Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-17 (of 17 Records) |
Query Trace: Poon AN[original query] |
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The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.
Walker K , Kalra D , Lowdon R , Chen G , Molik D , Soto DC , Dabbaghie F , Khleifat AA , Mahmoud M , Paulin LF , Raza MS , Pfeifer SP , Agustinho DP , Aliyev E , Avdeyev P , Barrozo ER , Behera S , Billingsley K , Chong LC , Choubey D , De Coster W , Fu Y , Gener AR , Hefferon T , Henke DM , Höps W , Illarionova A , Jochum MD , Jose M , Kesharwani RK , Kolora SRR , Kubica J , Lakra P , Lattimer D , Liew CS , Lo BW , Lo C , Lötter A , Majidian S , Mendem SK , Mondal R , Ohmiya H , Parvin N , Peralta C , Poon CL , Prabhakaran R , Saitou M , Sammi A , Sanio P , Sapoval N , Syed N , Treangen T , Wang G , Xu T , Yang J , Zhang S , Zhou W , Sedlazeck FJ , Busby B . F1000Res 2022 11 530 In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics. |
Protocol for a sequential, prospective meta-analysis to describe coronavirus disease 2019 (COVID-19) in the pregnancy and postpartum periods (preprint)
Smith ER , Oakley E , He S , Zavala R , Ferguson K , Miller L , Grandner GW , Abejirinde IO , Afshar Y , Ahmadzia H , Aldrovandi G , Akelo V , Tippett Barr BA , Bevilacqua E , Brandt JS , Broutet N , Fernández Buhigas I , Carrillo J , Clifton R , Conry J , Cosmi E , Delgado-López C , Divakar H , Driscoll AJ , Favre G , Flaherman V , Gale C , Gil MM , Godwin C , Gottlieb S , Hernandez Bellolio O , Kara E , Khagayi S , Kim CR , Knight M , Kotloff K , Lanzone A , Le Doare K , Lees C , Litman E , Lokken EM , Laurita Longo V , Magee LA , Martinez-Portilla RJ , McClure E , Metz TD , Money D , Mullins E , Nachega JB , Panchaud A , Playle R , Poon LC , Raiten D , Regan L , Rukundo G , Sanin-Blair J , Temmerman M , Thorson A , Thwin S , Tolosa JE , Townson J , Valencia-Prado M , Visentin S , von Dadelszen P , Adams Waldorf K , Whitehead C , Yang H , Thorlund K , Tielsch JM . medRxiv 2022 2020.11.08.20228056 We urgently need answers to basic epidemiological questions regarding SARS-CoV-2 infection in pregnant and postpartum women and its effect on their newborns. While many national registries, health facilities, and research groups are collecting relevant data, we need a collaborative and methodologically rigorous approach to better combine these data and address knowledge gaps, especially those related to rare outcomes. We propose that using a sequential, prospective meta-analysis (PMA) is the best approach to generate data for policy- and practice-oriented guidelines. As the pandemic evolves, additional studies identified retrospectively by the steering committee or through living systematic reviews will be invited to participate in this PMA. Investigators can contribute to the PMA by either submitting individual patient data or running standardized code to generate aggregate data estimates. For the primary analysis, we will pool data using two-stage meta-analysis methods. The meta-analyses will be updated as additional data accrue in each contributing study and as additional studies meet study-specific time or data accrual thresholds for sharing. At the time of publication, investigators of 25 studies, including more than 76,000 pregnancies, in 41 countries had agreed to share data for this analysis. Among the included studies, 12 have a contemporaneous comparison group of pregnancies without COVID-19, and four studies include a comparison group of non-pregnant women of reproductive age with COVID-19. Protocols and updates will be maintained publicly. Results will be shared with key stakeholders, including the World Health Organization (WHO) Maternal, Newborn, Child, and Adolescent Health (MNCAH) Research Working Group. Data contributors will share results with local stakeholders. Scientific publications will be published in open-access journals on an ongoing basis.Competing Interest StatementClare Whitehead declares a a relationship with the following entities, Ferring Pharmaceuticals COVID19 Investigational, Grant, NHMRC Fellowship (salary support). Alice Panchaud declares the following research grants to institution: H2020-Grant (Consortium member of Innovative medicine initiative call 13 topic 9) (ConcePTION), Efficacy and safety studies on Medicines EMA/2017/09/PE/11, Lot 4, WP 2 lead (CONSIGN: Study on impact of COVID-19 infection and medicines in pregnancy), Safety monitoring of COVID-19 vaccines in the EU Reopening of competition no. 20 under a framework contract following procurement procedure EMA/2017/09/PE (Lot 3) 4. Federal Office of Public Health (207000 CHF). (The COVI-Preg registry). Edward Mullins declares a relationship with the following entities National Institute for Health Research (Project grant for PAN COVID study) Deborah Money declares a relationship with the following entities, Canadian Institutes of Health Research (payments to my institution only), Public Health Agency of Canada (payments to my institution only), BC Womens Foundation (payments to my institution only) and is a Member of the COVID-19 Immunity Task Force sponsored by the Canadian government. Torri D. Metz declares a relationship with the following entities, Pfizer (site Principal Investigator for SARS-CoV-2 vaccination in pregnancy study, money paid to institution and member of Medical Advisory Board for SARS-CoV-2 vaccination in pregnancy study, money paid to me), NICHD (subcommittee Chair for the NICHD Maternal-Fetal Medicine Units Network Gestational Research Assessments of COVID-19 (GRAVID) study), and Society for Maternal-Fetal Medicine (board member). Erica Lokken declares a relationship with the following entity, US NIH (paid institution). Karen L. Kotloff declares a relationship with the following entity, Bill and Melinda Gates Foundation. Siran He declares a relationship with the following entity, Bill and Melinda Gates Foundtion (payments made to my institution). Valerie