Last data update: Jan 27, 2025. (Total: 48650 publications since 2009)
Records 1-30 (of 73 Records) |
Query Trace: Shu B[original query] |
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Discriminating north American swine influenza viruses with a portable, one-step, triplex real-time RT-PCR assay, and portable sequencing
Kirby MK , Shu B , Keller MW , Wilson MM , Rambo-Martin BL , Jang Y , Liddell J , Salinas Duron E , Nolting JM , Bowman AS , Davis CT , Wentworth DE , Barnes JR . Viruses 2024 16 (10) ![]() ![]() Swine harbors a genetically diverse population of swine influenza A viruses (IAV-S), with demonstrated potential to transmit to the human population, causing outbreaks and pandemics. Here, we describe the development of a one-step, triplex real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay that detects and distinguishes the majority of the antigenically distinct influenza A virus hemagglutinin (HA) clades currently circulating in North American swine, including the IAV-S H1 1A.1 (α), 1A.2 (β), 1A.3 (γ), 1B.2.2 (δ1) and 1B.2.1 (δ2) clades, and the IAV-S H3 2010.1 clade. We performed an in-field test at an exhibition swine show using in-field viral concentration and RNA extraction methodologies and a portable real-time PCR instrument, and rapidly identified three distinct IAV-S clades circulating within the N.A. swine population. Portable sequencing is used to further confirm the results of the in-field test of the swine triplex assay. The IAV-S triplex rRT-PCR assay can be easily transported and used in-field to characterize circulating IAV-S clades in North America, allowing for surveillance and early detection of North American IAV-S with human outbreak and pandemic potential. |
In-field detection and characterization of B/Victoria lineage deletion variant viruses causing early influenza activity and an outbreak in Louisiana, 2019
Shu B , Wilson MM , Keller MW , Tran H , Sokol T , Lee G , Rambo-Martin BL , Kirby MK , Hassell N , Haydel D , Hand J , Wentworth DE , Barnes JR . Influenza Other Respir Viruses 2024 18 (1) e13246 ![]() ![]() BACKGROUND: In 2019, the Louisiana Department of Health reported an early influenza B/Victoria (B/VIC) virus outbreak. METHOD: As it was an atypically large outbreak, we deployed to Louisiana to investigate it using genomics and a triplex real-time RT-PCR assay to detect three antigenically distinct B/VIC lineage variant viruses. RESULTS: The investigation indicated that B/VIC V1A.3 subclade, containing a three amino acid deletion in the hemagglutinin and known to be antigenically distinct to the B/Colorado/06/2017 vaccine virus, was the most prevalent circulating virus within the specimens evaluated (86/88 in real-time RT-PCR). CONCLUSION: This work underscores the value of portable platforms for rapid, onsite pathogen characterization. |
Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR (preprint)
Shu B , Kirby MK , Warnes C , Sessions WM , Davis WG , Liu J , Wilson MM , Wentworth DE , Barnes JR . bioRxiv 2019 818617 Influenza B viruses have two genetically and antigenically distinct lineages, B/Victoria/2/1987-like (VIC) and B/Yamagata/16/1988-like (YAM) viruses, that emerged in the 1980s and co-circulate annually during the influenza season. During the 2016-2017 influenza season, influenza B/VIC lineage variant viruses emerged with two (K162N163) or three (K162N163D164) amino acid (AA) deletions in the hemagglutinin protein. Hemagglutination inhibition assays demonstrate that these deletion variant influenza B/VIC viruses are antigenically distinct from each other and from the progenitor B/VIC virus that lacks the deletion. Therefore, there are currently four antigenically distinct HA proteins expressed by influenza B co-circulating: B/YAM, B/VIC V1A (no deletion), B/VIC V1A.1 (two-AA deletion), and B/VIC V1A.2 and V1A.3 (three-AA deletion). The prevalence of these viruses differs across geographic regions, making it critical to have a sensitive, rapid diagnostic assay(s) that detect and distinguish these Influenza B variant viruses during surveillance. Here, we present a real time RT-PCR assay that targets the influenza B/VIC deletion region in the HA gene and detects and distinguishes the influenza B/VIC V1A, B/VIC V1A.1, B/VIC V1A.2 and B/VIC V1A.3 variant viruses, with no cross-reactivity. This assay can be run as a multiplex reaction, allowing for increased testing efficiency and reduced cost. Coupling this assay with the CDC Human Influenza Virus Real-Time RT-PCR Diagnostic Panel Influenza B Lineage Genotyping Kit results in rapid detection and characterization of circulating influenza B viruses. Having accurate and detailed surveillance information on these distinct Influenza B variant viruses will provide insight into the prevalence and geographic distribution and could aid in vaccine recommendations. |
Prediagnostic blood levels of organochlorines and risk of non-Hodgkin lymphoma in three prospective cohorts in China and Singapore
Bassig BA , Shu XO , Sjödin A , Koh WP , Gao YT , Adams-Haduch J , Davis M , Wang R , Xiang YB , Engel LS , Purdue MP , Ji BT , Yang G , Jones RS , Langseth H , Hosgood HD , Grimsrud TK , Seow WJ , Wong JYY , Hu W , Chen D , Zheng W , Yuan JM , Lan Q , Rothman N . Int J Cancer 2020 146 (3) 839-849 Specific organochlorines (OCs) have been associated with non-Hodgkin lymphoma (NHL) with varying degrees of evidence. These associations have not been evaluated in Asia, where the high exposure and historical environmental contamination of certain OC pesticides (e.g., dichlorodiphenyltrichloroethane [DDT], hexachlorocyclohexane [HCH]) are different from Western populations. We evaluated NHL risk and prediagnostic blood levels of OC pesticides/metabolites and polychlorinated biphenyl congeners in a case-control study of 167 NHL cases and 167 controls nested within three prospective cohorts in Shanghai and Singapore. Conditional logistic regression was used to analyze lipid-adjusted OC levels and NHL risk. Median levels of p,p'-dichlorodiphenyldichloroethylene (p,p'-DDE), the primary DDT metabolite, and β-HCH were up to 12 and 65 times higher, respectively, in samples from the Asian cohorts compared to several cohorts in the United States and Norway. An increased risk of NHL was observed among those with higher β-HCH levels both overall (3rd vs. 1st tertile OR = 1.8, 95%CI = 1.0-3.2; p(trend) = 0.049) and after excluding cases diagnosed within 2 years of blood collection (3rd vs. 1st tertile OR = 2.0, 95%CI = 1.1-3.9; p(trend) = 0.03), and the association was highly consistent across the three cohorts. No significant associations were observed for other OCs, including p,p'-DDE. Our findings provide support for an association between β-HCH blood levels and NHL risk. This is a concern because substantial quantities of persistent, toxic residues of HCH are present in the environment worldwide. Although there is some evidence that DDT is associated with NHL, our findings for p,p'-DDE do not support an association. |
A Public Health Research Agenda for Managing Infodemics: Methods and Results of the First WHO Infodemiology Conference.
