Sequence Comparison of Avian Infectious Bronchitis Virus S1 Glycoproteins of the Florida Serotype and Five Variant Isolates from Georgia and California

The infectious bronchitis virus (IBV) spike glycoprotein S1 subunit is required to initiate infection and contains virus-neutralizing and serotype-specific epitope(s). Reported are the S1 gene nucleotide and predicted amino acid sequences for the Florida 18288 strain and isolates GA-92, CV-56b, CV-9437, CV-1686, and 1013. These sequences were compared with previously published gene sequences of IBV strains, and phylogenetic relationships are reported. The S1 amino acid sequence of Florida 18288 was 94.9% similar to the Connecticut strain, and GA-92 was 92.8% similar to the Arkansas 99 strain. S1 amino acid sequences of the California variants, CV-56b, CV-9437, and CV-1686, were 97.6–99.3% similar to one another and only 76.6%–76.8% similar to the Arkansas-type strains. Isolate 1013, also from California, was 84.0% similar to Ark DPI and 77.9% similar to CV-56b. When comparing 19 viruses isolated from the United States, sequence variations were observed between amino acids 55–96, 115–149, 255–309, and 378–395. Similar regions are reported to be involved in virus-neutralizing and/or serotype-specific epitopes. These data demonstrate that variant IBV strains continue to emerge, and unique variants may circulate among poultry in geographically isolated areas. This revised version was published online in July 2006 with corrections to the Cover Date.     

Latency characteristics in specific pathogen-free chickens 21 and 35 days after intra-tracheal inoculation with vaccine or field strains of infectious laryngotracheitis virus

ABSTRACT

Latency is an important feature of infectious laryngotracheitis virus (ILTV) yet is poorly understood. This study aimed to compare latency characteristics of vaccine (SA2) and field (CL9) strains of ILTV, establish an in vitro reactivation system and examine ILTV infection in peripheral blood mononuclear cells (PBMC) in specific pathogen-free chickens. Birds were inoculated with SA2 or CL9 ILTV and then bled and culled at 21 or 35 days post-inoculation (dpi). Swabs (conjunctiva, palatine cleft, trachea) and trigeminal ganglia (TG) were examined for ILTV DNA using PCR. Half of the TG, trachea and PBMC were co-cultivated with cell monolayers to assess in vitro reactivation of ILTV infection. ILTV DNA was detected in the trachea of approximately 50% of ILTV‐inoculated birds at both timepoints. At 21?dpi, ILTV was detected in the TG only in 29% and 17% of CL9- and SA2-infected birds, respectively. At 35?dpi, ILTV was detected in the TG only in 30% and 10% of CL9- and SA2-infected birds, respectively. Tracheal organ co-cultures from 30% and 70% of CL9- and SA2-infected birds, respectively, were negative for ILTV DNA at cull but yielded quantifiable DNA within 6 days post-explant (dpe). TG co-cultivation from 30% and 40% of CL9-and SA2-infected birds, respectively, had detectable ILTV DNA within 6 dpe. Latency characteristics did not substantially vary based on the strain of virus inoculated or between sampling timepoints. These results advance our understanding of ILTV latency and reactivation.

RESEARCH HIGHLIGHTS

• Following inoculation, latent ILTV infection was detected in a large proportion of chickens, irrespective of whether a field or vaccine strain was inoculated.

• In vitro reactivation of latent ILTV was readily detected in tracheal and trigeminal ganglia co-cultures using PCR.

• ILTV latency observed in SPF chickens at 21 days post-infection was not substantially different to 35 days post-infection.

     

2005-2019年理塘县法定传染病疫情分析

目的了解理塘县近15年法定传染病疫情形势及流行特征,为政府制定防控措施提供科学依据。方法对2005—2019年理塘县法定传染病疫情进行描述性流行病学分析。采用ArcGIS 10.3软件绘制各乡镇发病情况分布图,SPSS 21.0软件进行χ²检验、趋势性χ²检验。结果2005—2019年理塘县共计报告甲乙丙类传染病21种6154例,年均发病率为644.33/10万,发病呈上升趋势。死亡37例,年均死亡率3.87/10万,病死率0.60%。呼吸道传染病发病最高(341.12/10万);发病前3位的病种为肺结核(271.91/10万)、乙肝(103.24/10万)及包虫病(67.22/10万);肺结核、其他感染性腹泻病、艾滋病/HIV、梅毒发病呈上升趋势。3月、9月分别出现1次发病高峰;20~29岁、30~39岁和10~19岁组发病居前3位;男女性别比为1.24∶1;发病以农民、牧民及学生为主。结论2005-2019年理塘县法定传染病发病率较高且呈上升趋势,应针对高发传染病、上升趋势明显的传染病、重点人群进行分析研究,采取针对性措施控制疫情。     

Ten years of Pan-InfORM: modelling research for public health in Canada

Modelling and simulation methods can play an important role in guiding public health responses to infectious diseases and emerging health threats by projecting the plausible outcomes of decisions and interventions. The 2003 SARS epidemic marked a new chapter in disease modelling in Canada as it triggered a national discussion on the utility and uptake of modelling research in local and pandemic outbreaks. However, integration and application of model-based outcomes in public health requires knowledge translation and contextualization. We reviewed the history and performance of Pan-InfORM (Pandemic Influenza Outbreak Research Modelling), which created a national infrastructure in Canada with a mandate to develop innovative knowledge translation methodologies to inform policy makers through modelling frameworks that bridge the gaps between theory, policy, and practice. This review demonstrates the importance of a collaborative infrastructure as a “Community of Practice” to guide public health responses, especially in the context of emerging diseases with substantial uncertainty, such as the COVID-19 pandemic. Dedicated resources to modelling and knowledge translation activities can help create synergistic strategies at the global scale and optimize public health responses to protect at-risk populations and quell socioeconomic and health burden.     