Flaherman declares a relationship with the following entities, Bill and Melinda Gates Foundation (payments to my institution), Yellow Chair Foundati n (payments to my institution), Robert Woods Johnson Foundation (payments to my institution), CDC Foundation, California Health Care Foundation (payments to my institution), Tara Health Foundation (payments to my institution), UCSF Womens Health Center of Excellence (payments to my institution) and California Department of Health Care Services (payments made to my institution). Jose Sanin-Blair declares a relationship with the following entity, Ferring Pharmaceuticals which give a grant ($10,000) for the expenses of RECOGEST trial and is a part of the Columbian Federation of Perinatology Yalda Afshar declares a relationship with the following entities, Bill and Melinda Gates Foundation (payments made to my institution), CDC Foundation (payments made to my institution), Robert Woods Johnson Foundation (payments made to my institution), and UCLA Deans Office COVID-19 research (payments made to my institution). Rebecca Cliffton declares a relationship with the following entity, NIH HD36801 (MFMU Network DCC).Clinical TrialPROSPERO ID: 188955Funding StatementFunded by the Bill & Melinda Gates Foundation grant to Emily Smith (INV-022057) at George Washington University and a grant to Emily Smith via a grant from the Bill & Melinda Gates Foundation to Stephanie Gaw (INV-017035) at University of California San Francisco.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:This is a protocol paper and thus exempt from ethical approval. Ultimately, the meta-analysis study is exempt from human research ethics approval as the study authors will be synthesizing de-identified or aggregate data.I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesThis is a protocol paper and there is no related data to share. |
Risk of Adverse Maternal and Fetal Outcomes Associated with COVID-19 Variants of Concern: A Sequential Prospective Meta-Analysis (preprint)
Farooq F , Oakley E , Kerchner D , Hee Kim JY , Akelo V , Tippett Barr BA , Bevilacqua E , Bracero N , del Mar Gil M , Delgado-Lopez C , Favre G , Buhigas IF , Hillary Leung HY , Longo VL , Panchaud A , Poon LC , Martinez-Portilla RJ , Valencia-Prado M , Tielsch JM , Smith ER , Omore R , Ouma G , Onyango C , Otieno K , Were ZA , Were J , Maisonneuve E , Poncelet C , de Tejada BM , Quibel T , Monod C , Yu FNY , Kong CW , Lo TK , So PL , Leung WC , Meli F , Bonanni G , Romanzi F , Torcia E , di Ilio C , Aquise A , Rayo MN , Santacruz B , Gonzalez-Gea L , Laiseca S , Ferrer LN , Huertas MM , Rosario GM , Ramos NA , Gonzalez SV . medRxiv 2023 04 Introduction The main objective of this study is to conduct an individual patient data meta-analysis with collaborators from various countries to identify SARS-CoV-2 variants of concern associated with adverse maternal and neonatal outcomes. Methods Eligible studies included registries and single- or multi-site cohort studies that recruited pregnant and recently postpartum women with confirmed COVID-19. Studies must have enrolled at least 25 women within a defined catchment area. Studies also had to have data that overlapped more than a single COVID-19 variant time period. We invited principal investigators already participating in an ongoing sequential, prospective meta-analysis of perinatal COVID-19. Investigators shared individual patient data (IPD) with the technical team for review and analysis. We examined 31 outcomes related to: i) COVID-19 severity (n=5); ii) maternal morbidities including adverse birth outcomes (n=14); iii) fetal and neonatal morbidity and mortality (n=5) and iv) adverse birth outcomes (n=8). SARS-CoV-2 strains that have been identified as variants of concern (VOC) by the WHO were analyzed using the publicly available strain frequency data by Nextstrain.org and strains were classified as dominant when they were more than half of sequences in a given geographic area. We applied a 2-stage IPD meta-analytic framework to generate pooled relative risks, with 95% CI for each dominant variant and outcome pair when there were one or more studies with available data. Results Our data show that the Delta wave, compared to Omicron, was associated with a higher risk of all adverse COVID-19 severity outcomes in pregnancy including risk of hospitalization [RR 4.02 (95% CI 1.10, 14.69), n=1 study], risk of ICU admissions [RR 2.59 (95% CI 1.26, 5.30, n=3 studies], risk of critical care admission [RR 2.52 (95% CI 1.25, 5.08, n=3 studies], risk of needing ventilation [RR 3.96 (95% CI 1.47, 10.71), n=3 studies] and risk of pneumonia [RR 6.73 (95% CI 2.17, 20.90), n=3 studies]. The majority of maternal morbidity and mortality indicators were not at increased risk during any of the COVID-19 variant waves except hemorrhage, any Cesarean section, intrapartum Cesarean section and maternal composite outcome, although data was limited. Risk of fetal and neonatal morbidity and mortality did not show significant increases in risks during any of the COVID-19 waves except stillbirth and perinatal death during the Delta wave ([RR 4.84 (95% CI 1.37, 17.05, n=3 studies], [RR 6.03 (95%CI 1.63, 22.34), n=3 studies], respectively) when compared to the Pre-alpha wave. Adverse birth outcomes including very low birthweight and very preterm birth also showed increased risks during the Delta wave compared to the Pre-alpha wave. Discussion During periods of Delta strain predominance, all COVID-19 severity outcomes were more severe among pregnant women, compared to periods when other COVID-19 strains predominated. In addition, there are limited data comparing the impact of different variants on pregnancy outcomes. This highlights the importance of ongoing genomic surveillance among special populations. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. |
Reply to 'Reconciling disparate estimates of viral genetic diversity during human influenza infections'.