Calleja N , AbdAllah A , Abad N , Ahmed N , Albarracin D , Altieri E , Anoko JN , Arcos R , Azlan AA , Bayer J , Bechmann A , Bezbaruah S , Briand SC , Brooks I , Bucci LM , Burzo S , Czerniak C , De Domenico M , Dunn AG , Ecker UKH , Espinosa L , Francois C , Gradon K , Gruzd A , Gülgün BS , Haydarov R , Hurley C , Astuti SI , Ishizumi A , Johnson N , Johnson Restrepo D , Kajimoto M , Koyuncu A , Kulkarni S , Lamichhane J , Lewis R , Mahajan A , Mandil A , McAweeney E , Messer M , Moy W , Ndumbi Ngamala P , Nguyen T , Nunn M , Omer SB , Pagliari C , Patel P , Phuong L , Prybylski D , Rashidian A , Rempel E , Rubinelli S , Sacco P , Schneider A , Shu K , Smith M , Sufehmi H , Tangcharoensathien V , Terry R , Thacker N , Trewinnard T , Turner S , Tworek H , Uakkas S , Vraga E , Wardle C , Wasserman H , Wilhelm E , Würz A , Yau B , Zhou L , Purnat TD . JMIR Infodemiology 2021 1 (1) e30979 ![]() ![]() BACKGROUND: An infodemic is an overflow of information of varying quality that surges across digital and physical environments during an acute public health event. It leads to confusion, risk-taking, and behaviors that can harm health and lead to erosion of trust in health authorities and public health responses. Owing to the global scale and high stakes of the health emergency, responding to the infodemic related to the pandemic is particularly urgent. Building on diverse research disciplines and expanding the discipline of infodemiology, more evidence-based interventions are needed to design infodemic management interventions and tools and implement them by health emergency responders. OBJECTIVE: The World Health Organization organized the first global infodemiology conference, entirely online, during June and July 2020, with a follow-up process from August to October 2020, to review current multidisciplinary evidence, interventions, and practices that can be applied to the COVID-19 infodemic response. This resulted in the creation of a public health research agenda for managing infodemics. METHODS: As part of the conference, a structured expert judgment synthesis method was used to formulate a public health research agenda. A total of 110 participants represented diverse scientific disciplines from over 35 countries and global public health implementing partners. The conference used a laddered discussion sprint methodology by rotating participant teams, and a managed follow-up process was used to assemble a research agenda based on the discussion and structured expert feedback. This resulted in a five-workstream frame of the research agenda for infodemic management and 166 suggested research questions. The participants then ranked the questions for feasibility and expected public health impact. The expert consensus was summarized in a public health research agenda that included a list of priority research questions. RESULTS: The public health research agenda for infodemic management has five workstreams: (1) measuring and continuously monitoring the impact of infodemics during health emergencies; (2) detecting signals and understanding the spread and risk of infodemics; (3) responding and deploying interventions that mitigate and protect against infodemics and their harmful effects; (4) evaluating infodemic interventions and strengthening the resilience of individuals and communities to infodemics; and (5) promoting the development, adaptation, and application of interventions and toolkits for infodemic management. Each workstream identifies research questions and highlights 49 high priority research questions. CONCLUSIONS: Public health authorities need to develop, validate, implement, and adapt tools and interventions for managing infodemics in acute public health events in ways that are appropriate for their countries and contexts. Infodemiology provides a scientific foundation to make this possible. This research agenda proposes a structured framework for targeted investment for the scientific community, policy makers, implementing organizations, and other stakeholders to consider. |
MicroRNA, mRNA, and proteomics biomarkers and therapeutic targets for improving lung cancer treatment outcomes
Ye Qing , Raese Rebecca , Luo Dajie , Cao Shu , Wan Ying-Wooi , Qian Yong , Guo Nancy Lan . Cancers (Basel) 2023 15 (8) 2294 Simple Summary: This study identified a set of 73 microRNAs (miRNAs) that can accurately detect lung cancer tumors from normal lung tissues. Based on the consistent expression patterns associated with patient survival outcomes and in tumors vs. normal lung tissues, 10 miRNAs were considered to be putatively tumor suppressive and 4 miRNAs were deemed as oncogenic in lung cancer. From the list of genes that were targeted by the 73 diagnostic miRNAs, DGKE and WDR47 had significant associations with responses to both systemic therapies and radiotherapy in lung cancer. Based on our identified miRNA-regulated network, we discovered three drugs—BX-912, daunorubicin, and midostaurin—that can be repositioned to treat lung cancer, which was not known before. The majority of lung cancer patients are diagnosed with metastatic disease. This study identified a set of 73 microRNAs (miRNAs) that classified lung cancer tumors from normal lung tissues with an overall accuracy of 96.3% in the training patient cohort (n = 109) and 91.7% in unsupervised classification and 92.3% in supervised classification in the validation set (n = 375). Based on association with patient survival (n = 1016), 10 miRNAs were identified as potential tumor suppressors (hsa-miR-144, hsa-miR-195, hsa-miR-223, hsa-miR-30a, hsa-miR-30b, hsa-miR-30d, hsa-miR-335, hsa-miR-363, hsa-miR-451, and hsa-miR-99a), and 4 were identified as potential oncogenes (hsa-miR-21, hsa-miR-31, hsa-miR-411, and hsa-miR-494) in lung cancer. Experimentally confirmed target genes were identified for the 73 diagnostic miRNAs, from which proliferation genes were selected from CRISPR-Cas9/RNA interference (RNAi) screening assays. Pansensitive and panresistant genes to 21 NCCN-recommended drugs with concordant mRNA and protein expression were identified. DGKE and WDR47 were found with significant associations with responses to both systemic therapies and radiotherapy in lung cancer. Based on our identified miRNA-regulated molecular machinery, an inhibitor of PDK1/Akt BX-912, an anthracycline antibiotic daunorubicin, and a multi-targeted protein kinase inhibitor midostaurin were discovered as potential repositioning drugs for treating lung cancer. These findings have implications for improving lung cancer diagnosis, optimizing treatment selection, and discovering new drug options for better patient outcomes. |
Unmet needs for HIV ancillary care services by healthcare coverage and Ryan White HIV/AIDS program assistance.
