproducibility of Results
16.
Viruses ; 13(11)2021 10 31.
Article in English | MEDLINE | ID: covidwho-1488765

ABSTRACT

This study identified factors associated with hospital admission among people with laboratory-diagnosed COVID-19 cases in British Columbia. The study used data from the BC COVID-19 Cohort, which integrates data on all COVID-19 cases with data on hospitalizations, medical visits, emergency room visits, prescription drugs, chronic conditions and deaths. The analysis included all laboratory-diagnosed COVID-19 cases in British Columbia to 15 January 2021. We evaluated factors associated with hospital admission using multivariable Poisson regression analysis with robust error variance. Of the 56,874 COVID-19 cases included in the analysis, 2298 were hospitalized. Factors associated with increased hospitalization risk were as follows: male sex (adjusted risk ratio (aRR) = 1.27; 95% CI = 1.17-1.37), older age (p-trend < 0.0001 across age groups increasing hospitalization risk with increasing age [aRR 30-39 years = 3.06; 95% CI = 2.32-4.03, to aRR 80+ years = 43.68; 95% CI = 33.41-57.10 compared to 20-29 years-old]), asthma (aRR = 1.15; 95% CI = 1.04-1.26), cancer (aRR = 1.19; 95% CI = 1.09-1.29), chronic kidney disease (aRR = 1.32; 95% CI = 1.19-1.47), diabetes (treated without insulin aRR = 1.13; 95% CI = 1.03-1.25, requiring insulin aRR = 5.05; 95% CI = 4.43-5.76), hypertension (aRR = 1.19; 95% CI = 1.08-1.31), injection drug use (aRR = 2.51; 95% CI = 2.14-2.95), intellectual and developmental disabilities (aRR = 1.67; 95% CI = 1.05-2.66), problematic alcohol use (aRR = 1.63; 95% CI = 1.43-1.85), immunosuppression (aRR = 1.29; 95% CI = 1.09-1.53), and schizophrenia and psychotic disorders (aRR = 1.49; 95% CI = 1.23-1.82). In an analysis restricted to women of reproductive age, pregnancy (aRR = 2.69; 95% CI = 1.42-5.07) was associated with increased risk of hospital admission. Older age, male sex, substance use, intellectual and developmental disability, chronic comorbidities, and pregnancy increase the risk of COVID-19-related hospitalization.


Subject(s)
COVID-19 , Hospitalization , Mental Disorders/complications , Mental Health , Substance-Related Disorders/complications , Adult , Age Factors , Aged , Aged, 80 and over , British Columbia/epidemiology , COVID-19/complications , COVID-19/epidemiology , COVID-19/psychology , Cohort Studies , Comorbidity , Female , Humans , Male , Middle Aged , Pregnancy , Pregnancy Complications, Infectious , Risk Factors , Sex Factors , Young Adult
17.
Int J Infect Dis ; 114: 51-54, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1487755

ABSTRACT

Mutations in emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages can interfere with laboratory methods used to generate viral genome sequences for public health surveillance. We identified 20 mutations that are widespread in variant of concern lineages and affect widely used sequencing protocols by the ARTIC network and Freed et al. Three of these mutations disrupted sequencing of P.1 lineage specimens during a recent outbreak in British Columbia, Canada. We provide laboratory validation of protocol modifications that restored sequencing performance. The study findings indicate that genomic sequencing protocols require immediate updating to address emerging mutations. This work also suggests that routine monitoring and protocol updates will be necessary as SARS-CoV-2 continues to evolve. The bioinformatic and laboratory approaches used here provide guidance for this kind of assay maintenance.


Subject(s)
COVID-19 , SARS-CoV-2 , British Columbia , Genome, Viral/genetics , Genomics , Humans , Mutation
18.
Int J Infect Dis ; 114: 178-182, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1487753

ABSTRACT

This article reports a case of a 21-year-old woman with refractory B-cell acute lymphocytic leukaemia who presented with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). She remained positive for SARS-CoV-2 by viral culture for 78 days and by polymerase chain reaction (PCR) for 97 days. Sequencing of repeat samples over time demonstrated an increasing and dynamic repertoire of mutations.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , Female , Humans , Immunocompromised Host , Mutation , Virus Shedding , Young Adult
19.
mSystems ; 6(5): e0106821, 2021 Oct 26.
Article in English | MEDLINE | ID: covidwho-1476395

ABSTRACT

Wastewater-based genomic surveillance of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus shows promise to complement genomic epidemiology efforts. Multiplex tiling PCR is a desirable approach for targeted genome sequencing of SARS-CoV-2 in wastewater due to its low cost and rapid turnaround time. However, it is not clear how different multiplex tiling PCR primer schemes or wastewater sample matrices impact the resulting SARS-CoV-2 genome coverage. The objective of this work was to assess the performance of three different multiplex primer schemes, consisting of 150-bp, 400-bp, and 1,200-bp amplicons, as well as two wastewater sample matrices, influent wastewater and primary sludge, for targeted genome sequencing of SARS-CoV-2. Wastewater samples were collected weekly from five municipal wastewater treatment plants (WWTPs) in the Metro Vancouver region of British Columbia, Canada during a period of increased coronavirus disease 19 (COVID-19) case counts from February to April 2021. RNA extracted from clarified influent wastewater provided significantly higher genome coverage (breadth and median depth) than primary sludge samples across all primer schemes. Shorter amplicons appeared to be more resilient to sample RNA degradation but were hindered by greater primer pool complexity in the 150-bp scheme. The identified optimal primer scheme (400 bp) and sample matrix (influent) were capable of detecting the emergence of mutations associated with genomic variants of concern, for which the daily wastewater load significantly correlated with clinical case counts. Taken together, these results provide guidance on best practices for implementing wastewater-based genomic surveillance and demonstrate its ability to inform epidemiology efforts by detecting genomic variants of concern circulating within a geographic region. IMPORTANCE Monitoring the genomic characteristics of the SARS-CoV-2 virus circulating in a population can shed important insights into epidemiological aspects of the COVID-19 outbreak. Sequencing every clinical patient sample in a highly populous area is a difficult feat, and thus sequencing SARS-CoV-2 RNA in municipal wastewater offers great promise to augment genomic surveillance by characterizing a pooled population sample matrix, particularly during an escalating outbreak. Here, we assess different approaches and sample matrices for rapid targeted genome sequencing of SARS-CoV-2 in municipal wastewater. We demonstrate that the optimal approach is capable of detecting the emergence of SARS-CoV-2 genomic variants of concern, with strong correlations to clinical case data in the province of British Columbia. These results provide guidance on best practices on, as well as further support for, the application of wastewater genomic surveillance as a tool to augment current genomic epidemiology efforts.

20.
J Virol Methods ; 299: 114339, 2022 01.
Article in English | MEDLINE | ID: covidwho-1472084

ABSTRACT

The COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagnostic testing. Magnetic bead-based nucleic acid extraction protocols using 96-well plates on open liquid handlers are readily amenable to meet this need. Here, one such approach is rigorously optimized to minimize cross-well contamination while maintaining sensitivity.


Subject(s)
COVID-19 , Nucleic Acids , COVID-19 Testing , Humans , Indicators and Reagents , Magnetic Phenomena , Pandemics , RNA, Viral/genetics , SARS-CoV-2 , Sensitivity and Specificity
SELECTION OF CITATIONS
SEARCH DETAIL