Poon LLM , Song T , Wentworth DE , Holmes EC , Greenbaum BD , Peiris JSM , Cowling BJ , Ghedin E . Nat Genet 2019 51 (9) 1301-1303 In their Correspondence, Xue and Bloom1 identify an important discrepancy in the sequence data that we provided in our 2016 paper2 on the transmission of influenza virus in Hong Kong during the first wave of the H1N1 pandemic in 2009. The goal of the study was to provide a quantitative approach to characterizing the within-host genetic diversity of influenza virus and how this genomic information might be used in tracking transmission. We have determined that the potential source of this discrepancy was due to the technical limitations of the methods used at the time, which inadvertently led to the reporting of substantially higher levels of within-host diversity than were likely to be present. |
An early warning system for emerging SARS-CoV-2 variants.
Subissi L , von Gottberg A , Thukral L , Worp N , Oude Munnink BB , Rathore S , Abu-Raddad LJ , Aguilera X , Alm E , Archer BN , Attar Cohen H , Barakat A , Barclay WS , Bhiman JN , Caly L , Chand M , Chen M , Cullinane A , de Oliveira T , Drosten C , Druce J , Effler P , El Masry I , Faye A , Gaseitsiwe S , Ghedin E , Grant R , Haagmans BL , Herring BL , Iyer SS , Kassamali Z , Kakkar M , Kondor RJ , Leite JA , Leo YS , Leung GM , Marklewitz M , Moyo S , Mendez-Rico J , Melhem NM , Munster V , Nahapetyan K , Oh DY , Pavlin BI , Peacock TP , Peiris M , Peng Z , Poon LLM , Rambaut A , Sacks J , Shen Y , Siqueira MM , Tessema SK , Volz EM , Thiel V , van der Werf S , Briand S , Perkins MD , Van Kerkhove MD , Koopmans MPG , Agrawal A . Nat Med 2022 28 (6) 1110-1115 Global sequencing and surveillance capacity for SARS-CoV-2 must be strengthened and combined with multidisciplinary studies of infectivity, virulence and immune escape, in order to track the unpredictable evolution of the ongoing COVID-19 pandemic. | | In June 2020, the World Health Organization (WHO) SARS-CoV-2 evolution working group was established to track SARS-CoV-2 variants and their specific genetic changes and to monitor viral characteristics and their impact on medical and non-medical countermeasures, including vaccines against COVID-19. In November 2021, this working group transitioned to a formal WHO Technical Advisory Group on Virus Evolution (TAG-VE), with the aim of developing and implementing a global risk-monitoring framework for SARS-CoV-2 variants, based on a multidisciplinary approach that includes in silico, virological, clinical and epidemiological data. |
Adverse maternal, fetal, and newborn outcomes among pregnant women with SARS-CoV-2 infection: an individual participant data meta-analysis
Smith ER , Oakley E , Grandner GW , Ferguson K , Farooq F , Afshar Y , Ahlberg M , Ahmadzia H , Akelo V , Aldrovandi G , Tippett Barr BA , Bevilacqua E , Brandt JS , Broutet N , Fernández Buhigas I , Carrillo J , Clifton R , Conry J , Cosmi E , Crispi F , Crovetto F , Delgado-López C , Divakar H , Driscoll AJ , Favre G , Flaherman VJ , Gale C , Gil MM , Gottlieb SL , Gratacós E , Hernandez O , Jones S , Kalafat E , Khagayi S , Knight M , Kotloff K , Lanzone A , Le Doare K , Lees C , Litman E , Lokken EM , Laurita Longo V , Madhi SA , Magee LA , Martinez-Portilla RJ , McClure EM , Metz TD , Miller ES , Money D , Moungmaithong S , Mullins E , Nachega JB , Nunes MC , Onyango D , Panchaud A , Poon LC , Raiten D , Regan L , Rukundo G , Sahota D , Sakowicz A , Sanin-Blair J , Söderling J , Stephansson O , Temmerman M , Thorson A , Tolosa JE , Townson J , Valencia-Prado M , Visentin S , von Dadelszen P , Adams Waldorf K , Whitehead C , Yassa M , Tielsch JM . BMJ Glob Health 2023 8 (1) INTRODUCTION: Despite a growing body of research on the risks of SARS-CoV-2 infection during pregnancy, there is continued controversy given heterogeneity in the quality and design of published studies. METHODS: We screened ongoing studies in our sequential, prospective meta-analysis. We pooled individual participant data to estimate the absolute and relative risk (RR) of adverse outcomes among pregnant women with SARS-CoV-2 infection, compared with confirmed negative pregnancies. We evaluated the risk of