Dasgupta S , Crim SM , Dawson L , Kates J , Weiser J , Klein PW , Dempsey A , Hauck H , Lu JF , Shu F , Beer L . AIDS 2022 36 (10) 1399-1407 OBJECTIVE: To investigate unmet needs for HIV ancillary care services by health care coverage type and Ryan White HIV/AIDS Program (RWHAP) assistance among adults with HIV. DESIGN: We analyzed data using the 2017-2019 cycles of the CDC Medical Monitoring Project, an annual, cross-sectional study designed to produce nationally representative estimates of characteristics among adults with diagnosed HIV. METHODS: Unmet need was defined as needing, but not receiving, ≥1 HIV ancillary care service. We estimated prevalence ratios (PRs) and 95% confidence intervals (CIs) using predicted marginal means to examine associations between health care coverage type and unmet needs for HIV ancillary care services, adjusting for age. Associations were stratified by receipt of RWHAP assistance. RESULTS: Unmet needs for HIV ancillary care services were highest among uninsured persons (58.7%) and lowest among those with private insurance living ≥400% of the federal poverty level (FPL; 21.7%). Uninsured persons who received RWHAP assistance were less likely than those who did not receive RWHAP assistance to have unmet needs for HIV clinical support services (aPR: 0.21; 95% CI: 0.16-0.28) and other medical services (aPR: 0.75; 95% CI: 0.59-0.96), but not subsistence services (aPR: 0.97; 95% CI: 0.74-1.27). Unmet needs for other medical services and subsistence services did not differ by RWHAP assistance among those with Medicaid, Medicare, or other health care coverage. CONCLUSIONS: RWHAP helped reduce some needs for uninsured persons. However, with growing socioeconomic inequities following the COVID-19 pandemic, expanding access to needed services for all people with HIV could improve key outcomes. |
Multiplex Real-Time Reverse Transcription PCR for Influenza A Virus, Influenza B Virus, and Severe Acute Respiratory Syndrome Coronavirus 2.
Shu B , Kirby MK , Davis WG , Warnes C , Liddell J , Liu J , Wu KH , Hassell N , Benitez AJ , Wilson MM , Keller MW , Rambo-Martin BL , Camara Y , Winter J , Kondor RJ , Zhou B , Spies S , Rose LE , Winchell JM , Limbago BM , Wentworth DE , Barnes JR . Emerg Infect Dis 2021 27 (7) 1821-1830 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019, and the outbreak rapidly evolved into the current coronavirus disease pandemic. SARS-CoV-2 is a respiratory virus that causes symptoms similar to those caused by influenza A and B viruses. On July 2, 2020, the US Food and Drug Administration granted emergency use authorization for in vitro diagnostic use of the Influenza SARS-CoV-2 Multiplex Assay. This assay detects influenza A virus at 10(2.0), influenza B virus at 10(2.2), and SARS-CoV-2 at 10(0.3) 50% tissue culture or egg infectious dose, or as few as 5 RNA copies/reaction. The simultaneous detection and differentiation of these 3 major pathogens increases overall testing capacity, conserves resources, identifies co-infections, and enables efficient surveillance of influenza viruses and SARS-CoV-2. |
Population-based Estimates of COVID-19-like Illness, COVID-19 Illness, and Rates of Case Ascertainment, Hospitalizations, and Deaths - Non-Institutionalized New York City Residents, March-April 2020.
Alroy KA , Crossa A , Dominianni C , Sell J , Bartley K , Sanderson M , Fernandez S , Levanon Seligson A , Lim SW , Wang SM , Dumas SE , Perlman SE , Konty K , Olson DR , Gould LH , Greene SK . Clin Infect Dis 2021 73 (9) 1707-1710 Using a population-based, representative telephone survey, ~930,000 New York City residents had COVID-19 illness beginning March 20-April 30, 2020, a period with limited testing. For every 1000 persons estimated with COVID-19 illness, 141.8 were tested and reported as cases, 36.8 were hospitalized, and 12.8 died, varying by demographic characteristics. |
Disability among adults with diagnosed HIV in the United States, 2017
Chowdhury PP , Beer L , Shu F , Fagan J , Luke Shouse R . AIDS Care 2020 33 (12) 1-5 In the United States, one in four adults is living with a disability. Age-related changes, disease-related pathology and treatments can place a person with HIV at risk for a disability. We analyzed nationally representative data to describe disability status among adults ≥18 years with diagnosed HIV in the United States and Puerto Rico by demographic characteristics, health behaviors, quality of care, clinical outcomes and mental health status. We reported weighted percentages and prevalence ratios with predicted marginal means to evaluate significant differences between groups (P < .05). Overall, 44.5% reported any disability; the most frequently reported disabilities were related to mobility (24.8%) and cognition (23.9%). Persons who lived in households at or below the poverty level or who experienced homelessness in the last 12 months reported a higher prevalence of any disability than persons who were not poor or not homeless (60.2% vs. 33.4% and 61.8% vs. 42.8%, respectively). Prevalence of depression and anxiety was higher among persons with any disability compared with those with no disability (32.8% and 26.6% versus 10.1% and 7.0%, respectively). Enhancing support from clinicians and ancillary providers may help optimize long-term health outcomes among HIV-positive persons with disabilities. |
Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR.
Shu B , Kirby MK , Warnes C , Sessions WM , Davis WG , Liu J , Wilson MM , Lindstrom S , Wentworth DE , Barnes JR . Euro Surveill 2020 25 (41) ![]() ![]() BackgroundDuring the 2016/17 influenza season, influenza B/VIC lineage variant viruses emerged with two (K(162)N(163)) or three (K(162)N(163)D(164)) amino acid (aa) deletions in the haemagglutinin (HA) protein. There are currently five antigenically distinct HA proteins expressed by co-circulating influenza B viruses: B/YAM, B/VIC V1A (no deletion), B/VIC V1A-2DEL (2 aa deletion) and two antigenically distinguishable groups of B/VIC V1A-3DEL (3 aa deletion). The prevalence of these viruses differs across geographical regions, making it critical to have a sensitive, rapid diagnostic assay that detects and distinguishes these influenza B variant viruses during surveillance.AimOur objective was to develop a real-time RT-PCR (rRT-PCR) assay for detection and discrimination of influenza B/VIC lineage variant viruses.MethodsWe designed a diagnostic assay with one pair of conserved primers and three probes specific to each genetic group. We used propagated influenza B/VIC variant viruses and clinical specimens to assess assay performance.ResultsThis rRT-PCR assay detects and distinguishes the influenza B/VIC V1A, B/VIC V1A-2DEL, and B/VIC V1A-3DEL variant viruses, with no cross-reactivity. This assay can be run as a multiplex reaction, allowing for increased testing efficiency and reduced cost.ConclusionCoupling this assay with the Centers for Disease Control and Prevention's Human Influenza Virus Real-Time RT-PCR Diagnostic Panel Influenza B Lineage Genotyping Kit results in rapid detection and characterisation of circulating influenza B viruses. Detailed surveillance information on these distinct influenza B variant viruses will provide insight into their prevalence and geographical distribution and could aid in vaccine recommendations. |