Hybrid Approach to Estimation of Underreporting of Tuberculosis Case Notification in High-Burden Settings With Weak Surveillance Infrastructure: Design and Implementation of an Inventory Study

BackgroundThe greatest risk of infectious disease undernotification occurs in settings with limited capacity to detect it reliably. World Health Organization guidance on the measurement of misreporting is paradoxical, requiring robust, independent systems to assess surveillance rigor. Methods are needed to estimate undernotification in settings with incomplete, flawed, or weak surveillance systems. This study attempted to design a tuberculosis (TB) inventory study that balanced rigor with feasibility for high-need settings.ObjectiveThis study aims to design a hybrid TB inventory study for contexts without World Health Organization preconditions. We estimated the proportion of TB cases that were not reported to the Ministry of Health in 2015. The study sought to describe TB surveillance coverage and quality at different levels of TB care provision. Finally, we aimed to identify structural-, facility-, and provider-level barriers to notification and reasons for underreporting, nonreporting, and overreporting.MethodsRetrospective partial digitalization of paper-based surveillance and facility records preceded deterministic and probabilistic record linkage; a hybrid of health facilities and laboratory census with a stratified sampling of HFs with no capacity to notify leveraged a priori knowledge. Distinct extrapolation methods were applied to the sampled health facilities to estimate bacteriologically confirmed versus clinical TB. In-depth interviews and focus groups were used to identify causal factors responsible for undernotification and test the acceptability of remedies.ResultsThe hybrid approach proved viable and instructive. High-specificity verification of paper-based records in the field was efficient and had minimal errors. Limiting extrapolation to clinical cases improved precision. Probabilistic record linkage is computationally intensive, and the choice of software influences estimates. Record absence, decay, and overestimation of the private sector TB treatment behavior threaten validity, meriting mitigation. Data management demands were underestimated. Treatment success was modest in all sectors (R=37.9%–72.0%) and did not align with treatment success reported by the state (6665/8770, 75.99%). One-fifth of TB providers (36/178, 20%) were doubtful that the low volume of patients with TB treated in their facility merited mastery of the extensive TB notification forms and procedures.ConclusionsSubnational inventory studies can be rigorous, relevant, and efficient in countries that need them even in the absence of World Health Organization preconditions, if precautions are taken. The use of triangulation techniques, with minimal recourse to sampling and extrapolation, and the privileging of practical information needs of local decision makers yield reasonable misreporting estimates and viable policy recommendations.     

Confirmed Cases of Ophidiomycosis in Museum Specimens from as Early as 1945, United States

Ophidiomycosis represents a conservation threat to wild snake populations. The disease was reported in North America early in the 21st century, but the history of ophidiomycosis has not been investigated. We examined museum specimens and confirmed cases of ophidiomycosis >50 years before the disease’s reported emergence.     

2015—2020年湖南省感染性腹泻病原学及分子流行病学特征分析

目的 了解湖南省感染性腹泻的病原谱,追踪其分子流行病学演变趋势,为感染性腹泻的综合防治提供科学依据。 方法 通过哨点监测结合暴发疫情监测的方法,收集2015—2020年湖南省感染性腹泻标本,对细菌病原采用细菌培养、生化鉴定进行检测;对病毒病原采用分子生物学方法进行分型鉴定,并对部分PCR阳性标本进行序列测定。 结果 哨点医院主动监测的总阳性率为35.61%,病毒检出率20.26%高于细菌检出率11.26%,混合病原感染检出率为4.09%。细菌病原谱以沙门菌O∶4群鼠伤寒型为主,病毒病原谱以轮状病毒A组G9P[8]型和诺如病毒GⅡ.4Sydney[P31]型感染为主。不同监测、不同年份的病原谱构成及其基因型变迁规律各不相同:哨点医院监测细菌阳性率低而病毒阳性率高时,诺如暴发疫情随之增加;暴发疫情中诺如病毒感染为86.78%,其中69.43%为GⅡ型感染,12.42%为GⅠ型感染,混合感染占3.03%。诺如病毒暴发疫情具有明显季节性,优势基因型为GⅡ.2[P16]占42.97%。 结论 2015—2020年湖南省感染性腹泻病毒类病原体高于细菌类,鼠伤寒沙门菌、A组轮状病毒G9P[8]和诺如病毒GⅡ.4 Sydney [P31]是最主要的病原体和优势血清/基因型;GⅡ.2 [P16]是诺如病毒暴发流行的优势基因型;通过连续哨点监测的数据支持,提前为暴发疫情做好了防控,促成了湖南省感染性腹泻发病率的平稳下降。     

Genomic Analysis of Novel Poxvirus Brazilian Porcupinepox Virus,Brazil, 2019

We obtained the complete sequence of a novel poxvirus, tentatively named Brazilian porcupinepox virus, from a wild porcupine (Coendou prehensilis) in Brazil that had skin and internal lesions characteristic of poxvirus infection. The impact of this lethal poxvirus on the survival of this species and its potential zoonotic importance remain to be investigated.     

SARS-CoV-2 Serial Interval Variation,Montana, USA,March 1–July 31, 2020

We report mean severe acute respiratory syndrome coronavirus 2 serial intervals for Montana, USA, from 583 transmission pairs; infectors’ symptom onset dates occurred during March 1–July 31, 2020. Our estimate was 5.68 (95% CI 5.27–6.08) days, SD 4.77 (95% CI 4.33–5.19) days. Subperiod estimates varied temporally by nonpharmaceutical intervention type and fluctuating incidence.