bias using a modified Newcastle-Ottawa Scale. RESULTS: We screened 137 studies and included 12 studies in 12 countries involving 13 136 pregnant women.Pregnant women with SARS-CoV-2 infection-as compared with uninfected pregnant women-were at significantly increased risk of maternal mortality (10 studies; n=1490; RR 7.68, 95% CI 1.70 to 34.61); admission to intensive care unit (8 studies; n=6660; RR 3.81, 95% CI 2.03 to 7.17); receiving mechanical ventilation (7 studies; n=4887; RR 15.23, 95% CI 4.32 to 53.71); receiving any critical care (7 studies; n=4735; RR 5.48, 95% CI 2.57 to 11.72); and being diagnosed with pneumonia (6 studies; n=4573; RR 23.46, 95% CI 3.03 to 181.39) and thromboembolic disease (8 studies; n=5146; RR 5.50, 95% CI 1.12 to 27.12).Neonates born to women with SARS-CoV-2 infection were more likely to be admitted to a neonatal care unit after birth (7 studies; n=7637; RR 1.86, 95% CI 1.12 to 3.08); be born preterm (7 studies; n=6233; RR 1.71, 95% CI 1.28 to 2.29) or moderately preterm (7 studies; n=6071; RR 2.92, 95% CI 1.88 to 4.54); and to be born low birth weight (12 studies; n=11 930; RR 1.19, 95% CI 1.02 to 1.40). Infection was not linked to stillbirth. Studies were generally at low or moderate risk of bias. CONCLUSIONS: This analysis indicates that SARS-CoV-2 infection at any time during pregnancy increases the risk of maternal death, severe maternal morbidities and neonatal morbidity, but not stillbirth or intrauterine growth restriction. As more data become available, we will update these findings per the published protocol. |
Clinical risk factors of adverse outcomes among women with COVID-19 in the pregnancy and postpartum period: A sequential, prospective meta-analysis.
Smith ER , Oakley E , Grandner GW , Rukundo G , Farooq F , Ferguson K , Baumann S , Waldorf KA , Afshar Y , Ahlberg M , Ahmadzia H , Akelo V , Aldrovandi G , Bevilacqua E , Bracero N , Brandt JS , Broutet N , Carrillo J , Conry J , Cosmi E , Crispi F , Crovetto F , Gil MDM , Delgado-Lpez C , Divakar H , Driscoll AJ , Favre G , Buhigas IF , Flaherman V , Gale C , Godwin CL , Gottlieb S , Gratacs E , He S , Hernandez O , Jones S , Joshi S , Kalafat E , Khagayi S , Knight M , Kotloff K , Lanzone A , Longo VL , LeDoare K , Lees C , Litman E , Lokken EM , Madhi SA , Magee LA , Martinez-Portilla RJ , Metz TD , Miller ES , Money D , Moungmaithong S , Mullins E , Nachega JB , Nunes MC , Onyango D , Panchaud A , Poon LC , Raiten D , Regan L , Sahota D , Sakowicz A , Sanin-Blair J , Stephansson O , Temmerman M , Thorson A , Thwin SS , TippettBarr BA , Tolosa JE , Tug N , Valencia-Prado M , Visentin S , vonDadelszen P , Whitehead C , Wood M , Yang H , Zavala R , Tielsch JM . Am J Obstet Gynecol 2022 228 (2) 161-177 OBJECTIVE: This sequential, prospective meta-analysis (sPMA) sought to identify risk factors among pregnant and postpartum women with COVID-19 for adverse outcomes related to: disease severity, maternal morbidities, neonatal mortality and morbidity, adverse birth outcomes. DATA SOURCES: We prospectively invited study investigators to join the sPMA via professional research networks beginning in March 2020. STUDY ELIGIBILITY CRITERIA: Eligible studies included those recruiting at least 25 consecutive cases of COVID-19 in pregnancy within a defined catchment area. STUDY APPRAISAL AND SYNTHESIS METHODS: We included individual patient data from 21 participating studies. Data quality was assessed, and harmonized variables for risk factors and outcomes were constructed. Duplicate cases were removed. Pooled estimates for the absolute and relative risk of adverse outcomes comparing those with and without each risk factor were generated using a two-stage meta-analysis. RESULTS: We collected data from 33 countries and territories, including 21,977 cases of SARS-CoV-2 infection in pregnancy or postpartum. We found that women with comorbidities (pre-existing diabetes, hypertension, cardiovascular disease) versus those without were at higher risk for COVID-19 severity and pregnancy health outcomes (fetal death, preterm birth, low birthweight). Participants with COVID-19 and HIV were 1.74 times (95% CI: 1.12, 2.71) more likely to be admitted to