The first report of human infection with avian influenza A(H9N2) virus in Oman: the need for a One Health approach
Al-Mayahi Z , Al Kindi H , Davis CT , Al-Rawahi B , Al-Yaqoubi F , Jang Y , Jones J , Barnes JR , Davis W , Shu B , Lynch B , Wentworth DE , Al-Maskari Z , Al Maani A , Al Abri S . Int J Infect Dis 2019 91 169-173 After detection of the first human case of avian influenza A subtype H9N2 in 1998, more than 40 cases were diagnosed worldwide. The spread of the virus, on the other hand, is more remarkable and significant in global poultry populations causing notable economic losses despite its low pathogenicity. Many surveillance studies and activities conducted in several countries proved the predominance of this virus subtype. We present a case report of A(H9N2) virus infection in a 14-month-old female from Oman. It is the first A(H9N2) human case reported from Oman and the Gulf Cooperation Countries and the second country outside of southern and eastern Asia, cases were also detected in Egypt. The patient had bronchial asthma and presented with high-grade temperature and symptoms of lower respiratory tract infection that necessitated admission to a high dependency unit in a tertiary care hospital. It is of urgency that a multisectoral One Health approach be established to combat the threat of avian influenza at the animal-human interface. In addition to enhancements of surveillance and control in poultry, there is a need to develop screening and preventive programs for high-risk occupations. |
Depression prevalence, antidepressant treatment status, and association with sustained HIV viral suppression among adults living with HIV in care in the United States, 2009-2014
Gokhale RH , Weiser J , Sullivan PS , Luo Q , Shu F , Bradley H . AIDS Behav 2019 23 (12) 3452-3459 Previous research indicates a high burden of depression among adults living with HIV and an association between depression and poor HIV clinical outcomes. National estimates of diagnosed depression, depression treatment status, and association with HIV clinical outcomes are lacking. We used 2009-2014 data from the Medical Monitoring Project to estimate diagnosed depression, antidepressant treatment status, and associations with sustained viral suppression (all viral loads in past year < 200 copies/mL). Data were obtained through interview and medical record abstraction and were weighted to account for unequal selection probabilities and non-response. Of adults receiving HIV medical care in the U.S. and prescribed ART, 27% (95% confidence interval [CI] 25-29%) had diagnosed depression during the surveillance period; the majority (65%) were prescribed antidepressants. The percentage with sustained viral suppression was highest among those without depression (72%, CI 71-73%) and lowest among those with untreated depression (66%, CI 64-69%). Compared to those without depression, those with a depression diagnosis were less likely to achieve sustained viral suppression (aPR 0.95, CI 0.93-0.97); this association held for persons with treated depression compared to no depression (aPR 0.96, CI 0.94-0.99) and untreated depression compared to no depression (aPR 0.92, CI 0.89-0.96). The burden of depression among adults living with HIV in care is high. While in our study depression was only minimally associated with a lower prevalence of sustained viral suppression, diagnosing and treating depression in persons living with HIV remains crucial in order to improve mental health and avoid other poor health outcomes. |
A ten-year China-US laboratory collaboration: improving response to influenza threats in China and the world, 2004-2014.
Shu Y , Song Y , Wang D , Greene CM , Moen A , Lee CK , Chen Y , Xu X , McFarland J , Xin L , Bresee J , Zhou S , Chen T , Zhang R , Cox N . BMC Public Health 2019 19 520 ![]() ![]() The emergence of severe acute respiratory syndrome (SARS) underscored the importance of influenza detection and response in China. From 2004, the Chinese National Influenza Center (CNIC) and the United States Centers for Disease Control and Prevention (USCDC) initiated Cooperative Agreements to build capacity in influenza surveillance in China. From 2004 to 2014, CNIC and USCDC collaborated on the following activities: 1) developing human technical expertise in virology and epidemiology in China; 2) developing a comprehensive influenza surveillance system by enhancing influenza-like illness (ILI) reporting and virological characterization; 3) strengthening analysis, utilization and dissemination of surveillance data; and 4) improving early response to influenza viruses with pandemic potential. Since 2004, CNIC expanded its national influenza surveillance and response system which, as of 2014, included 408 laboratories and 554 sentinel hospitals. With support from USCDC, more than 2500 public health staff from China received virology and epidemiology training, enabling > 98% network laboratories to establish virus isolation and/or nucleic acid detection techniques. CNIC established viral drug resistance surveillance and platforms for gene sequencing, reverse genetics, serologic detection, and vaccine strains development. CNIC also built a bioinformatics platform to strengthen data analysis and utilization, publishing weekly on-line influenza surveillance reports in English and Chinese. The surveillance system collects 200,000-400,000 specimens and tests more than 20,000 influenza viruses annually, which provides valuable information for World Health Organization (WHO) influenza vaccine strain recommendations. In 2010, CNIC became the sixth WHO Collaborating Centre for Influenza. CNIC has strengthened virus and data sharing, and has provided training and reagents for other countries to improve global capacity for influenza control and prevention. The collaboration's successes were built upon shared mission and values, emphasis on long-term capacity development and sustainability, and leadership commitment. |
Taxonomy of the order Bunyavirales: update 2019.
Abudurexiti A , Adkins S , Alioto D , Alkhovsky SV , Avsic-Zupanc T , Ballinger MJ , Bente DA , Beer M , Bergeron E , Blair CD , Briese T , Buchmeier MJ , Burt FJ , Calisher CH , Chang C , Charrel RN , Choi IR , Clegg JCS , de la Torre JC , de Lamballerie X , Deng F , Di Serio F , Digiaro M , Drebot MA , Duan X , Ebihara H , Elbeaino T , Ergunay K , Fulhorst CF , Garrison AR , Gao GF , Gonzalez JJ , Groschup MH , Gunther S , Haenni AL , Hall RA , Hepojoki J , Hewson R , Hu Z , Hughes HR , Jonson MG , Junglen S , Klempa B , Klingstrom J , Kou C , Laenen L , Lambert AJ , Langevin SA , Liu D , Lukashevich IS , Luo T , Lu C , Maes P , de Souza WM , Marklewitz M , Martelli GP , Matsuno K , Mielke-Ehret N , Minutolo M , Mirazimi A , Moming A , Muhlbach HP , Naidu R , Navarro B , Nunes MRT , Palacios G , Papa A , Pauvolid-Correa A , Paweska JT , Qiao J , Radoshitzky SR , Resende RO , Romanowski V , Sall AA , Salvato MS , Sasaya T , Shen S , Shi X , Shirako Y , Simmonds P , Sironi M , Song JW , Spengler JR , Stenglein MD , Su Z , Sun S , Tang S , Turina M , Wang B , Wang C , Wang H , Wang J , Wei T , Whitfield AE , Zerbini FM , Zhang J , Zhang L , Zhang Y , Zhang YZ , Zhang Y , Zhou X , Zhu L , Kuhn JH . Arch Virol 2019 164 (7) 1949-1965 ![]() In February 2019, following the annual taxon ratification vote, the order Bunyavirales was amended by creation of two new families, four new subfamilies, 11 new genera and 77 new species, merging of two species, and deletion of one species. This article presents the updated taxonomy of the order Bunyavirales now accepted by the International Committee on Taxonomy of Viruses (ICTV). |
Non-persistence to antiretroviral therapy among adults receiving HIV medical care in the United States
Nyaku M , Beer L , Shu F . AIDS Care 2018 31 (5) 1-10 Not taking medicine over a specific period of time-non-persistence to antiretroviral therapy (ART)-may be associated with higher HIV-viral load. However, national estimates of non-persistence among U.S. HIV patients are lacking. We examined the association between non-persistence and various factors, including sustained HIV-viral suppression (VS) stratified by adherence, and assessed reasons for non-persistence using Medical Monitoring Project (MMP) data. MMP conducts clinical and behavioral surveillance among cross-sectional representative samples of adults receiving HIV care in the U.S. We analyzed weighted MMP interview and medical record abstraction data collected between 6/2011-5/2015 from 18,423 patients self-reporting ART use. We defined non-persistence as a self-initiated decision to not take ART for >/=2 consecutive days in the past 12-months, non-adherence as missing >/=1 ART dose during the past 3-days and sustained VS as all HIV-viral loads documented in medical record during the past 12-months as undetectable or <200 copies/mL. We used Rao-Scott chi-square tests to examine the association between non-persistence and sociodemographic, behavioral, clinical, and medication-related factors. We examined the association between non-persistence and sustained VS, stratified by adherence, and present prevalence ratios (PRs) with 95% confidence intervals (CIs). Reasons for non-persistence were assessed. Overall, 7% of patients reported non-persistence. Drug use, depression and medication side effects were associated with non-persistence (P < 0.01). Non-persistence was associated with the lack of sustained VS (PR: .66, CI:63-.70); this association did not differ by adherence level. However, VS was lower among the non-persistent/adherent compared with the persistent/non-adherent [51% (CI:47-54) versus 61% (CI:36-46), P < 0.01]. The most prevalent reason for non-persistence was treatment fatigue (38%). Though few persons in HIV care reported non-persistence, our findings suggest that non-persistence is associated with lack of sustained VS, regardless of adherence. Routine screening for non-persistence during clinical appointments and counseling for those at risk for non-persistence may help improve clinical outcomes. |
Inter- and intra-host sequence diversity reveal the emergence of viral variants during an overwintering epidemic caused by dengue virus serotype 2 in southern Taiwan
Ko HY , Li YT , Chao DY , Chang YC , Li ZT , Wang M , Kao CL , Wen TH , Shu PY , Chang GJ , King CC . PLoS Negl Trop Dis 2018 12 (10) e0006827 Purifying selection during dengue viral infection has been suggested as the driving force of viral evolution and the higher complexity of the intra-host quasi-species is thought to offer an adaptive advantage for arboviruses as they cycle between arthropod and vertebrate hosts. However, very few studies have been performed to investigate the viral genetic changes within (intra-host) and between (inter-host) humans in a spatio-temporal scale. Viruses of different serotypes from various countries imported to Taiwan cause annual outbreaks. During 2001-2003, two consecutive outbreaks were caused by dengue virus serotype 2 (DENV-2) and resulted in a larger-scale epidemic with more severe dengue cases in the following year. Phylogenetic analyses showed that the viruses from both events were similar and related to the 2001 DENV-2 isolate from the Philippines. We comprehensively analyzed viral sequences from representative dengue patients and identified three consensus genetic variants, group Ia, Ib and II, with different spatio-temporal population dynamics. The phylodynamic analysis suggested group Ib variants, characterized by lower genetic diversity, transmission rate, and intra-host variant numbers, might play the role of maintenance variants. The residential locations among the patients infected by group Ib variants were in the outer rim of case clusters throughout the 2001-2003 period whereas group Ia and II variants were located in the centers of case clusters, suggesting that group Ib viruses might serve as "sheltered overwintering" variants in an undefined ecological niche. Further deep sequencing of the viral envelope (E) gene directly from individual patient serum samples confirmed the emergence of variants belonging to three quasi-species (group Ia, Ib, and II) and the ancestral role of the viral variants in the latter phase of the 2001 outbreak contributed to the later, larger-scale epidemic beginning in 2002. These findings enhanced our understanding of increasing epidemic severity over time in the same epidemic area. It also highlights the importance of combining phylodynamic and deep sequencing analysis as surveillance tools for detecting dynamic changes in viral variants, particularly searching for and monitoring any specific viral subpopulation. Such subpopulations might have selection advantages in both fitness and transmissibility leading to increased epidemic severity. |
Factors associated with prolonged viral shedding in patients with avian influenza A(H7N9) virus infection
Wang Y , Guo Q , Yan Z , Zhou D , Zhang W , Zhou S , Li YP , Yuan J , Uyeki TM , Shen X , Wu W , Zhao H , Wu YF , Shang J , He Z , Yang Y , Zhao H , Hong Y , Zhang Z , Wu M , Wei T , Deng X , Deng Y , Cai LH , Lu W , Shu H , Zhang L , Luo H , Ing Zhou Y , Weng H , Song K , Yao L , Jiang M , Zhao B , Chi R , Guo B , Fu L , Yu L , Min H , Chen P , Chen S , Hong L , Mao W , Huang X , Gu L , Li H , Wang C , Cao B . J Infect Dis 2018 217 (11) 1708-1717 Background: Data are limited on the impact of neuraminidase inhibitor (NAI) treatment on avian influenza A(H7N9) virus RNA shedding. Methods: In this multicenter, retrospective study, data were collected from adults hospitalized with A(H7N9) infection during 2013-2017 in China. We compared clinical features and A(H7N9) shedding among patients with different NAI doses and combination therapies and evaluated factors associated with A(H7N9) shedding, using Cox proportional hazards regression. Results: Among 478 patients, the median age was 56 years, 71% were male, and 37% died. The median time from illness onset to NAI treatment initiation was 8 days (interquartile range [IQR], 6-10 days), and the median duration of A(H7N9) RNA detection from onset was 15.5 days (IQR, 12-20 days). A(H7N9) RNA shedding was shorter in survivors than in patients who died (P < .001). Corticosteroid administration (hazard ratio [HR], 0.62 [95% confidence interval {CI}, .50-.77]) and delayed NAI treatment (HR, 0.90 [95% CI, .91-.96]) were independent risk factors for prolonged A(H7N9) shedding. There was no significant difference in A(H7N9) shedding duration between NAI combination treatment and monotherapy (P = .65) or between standard-dose and double-dose oseltamivir treatment (P = .70). Conclusions: Corticosteroid therapy and delayed NAI treatment were associated with prolonged A(H7N9) RNA shedding. NAI combination therapy and double-dose oseltamivir treatment were not associated with a reduced A(H7N9) shedding duration as compared to standard-dose oseltamivir. |
Detection of Influenza C Viruses Among Outpatients and Patients Hospitalized for Severe Acute Respiratory Infection, Minnesota, 2013-2016.