the ICU. Pregnant women who were underweight before pregnancy were at higher risk of ICU admission (RR 5.53, 95% CI: 2.27, 13.44), ventilation (RR 9.36, 95% CI: 3.87, 22.63), and pregnancy-related death (RR 14.10, 95% CI: 2.83, 70.36). Pre-pregnancy obesity was also a risk factor for severe COVID-19 outcomes including ICU admission (RR 1.81, 95% CI: 1.26,2.60), ventilation (RR 2.05, 95% CI: 1.20,3.51), any critical care (RR 1.89, 95% CI: 1.28,2.77), and pneumonia (RR 1.66, 95% CI: 1.18,2.33). Anemic pregnant women with COVID-19 also had increased risk of ICU admission (RR 1.63, 95% CI: 1.25, 2.11) and death (RR 2.36, 95% CI: 1.15, 4.81). CONCLUSION: We found that pregnant women with comorbidities including diabetes, hypertension, and cardiovascular disease were at increased risk for severe COVID-19-related outcomes, maternal morbidities, and adverse birth outcomes. We also identified several less commonly-known risk factors, including HIV infection, pre-pregnancy underweight, and anemia. Although pregnant women are already considered a high-risk population, special priority for prevention and treatment should be given to pregnant women with these additional risk factors. |
Protocol for a sequential, prospective meta-analysis to describe coronavirus disease 2019 (COVID-19) in the pregnancy and postpartum periods.
Smith ER , Oakley E , He S , Zavala R , Ferguson K , Miller L , Grandner GW , Abejirinde IO , Afshar Y , Ahmadzia H , Aldrovandi G , Akelo V , Tippett Barr BA , Bevilacqua E , Brandt JS , Broutet N , Fernández Buhigas I , Carrillo J , Clifton R , Conry J , Cosmi E , Delgado-López C , Divakar H , Driscoll AJ , Favre G , Flaherman V , Gale C , Gil MM , Godwin C , Gottlieb S , Hernandez Bellolio O , Kara E , Khagayi S , Kim CR , Knight M , Kotloff K , Lanzone A , Le Doare K , Lees C , Litman E , Lokken EM , Laurita Longo V , Magee LA , Martinez-Portilla RJ , McClure E , Metz TD , Money D , Mullins E , Nachega JB , Panchaud A , Playle R , Poon LC , Raiten D , Regan L , Rukundo G , Sanin-Blair J , Temmerman M , Thorson A , Thwin S , Tolosa JE , Townson J , Valencia-Prado M , Visentin S , von Dadelszen P , Adams Waldorf K , Whitehead C , Yang H , Thorlund K , Tielsch JM . PLoS One 2022 17 (6) e0270150 We urgently need answers to basic epidemiological questions regarding SARS-CoV-2 infection in pregnant and postpartum women and its effect on their newborns. While many national registries, health facilities, and research groups are collecting relevant data, we need a collaborative and methodologically rigorous approach to better combine these data and address knowledge gaps, especially those related to rare outcomes. We propose that using a sequential, prospective meta-analysis (PMA) is the best approach to generate data for policy- and practice-oriented guidelines. As the pandemic evolves, additional studies identified retrospectively by the steering committee or through living systematic reviews will be invited to participate in this PMA. Investigators can contribute to the PMA by either submitting individual patient data or running standardized code to generate aggregate data estimates. For the primary analysis, we will pool data using two-stage meta-analysis methods. The meta-analyses will be updated as additional data accrue in each contributing study and as additional studies meet study-specific time or data accrual thresholds for sharing. At the time of publication, investigators of 25 studies, including more than 76,000 pregnancies, in 41 countries had agreed to share data for this analysis. Among the included studies, 12 have a contemporaneous comparison group of pregnancies without COVID-19, and four studies include a comparison group of non-pregnant women of reproductive age with COVID-19. Protocols and updates will be maintained publicly. Results will be shared with key stakeholders, including the World Health Organization (WHO) Maternal, Newborn, Child, and Adolescent Health (MNCAH) Research Working Group. Data contributors will share results with local stakeholders. Scientific publications will be published in open-access journals on an ongoing basis. |
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse.
Konings F , Perkins MD , Kuhn JH , Pallen MJ , Alm EJ , Archer BN , Barakat A , Bedford T , Bhiman JN , Caly L , Carter LL , Cullinane A , de Oliveira T , Druce J , El Masry I , Evans R , Gao GF , Gorbalenya AE , Hamblion E , Herring BL , Hodcroft E , Holmes EC , Kakkar M , Khare S , Koopmans MPG , Korber B , Leite J , MacCannell D , Marklewitz M , Maurer-Stroh S , Rico JAM , Munster VJ , Neher R , Munnink BO , Pavlin BI , Peiris M , Poon L , Pybus O , Rambaut A , Resende P , Subissi L , Thiel V , Tong S , van der Werf S , von Gottberg A , Ziebuhr J , Van Kerkhove MD . Nat Microbiol 2021 6 (7) 821-823 A group convened and led by the Virus Evolution Working Group of the World Health Organization reports on its deliberations and announces a naming scheme that will enable clear communication about SARS-CoV-2 variants of interest and concern. | | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has a linear, unsegmented, positive-sense RNA genome. As with all viruses, SARS-CoV-2 continuously adapts to changing environments in real time via random genome mutations that are subject to natural selection. Most mutations are neutral or detrimental to the virus; however, a small number of mutations may provide a selective advantage, such as escape from the host immune system or resistance to antiviral drugs. Such mutations may also lead to increased fitness for transmissibility. As mutated forms of viruses or variants spread from person to person, they will eventually be detected at the population level. |
Addressing ethical challenges in US-based HIV phylogenetic research.
Dawson L , Benbow N , Fletcher FE , Kassaye S , Killelea A , Latham SR , Lee LM , Leitner T , Little SJ , Mehta SR , Martinez O , Minalga B , Poon A , Rennie S , Sugarman J , Sweeney P , Torian LV , Wertheim JO . J Infect Dis 2020 222 (12) 1997-2006 In recent years, phylogenetic analysis of HIV sequence data has been used in research studies to investigate transmission patterns between individuals and groups, including analysis of data from HIV prevention clinical trials; in molecular epidemiology; and in public health surveillance programs. Phylogenetic analysis can provide valuable information to inform HIV prevention efforts, but it also has risks, including stigma and marginalization of groups, or potential identification of HIV transmission between individuals. In response to these concerns, an interdisciplinary working group was assembled to address ethical challenges in United States-based HIV phylogenetic research. The working group developed recommendations regarding (1) study design; (2) data security, access, and sharing; (3) community engagement; (4) legal issues; and (5) communication and dissemination. The working group also identified areas for future research and scholarship to promote ethical conduct of HIV phylogenetic research. |
Acceptability and willingness of HIV pre-exposure prophylaxis amongst female sex workers in China
Poon AN , Han L , Li Z , Zhou C , Li Y , Huang L , Liao M , Shepard C , Bulterys M . AIDS Care 2019 31 (12) 1555-1564 HIV pre-exposure prophylaxis (PrEP) is a highly effective prevention method. It is an attractive self-initiated approach to reduce the spread of HIV amongst female sex workers (FSW). PrEP, however, has not yet achieved its potential to reduce HIV infections partially due to a general lack of awareness from women who may benefit. Aims of this cross-sectional study of 1,466 FSW in China were to understand: levels of awareness of and willingness to use PrEP among female sex workers (FSW) in China, and factors contributing to willingness to use PrEP. We found that awareness (10.2%) and willingness (35.5%) to use PrEP were low in our survey areas. Low PrEP willingness is likely reflective of the overall poor knowledge and understanding of HIV risk and prevention. FSW that demonstrated greater HIV knowledge through having been tested or having greater decision-making involvement in condom use were more willing to use PrEP. Study findings may be used to inform future HIV prevention activities, including possible use of PrEP among FSW at higher risk of incident HIV infection in China. |
Rotavirus vaccine effectiveness in Hong Kong children
Yeung KH , Tate JE , Chan CC , Chan MC , Chan PK , Poon KH , Siu SL , Fung GP , Ng KL , Chan IM , Yu PT , Ng CH , Lau YL , Nelson EA . Vaccine 2016 34 (41) 4935-4942 BACKGROUND: Rotavirus is a common infectious cause of childhood hospitalisation in Hong Kong. Rotavirus vaccines have been used in the private sector since licensure in 2006 but have not been incorporated in the government's universal Childhood Immunisation Programme. This study aimed to evaluate rotavirus vaccine effectiveness against hospitalisation. METHODS: This case-control study was conducted in the 2014/2015 rotavirus season in six public hospitals. Hospitalised acute gastroenteritis patients meeting inclusion criteria were recruited and copies of their immunisation records were collected. Case-patients were defined as enrolled subjects with stool specimens obtained in the first 48h of hospitalisation that tested positive for rotavirus, whereas control-patients were those with stool specimens obtained in the first 48h of hospitalisation testing negative for rotavirus. Vaccine effectiveness for administration of at least one dose of either Rotarix(R) (GlaxoSmithKline Biologicals) or RotaTeq(R) (Merck Research Laboratories) was calculated as 1 minus the odds ratio for rotavirus vaccination history for case-patients versus control-patients. RESULTS: Among the 525 eligible subjects recruited, immunisation records were seen in 404 (77%) subjects. 31% (162/525 and 126/404) tested positive for rotavirus. In the 404 subjects assessed for vaccine effectiveness, 2.4% and 24% received at least 1 dose of either rotavirus vaccine in case- and control-patients respectively. The unmatched vaccine effectiveness against hospitalisation for administration of at least one dose of either rotavirus vaccines was 92% (95% confidence interval [CI]: 75%, 98%). The matched analyses by age only and both age and admission date showed 96% (95% CI: 72%, 100%) and 89% (95% CI: 51%, 97%) protection against rotavirus hospitalisation respectively. CONCLUSIONS: Rotavirus vaccine is highly effective in preventing hospitalisation from rotavirus disease in young Hong Kong children. |
The spread of hepatitis C virus genotype 1a in North America: a retrospective phylogenetic study.