Thielen BK , Friedlander H , Bistodeau S , Shu B , Lynch B , Martin K , Bye E , Como-Sabetti K , Boxrud D , Strain AK , Chaves SS , Steffens A , Fowlkes AL , Lindstrom S , Lynfield R . Clin Infect Dis 2018 66 (7) 1092-1098 ![]() ![]() Background: Existing literature suggests that influenza C typically causes mild respiratory tract disease. However, clinical and epidemiological data are limited. Methods: Four outpatient clinics and 3 hospitals submitted clinical data and respiratory specimens through a surveillance network for acute respiratory infection (ARI) from May 2013 through December 2016. Specimens were tested using multitarget nucleic acid amplification for 19-22 respiratory pathogens, including influenza C. Results: Influenza C virus was detected among 59 of 10 202 (0.58%) hospitalized severe ARI cases and 11 of 2282 (0.48%) outpatients. Most detections occurred from December to March, 73% during the 2014-2015 season. Influenza C detections occurred among patients of all ages, with rates being similar between inpatients and outpatients. The highest rate of detection occurred among children aged 6-24 months (1.2%). Among hospitalized cases, 7 required intensive care. Medical comorbidities were reported in 58% of hospitalized cases and all who required intensive care. At least 1 other respiratory pathogen was detected in 40 (66%) cases, most commonly rhinovirus/enterovirus (25%) and respiratory syncytial virus (20%). The hemagglutinin-esterase-fusion gene was sequenced in 37 specimens, and both C/Kanagawa and C/Sao Paulo lineages were detected in inpatients and outpatients. Conclusions: We found seasonal circulation of influenza C with year-to-year variability. Detection was most frequent among young children but occurred in all ages. Some cases that were positive for influenza C, particularly those with comorbid conditions, had severe disease, suggesting a need for further study of the role of influenza C virus in the pathogenesis of respiratory disease. |
Avian influenza A(H7N2) virus in human exposed to sick cats, New York, USA, 2016
Marinova-Petkova A , Laplante J , Jang Y , Lynch B , Zanders N , Rodriguez M , Jones J , Thor S , Hodges E , De La Cruz JA , Belser J , Yang H , Carney P , Shu B , Berman L , Stark T , Barnes J , Havers F , Yang P , Trock SC , Fry A , Gubareva L , Bresee JS , Stevens J , Daskalakis D , Liu D , Lee CT , Torchetti MK , Newbury S , Cigel F , Toohey-Kurth K , St George K , Wentworth DE , Lindstrom S , Davis CT . Emerg Infect Dis 2017 23 (12) 2046-9 An outbreak of influenza A(H7N2) virus in cats in a shelter in New York, NY, USA, resulted in zoonotic transmission. Virus isolated from the infected human was closely related to virus isolated from a cat; both were related to low pathogenicity avian influenza A(H7N2) viruses detected in the United States during the early 2000s. |
Cohort profile: the China Ageing REespiratory infections Study (CARES), a prospective cohort study in older adults in Eastern China
Cowling BJ , Xu C , Tang F , Zhang J , Shen J , Havers F , Wendladt R , Leung NH , Greene C , Iuliano AD , Shifflett P , Song Y , Zhang R , Kim L , Chen Y , Chu DK , Zhu H , Shu Y , Yu H , Thompson MG . BMJ Open 2017 7 (10) e017503 PURPOSE: This study was established to provide direct evidence on the incidence of laboratory-confirmed influenza virus and respiratory syncytial virus (RSV) infections in older adults in two cities in Jiangsu Province, China, and the potential impact of acute respiratory infections on frailty. PARTICIPANTS: The cohort was enrolled in Suzhou and Yancheng, two cities in Jiangsu Province in Eastern China. Between November 2015 and March 2016, we enrolled 1532 adults who were 60-89 years of age, and collected blood samples along with baseline data on demographics, general health, chronic diseases, functional status and cognitive function through face-to-face interviews using a standardised questionnaire. Participants are being followed weekly throughout the year to identify acute respiratory illnesses. We schedule home visits to ill participants to collect mid-turbinate nasal and oropharyngeal swabs for laboratory testing and detailed symptom information for the acute illness. Regular follow-up including face-to-face interviews and further blood draws will take place every 6-12 months. FINDINGS TO DATE: As of 3 September 2016, we had identified 339 qualifying acute respiratory illness events and 1463 (95%) participants remained in the study. Laboratory testing is ongoing. FUTURE PLANS: We plan to conduct laboratory testing to estimate the incidence of influenza virus and RSV infections in older adults. We plan to investigate the impact of these infections on frailty and functional status to determine the association of pre-existing immune status with protection against influenza and RSV infection in unvaccinated older adults, and to assess the exposure to avian influenza viruses in this population. |
Clusters of human infections with avian influenza A(H7N9) virus in China, March 2013 to June 2015
Liu B , Havers FP , Zhou L , Zhong H , Wang X , Mao S , Li H , Ren R , Xiang N , Shu Y , Zhou S , Liu F , Chen E , Zhang Y , Widdowson MA , Li Q , Feng Z . J Infect Dis 2017 216 S548-s554 Multiple clusters of human infections with novel avian influenza A(H7N9) virus have occurred since the virus was first identified in spring 2013. However, in many situations it is unclear whether these clusters result from person-to-person transmission or exposure to a common infectious source. We analyzed the possibility of person-to-person transmission in each cluster and developed a framework to assess the likelihood that person-to-person transmission had occurred. We described 21 clusters with 22 infected contact cases that were identified by the Chinese Center for Disease Control and Prevention from March 2013 through June 2015. Based on detailed epidemiological information and the timing of the contact case patients' exposures to infected persons and to poultry during their potential incubation period, we graded the likelihood of person-to-person transmission as probable, possible, or unlikely. We found that person-to-person transmission probably occurred 12 times and possibly occurred 4 times; it was unlikely in 6 clusters. Probable nosocomial transmission is likely to have occurred in 2 clusters. Limited person-to-person transmission is likely to have occurred on multiple occasions since the H7N9 virus was first identified. However, these transmission events represented a small fraction of all identified cases of H7N9 human infection, and sustained person-to-person transmission was not documented. |