Joy JB , McCloskey RM , Nguyen T , Liang RH , Khudyakov Y , Olmstead A , Krajden M , Ward JW , Harrigan PR , Montaner JS , Poon AF . Lancet Infect Dis 2016 16 (6) 698-702 BACKGROUND: The timing of the initial spread of hepatitis C virus genotype 1a in North America is controversial. In particular, how and when hepatitis C virus reached extraordinary prevalence in specific demographic groups remains unclear. We quantified, using all available hepatitis C virus sequence data and phylodynamic methods, the timing of the spread of hepatitis C virus genotype 1a in North America. METHODS: We screened 45 316 publicly available sequences of hepatitis C virus genotype 1a for location and genotype, and then did phylogenetic analyses of available North American sequences from five hepatitis C virus genes (E1, E2, NS2, NS4B, NS5B), with an emphasis on including as many sequences with early collection dates as possible. We inferred the historical population dynamics of this epidemic for all five gene regions using Bayesian skyline plots. FINDINGS: Most of the spread of genotype 1a in North America occurred before 1965, and the hepatitis C virus epidemic has undergone relatively little expansion since then. The effective population size of the North American epidemic stabilised around 1960. These results were robust across all five gene regions analysed, although analyses of each gene separately show substantial variation in estimates of the timing of the early exponential growth, ranging roughly from 1940 for NS2, to 1965 for NS4B. INTERPRETATION: The expansion of genotype 1a before 1965 suggests that nosocomial or iatrogenic factors rather than past sporadic behavioural risk (ie, experimentation with injection drug use, unsafe tattooing, high risk sex, travel to high endemic areas) were key contributors to the hepatitis C virus epidemic in North America. Our results might reduce stigmatisation around screening and diagnosis, potentially increasing rates of screening and treatment for hepatitis C virus. FUNDING: The Canadian Institutes of Health Research, Michael Smith Foundation for Health Research, and BC Centre for Excellence in HIV/AIDS. |
Asymptomatic MERS-CoV infection in humans possibly linked to infected dromedaries imported from Oman to United Arab Emirates, May 2015
Al Hammadi ZM , Chu DK , Eltahir YM , Al Hosani F , Al Mulla M , Tarnini W , Hall AJ , Perera RA , Abdelkhalek MM , Peiris JS , Al Muhairi SS , Poon LL . Emerg Infect Dis 2015 21 (12) 2197-200 In May 2015 in United Arab Emirates, asymptomatic Middle East respiratory syndrome coronavirus infection was identified through active case finding in 2 men with exposure to infected dromedaries. Epidemiologic and virologic findings suggested zoonotic transmission. Genetic sequences for viruses from the men and camels were similar to those for viruses recently detected in other countries. |
Differences in risk behaviours and HIV/STI prevalence between low-fee and medium-fee female sex workers in three provinces in China
Han L , Zhou C , Li Z , Poon AN , Rou K , Fuller S , Li Y , Shen L , Kang D , Huang L , Liao M , Fu X , Shepard C , Wu Z , Bulterys M . Sex Transm Infect 2015 92 (4) 309-15 OBJECTIVES: To better understand risk behaviours and factors associated with low-fee female sex workers (FSW) and support HIV/sexually transmitted infections (STI) epidemic control among this key population in China. METHODS: A cross-sectional study using convenience sampling to recruit 1487 eligible low-fee and medium-fee FSW was conducted in 2012 in three provinces. The participants were interviewed using a structured questionnaire and tested for HIV-1, herpes simplex virus (HSV)-2 and syphilis antibody. Log-binomial modelling was used to estimate prevalence ratios (PR) and examine factors associated with low-fee sex work. RESULTS: Prevalence of HIV-1, syphilis and HSV-2 antibody positive were 0.5%, 4.8% and 27.8%, respectively. Low-fee FSW were more likely to have HSV-2 infection (adjusted prevalence ratio (APR)=1.3, 95% CI 1.1 to 1.7), but not more likely to have HIV-1 and syphilis infection compared with medium-fee FSW. Compared with medium-fee FSW, low-fee FSW were more likely to be ≥35 years of age (APR=2.1, 95% CI 1.3 to 3.6), engage in sex work ≥6 days/per week (APR=1.7, 95% CI 1.2 to 2.6), have ≥3 clients per day (APR=2.2, 95% CI 1.5 to 3.3), have clients decide condom use (APR=1.6, 95% CI 1.1 to 2.3), fail to persuade clients to use condoms (APR=1.6, 95% CI 1.1 to 2.6), express willingness to have unprotected sex in return for receipt of a higher fee (APR=1.8, 95% CI 1.2 to 2.8), have had genital symptoms in the past year (APR=1.4, 95% CI 1.1 to 1.8) and have migrated from another city. CONCLUSIONS: Low-fee FSW in China have unique risks for acquiring HIV/STI, in part due to greater economic pressures. Tailored interventions targeting low-fee FSW and incorporating their prevailing perception of HIV/STI risks and condom use negotiation challenges that they face are urgently needed. |
Transmission of H7N9 influenza viruses with polymorphism at PB2 residue 627 in chickens and ferrets.