Mild respiratory illness among young children caused by highly pathogenic avian influenza A (H5N1) virus infection in Dhaka, Bangladesh, 2011
Chakraborty A , Rahman M , Hossain MJ , Khan SU , Haider MS , Sultana R , Ali Rimi N , Islam MS , Haider N , Islam A , Sultana Shanta I , Sultana T , Al Mamun A , Homaira N , Goswami D , Nahar K , Alamgir ASM , Rahman M , Mahbuba Jamil K , Azziz-Baumgartner E , Simpson N , Shu B , Lindstrom S , Gerloff N , Davis CT , Katz JM , Mikolon A , Uyeki TM , Luby SP , Sturm-Ramirez K . J Infect Dis 2017 216 S520-s528 Background: In March 2011, a multidisciplinary team investigated 2 human cases of highly pathogenic avian influenza A(H5N1) virus infection, detected through population-based active surveillance for influenza in Bangladesh, to assess transmission and contain further spread. Methods: We collected clinical and exposure history of the case patients and monitored persons coming within 1 m of a case patient during their infectious period. Nasopharyngeal wash specimens from case patients and contacts were tested with real-time reverse-transcription polymerase chain reaction, and virus culture and isolates were characterized. Serum samples were tested with microneutralization and hemagglutination inhibition assays. We tested poultry, wild bird, and environmental samples from case patient households and surrounding areas for influenza viruses. Results: Two previously healthy case patients, aged 13 and 31 months, had influenzalike illness and fully recovered. They had contact with poultry 7 and 10 days before illness onset, respectively. None of their 57 contacts were subsequently ill. Clade 2.2.2.1 highly pathogenic avian influenza H5N1 viruses were isolated from the case patients and from chicken fecal samples collected at the live bird markets near the patients' dwellings. Conclusion: Identification of H5N1 cases through population-based surveillance suggests possible additional undetected cases throughout Bangladesh and highlights the importance of surveillance for mild respiratory illness among populations frequently exposed to infected poultry. |
Risk factors for influenza A(H7N9) Disease in China, a matched case control study, October 2014 to April 2015
Zhou L , Ren R , Ou J , Kang M , Wang X , Havers F , Huo X , Liu X , Sun Q , He Y , Liu B , Wu S , Wang Y , Sui H , Zhang Y , Tang S , Chang C , Xiang L , Wang D , Zhao S , Zhou S , Chen T , Xiang N , Greene CM , Zhang Y , Shu Y , Feng Z , Li Q . Open Forum Infect Dis 2016 3 (3) ofw182 Background. Human infections with avian influenza A(H7N9) virus have been associated with exposure to poultry and live poultry markets (LPMs). We conducted a case-control study to identify additional and more specific risk factors. Methods. Cases were laboratory-confirmed A(H7N9) infections in persons in China reported from October 1, 2014 to April 30, 2015. Poultry workers, those with insufficient data, and those refusing participation were excluded. We matched up to 4 controls per case by sex, age, and residential community. Using conditional logistic regression, we examined associations between A(H7N9) infection and potential risk factors. Results. Eighty-five cases and 334 controls were enrolled with similar demographic characteristics. Increased risk of A(H7N9) infection was associated with the following: visiting LPMs (adjusted odds ratio [aOR], 6.3; 95% confidence interval [CI], 2.6-15.3), direct contact with live poultry in LPMs (aOR, 4.1; 95% CI, 1.1-15.6), stopping at a live poultry stall when visiting LPMs (aOR, 2.7; 95% CI, 1.1-6.9), raising backyard poultry at home (aOR, 7.7; 95% CI, 2.0-30.5), direct contact with backyard poultry (aOR, 4.9; 95% CI, 1.1-22.1), and having ≥1 chronic disease (aOR, 3.1; 95% CI, 1.5-6.5). Conclusions. Our study identified raising backyard poultry at home as a risk factor for illness with A(H7N9), suggesting the need for enhanced avian influenza surveillance in rural areas. |
Sero-epidemiologic study of influenza A(H7N9) infection among exposed populations, China 2013-2014
Xiang N , Bai T , Kang K , Yuan H , Zhou S , Ren R , Li X , Wu J , Deng L , Zeng G , Wang X , Mao S , Shi J , Gao R , Chen T , Zou S , Li D , Havers F , Widdowson MA , Greene CM , Zhang Y , Ni D , Liu X , Li Q , Shu Y . Influenza Other Respir Viruses 2017 11 (2) 170-176 BACKGROUND: The first human infections of novel avian influenza A(H7N9) virus were identified in China in March 2013. Sentinel surveillance systems and contact tracing may not identify mild and asymptomatic human infections of influenza A(H7N9) virus. OBJECTIVES: We assessed the seroprevalence of antibodies to influenza A(H7N9) virus in three populations during the early stages of the epidemic. PATIENTS/METHODS: From March 2013 to May 2014, we collected sera from the general population, poultry workers, and contacts of confirmed infections in nine Chinese provinces reporting human A(H7N9) infections and, for contacts, second sera 2-3 weeks later. We screened for A(H7N9) antibodies by advanced hemagglutination inhibition (HI) assay and tested sera with HI titers ≥20 by modified microneutralization (MN) assay. MN titers ≥20 or fourfold increases in paired sera were considered seropositive. RESULTS: Among general population sera (n=1480), none were seropositive. Among poultry worker sera (n=1866), 28 had HI titers ≥20; two (0.11%, 95% CI: 0.02-0.44) were positive by MN. Among 61 healthcare and 117 non-healthcare contacts' sera, five had HI titers ≥20, and all were negative by MN. There was no seroconversion among 131 paired sera. CONCLUSIONS: There was no evidence of widespread transmission of influenza A(H7N9) virus during March 2013 to May 2014, although A(H7N9) may have caused rare, previously unrecognized infections among poultry workers. Although the findings suggest that there were few undetected cases of influenza A(H7N9) early in the epidemic, it is important to continue monitoring transmission as virus and epidemic evolve. |
A large outbreak of acute gastroenteritis caused by the human norovirus GII.17 strain at a university in Henan Province, China.