Luk GS , Leung CY , Sia SF , Choy KT , Zhou J , Ho CC , Cheung PP , Lee EF , Wai CK , Li PC , Ip SM , Poon LL , Lindsley WG , Peiris M , Yen HL . J Virol 2015 Poultry exposure is a major risk factor for human H7N9 zoonotic infections of which the mode of transmission remains unclear. We studied the transmission of genetically related poultry and human H7N9 influenza viruses differed by four amino acids including the host determinant PB2 residue 627. A/Silkie Chicken/HK/1772/2014 (SCk1772) and A/HK/3263/14 (HK3263) replicated to comparable titers in chickens with superior oropharyngeal over cloacal shedding; both viruses transmitted efficiently among chickens via direct contact but inefficiently via airborne route. Interspecies transmission via the airborne route was observed for ferrets exposed to the SCk1772 or HK3263 infected chickens while low numbers of copies of influenza viral genome were detected in the air, predominantly at particle sizes larger than 4mum. In ferrets, the human isolate HK3263 replicated to higher titers and transmitted more efficiently via direct contact than SCk1772. We monitored "intra-host" and "inter-host" adaptive changes at PB2 residue 627 during infection and transmission of the SCK1772 that carried E627 and HK3263 that carried V/K/E polymorphism at 60%, 20%, and 20%, respectively. For SCk1772, positive selection for K627 over E627 was observed in ferrets during the chicken-to-ferret or ferret-to-ferret transmission. For HK3263 that contained V/K/E polymorphism, mixed V627 and E627 genotypes were transmitted among chickens while either V627 or K627 was transmitted from chicken-to-ferret or ferret-to-ferret with a narrow transmission bottleneck. Overall, our results suggest direct contact as the main mode for H7N9 transmission and identify the PB2-V627 genotype with uncompromised fitness and transmissibility in both avian and mammalian species. IMPORTANCE: We studied the modes of H7N9 transmission, as this information is crucial for developing effective control measures for prevention. Using chicken (SCk1772) and human (HK3263) H7N9 isolates that differed by four amino acids, including the host determinant PB2 residue 627, we observed both viruses transmitted efficiently among chickens via direct contact but inefficiently via airborne route. Chicken-to-ferret transmission via airborne route was observed along with the detection of viral genome in the air at low copies. In ferrets, HK3263 transmitted more efficiently than SCk1772 via direct contact. During the transmission of SCk1772 that contained E and HK3263 that contained V/K/E polymorphism at PB2 residue 627, positive selections of E627 and K627 were observed in chickens and ferrets, respectively. In addition, PB2-V627 was transmitted and stably maintained in both avian and mammalian species. Our results support applying intervention strategies that minimize direct and indirect contact at the poultry markets during epidemics. |
A molecular phylogenetics-based approach for identifying recent hepatitis C virus transmission events.
Olmstead AD , Joy JB , Montoya V , Luo I , Poon AF , Jacka B , Lamoury F , Applegate T , Montaner J , Khudyakov Y , Grebely J , Cook D , Harrigan PR , Krajden M . Infect Genet Evol 2015 33 101-9 Improved surveillance methods are needed to better understand the current hepatitis C virus (HCV) disease burden and to monitor the impact of prevention and treatment interventions on HCV transmission dynamics. Sanger sequencing (HCV NS5B, HVR1 and Core-E1-HVR1) and phylogenetics were applied to samples from individuals diagnosed with HCV in British Columbia, Canada in 2011. This included individuals with two or three sequential samples collected <1year apart. Patristic distances between sequential samples were used to set cutoffs to identify recent transmission clusters. Factors associated with transmission clustering were analyzed using logistic regression. From 618 individuals, 646 sequences were obtained. Depending on the cutoff used, 63 (10%) to 92 (15%) unique individuals were identified within transmission clusters of predicted recent origin. Clustered individuals were more likely to be <40years old (Adjusted Odds Ratio (AOR) 2.12, 95% CI 1.21-3.73), infected with genotype 1a (AOR 6.60, 95% CI 1.98-41.0), and to be seroconverters with estimated infection duration of <1year (AOR 3.13, 95% CI 1.29-7.36) or >1year (AOR 2.19, 95% CI 1.22-3.97). CONCLUSION: Systematic application of molecular phylogenetics may be used to enhance traditional surveillance methods through identification of recent transmission clusters. |
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