Huang XY , Su J , Lu QC , Li SZ , Zhao JY , Li ML , Li Y , Shen XJ , Zhang BF , Wang HF , Mu YJ , Wu SY , Du YH , Liu LC , Chen WJ , Klena JD , Xu BL . Infect Dis Poverty 2017 6 (1) 6 ![]() BACKGROUND: Human noroviruses are a major cause of viral gastroenteritis and are the main etiological agents of acute gastroenteritis outbreaks. An increasing number of outbreaks and sporadic cases of norovirus have been reported in China in recent years. There was a large acute gastroenteritis outbreak at a university in Henan Province, China in the past five years. We want to identify the source, transmission routes of the outbreak by epidemiological investigation and laboratory testing in order to provide the effective control measures. METHODS: The clinical cases were investigated, and analysed by descriptive epidemiological methods according to factors such as time, department, grade and so on. Samples were collected from clinical cases, healthy persons, the environment, water, and food at the university. These samples were tested for potential bacteria and viruses. The samples that tested positive for norovirus were selected for whole genome sequencing and the sequences were then analysed. RESULTS: From 4 March to 3 April 2015, a total of 753 acute diarrhoea cases were reported at the university; the attack rate was 3.29%. The epidemic curve showed two peaks, with the main peak occurring between 10 and 20 March, accounting for 85.26% of reported cases. The rates of norovirus detection in samples from confirmed cases, people without symptoms, and environmental samples were 32.72%, 17.39%, and 9.17%, respectively. The phylogenetic analysis showed that the norovirus belonged to the genotype GII.17. CONCLUSIONS: This is the largest and most severe outbreak caused by genotype GII.17 norovirus in recent years in China. The GII.17 viruses displayed high epidemic activity and have become a dominant strain in China since the winter of 2014, having replaced the previously dominant GII.4 Sydney 2012 strain. |
Assessing change in avian influenza A(H7N9) virus infections during the fourth epidemic - China, September 2015-August 2016
Xiang N , Li X , Ren R , Wang D , Zhou S , Greene CM , Song Y , Zhou L , Yang L , Davis CT , Zhang Y , Wang Y , Zhao J , Li X , Iuliano AD , Havers F , Olsen SJ , Uyeki TM , Azziz-Baumgartner E , Trock S , Liu B , Sui H , Huang X , Zhang Y , Ni D , Feng Z , Shu Y , Li Q . MMWR Morb Mortal Wkly Rep 2016 65 (49) 1390-1394 Since human infections with avian influenza A(H7N9) virus were first reported by the Chinese Center for Disease Control and Prevention (China CDC) in March 2013, mainland China has experienced four influenza A(H7N9) virus epidemics. Prior investigations demonstrated that age and sex distribution, clinical features, and exposure history of A(H7N9) virus human infections reported during the first three epidemics were similar. In this report, epidemiology and virology data from the most recent, fourth epidemic (September 2015-August 2016) were compared with those from the three earlier epidemics. Whereas age and sex distribution and exposure history in the fourth epidemic were similar to those in the first three epidemics, the fourth epidemic demonstrated a greater proportion of infected persons living in rural areas, a continued spread of the virus to new areas, and a longer epidemic period. The genetic markers of mammalian adaptation and antiviral resistance remained similar across each epidemic, and viruses from the fourth epidemic remained antigenically well matched to current candidate vaccine viruses. Although there is no evidence of increased human-to-human transmissibility of A(H7N9) viruses, the continued geographic spread, identification of novel reassortant viruses, and pandemic potential of the virus underscore the importance of rigorous A(H7N9) virus surveillance and continued risk assessment in China and neighboring countries. |
Comparison of the first three waves of avian influenza A(H7N9) virus circulation in the mainland of the People's Republic of China
Xiang N , Iuliano AD , Zhang Y , Ren R , Geng X , Ye B , Tu W , Li CA , Lv Y , Yang M , Zhao J , Wang Y , Yang F , Zhou L , Liu B , Shu Y , Ni D , Feng Z , Li Q . BMC Infect Dis 2016 16 (1) 734 ![]() BACKGROUND: H7N9 human cases were first detected in mainland China in March 2013. Circulation of this virus has continued each year shifting to typical winter months. We compared the clinical and epidemiologic characteristics for the first three waves of virus circulation. METHODS: The first wave was defined as reported cases with onset dates between March 31-September 30, 2013, the second wave was defined as October 1, 2013-September 30, 2014 and the third wave was defined as October 1, 2014-September 30, 2015. We used simple descriptive statistics to compare characteristics of the three distinct waves of virus circulation. RESULTS: In mainland China, 134 cases, 306 cases and 219 cases were detected and reported in first three waves, respectively. The median age of cases was statistically significantly older in the first wave (61 years vs. 56 years, 56 years, p < 0.001) compared to the following two waves. Most reported cases were among men in all three waves. There was no statistically significant difference between case fatality proportions (33, 42 and 45%, respectively, p = 0.08). There were no significant statistical differences for time from illness onset to first seeking healthcare, hospitalization, lab confirmation, initiation antiviral treatment and death between the three waves. A similar percentage of cases in all waves reported exposure to poultry or live poultry markets (87%, 88%, 90%, respectively). There was no statistically significant difference in the occurrence of severe disease between the each of the first three waves of virus circulation. Twenty-one clusters were reported during these three waves (4, 11 and 6 clusters, respectively), of which, 14 were considered to be possible human-to-human transmission. CONCLUSION: Though our case investigation for the first three waves found few differences between the epidemiologic and clinical characteristics, there is continued international concern about the pandemic potential of this virus. Since the virus continues to circulate, causes more severe disease, has the ability to mutate and become transmissible from human-to-human, and there is limited natural protection from infection in communities, it is critical that surveillance systems in China and elsewhere are alert to the influenza H7N9 virus. |
A Novel Rapidly Growing Mycobacterium Species Causing an Abdominal Cerebrospinal Fluid Pseudocyst Infection.
Hussain CK , de Man TJ , Toney NC , Kamboj K , Balada-Llasat JM , Wang SH . Open Forum Infect Dis 2016 3 (3) ofw146 ![]() Nontuberculous mycobacteria (NTM) are a rare cause of ventriculoperitoneal shunt infections. We describe the isolation and identification of a novel, rapidly growing, nonpigmented NTM from an abdominal cerebrospinal fluid pseudocyst. The patient presented with fevers, nausea, and abdominal pain and clinically improved after shunt removal. NTM identification was performed by amplicon and whole-genome sequencing. |
Selection of antigenically advanced variants of seasonal influenza viruses
Li C , Hatta M , Burke DF , Ping J , Zhang Y , Ozawa M , Taft AS , Das SC , Hanson AP , Song J , Imai M , Wilker PR , Watanabe T , Watanabe S , Ito M , Iwatsuki-Horimoto K , Russell CA , James SL , Skepner E , Maher EA , Neumann G , Klimov AI , Kelso A , McCauley J , Wang D , Shu Y , Odagiri T , Tashiro M , Xu X , Wentworth DE , Katz JM , Cox NJ , Smith DJ , Kawaoka Y . Nat Microbiol 2016 1 (6) 16058 Influenza viruses mutate frequently, necessitating constant updates of vaccine viruses. To establish experimental approaches that may complement the current vaccine strain selection process, we selected antigenic variants from human H1N1 and H3N2 influenza virus libraries possessing random mutations in the globular head of the haemagglutinin protein (which includes the antigenic sites) by incubating them with human and/or ferret convalescent sera to human H1N1 and H3N2 viruses. We also selected antigenic escape variants from human viruses treated with convalescent sera and from mice that had been previously immunized against human influenza viruses. Our pilot studies with past influenza viruses identified escape mutants that were antigenically similar to variants that emerged in nature, establishing the feasibility of our approach. Our studies with contemporary human influenza viruses identified escape mutants before they caused an epidemic in 2014-2015. This approach may aid in the prediction of potential antigenic escape variants and the selection of future vaccine candidates before they become widespread in nature. |
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