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In thoracoscopic segmentectomy, accurate preoperative identification of intersegmental vessels, bronchi, and the surgical safety margin is vital. We applied three dimensional computed tomography bronchography and angiography (3D-CTBA) reconstruction to appropriately plan thoracoscopic segmentectomy for Patients with pulmonary nodules. In this study, we evaluated the effectiveness and accuracy of 3D-CTBA reconstruction for the identification of segmental anatomical structures and variation during thoracoscopic segmentectomy.We retrospectively analyzed data of 30 patients who underwent 3D-CTBA reconstruction before thoracoscopic segmentectomy between January and May 2019 in the Department of Thoracic Surgery, First Affiliated Hospital of Nanchang University. We compared the individual target segment arteries, veins, and bronchi identified during surgery with the preoperative 3D-CTBA model to evaluate its effectiveness and accuracy. The accuracy of the preoperative 3D-CTBA model for the identification of target segmental arteries, veins, and bronchi was 99.08% (108/109), 98.39% (122/124), and 100% (118/118), respectively. Through 3DCTBA modeling, we found mediastinal and interlobar types of lingular segmental arteries in six patients, and central veins were not found in seven patients. In addition, we detected rare anatomical variations in two patients; one patient had the right apical segmental bronchus that stemmed solely from the right primary bronchus (tracheal bronchus), and the other had rare right basal segmental variant bronchi and vessels. The 3D-CTBA model can precisely predict segmental bronchi and vessels and identify anatomical structure variations before operation, which can aid surgeons to avoid incorrect operation and improve surgical efficiency. This has important implications for thoracoscopic segmentectomy.

The Camp Fire, California's deadliest wildfire, began November 8, 2018, and was extinguished November 25 (1). Approximately 1,100 evacuees from the fire sought emergency shelter. On November 10, acute gastroenteritis (AGE) was reported in two evacuation shelters; norovirus illness was suspected, because it is commonly detected in shelter-associated AGE outbreaks. Norovirus is highly contagious and resistant to several disinfectants. Butte County Public Health Department (BCPHD), assisted by the California Department of Public Health (CDPH), initiated active surveillance to identify cases, confirm the etiology, and assess shelter infection prevention and control (IPC) practices to guide recommendations. During November 8-30, a total of 292 patients with AGE were identified among nine evacuation shelters; norovirus was detected in 16 of 17 unique patient stool specimens. Shelter IPC assessments revealed gaps in illness surveillance, isolation practices, cleaning, disinfection, and handwashing. CDPH and BCPHD collaborated with partner agencies to implement AGE screening, institute isolation protocols and 24-hour cleaning services, and promote proper hand hygiene. During disasters with limited resources, damaged infrastructure, and involvement of multiple organizations, establishing shelter disease surveillance and IPC is difficult. However, prioritizing effective surveillance and IPC at shelter activation is necessary to prevent, identify, and contain outbreaks.

SARS-CoV-2 infection elicits a distinct host response in nasal swabs and blood that can be used to diagnose COVID-19., Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease-19 (COVID-19), has emerged as the cause of a global pandemic. We used RNA sequencing to analyze 286 nasopharyngeal (NP) swab and 53 whole-blood (WB) samples from 333 patients with COVID-19 and controls. Overall, a muted immune response was observed in COVID-19 relative to other infections (influenza, other seasonal coronaviruses, and bacterial sepsis), with paradoxical down-regulation of several key differentially expressed genes. Hospitalized patients and outpatients exhibited up-regulation of interferon-associated pathways, although heightened and more robust inflammatory responses were observed in hospitalized patients with more clinically severe illness. Two-layer machine learning–based host classifiers consisting of complete (>1000 genes), medium (

Noroviruses are a leading cause of acute gastroenteritis (AGE) among adults and children worldwide. NoroSurv is a global network for norovirus strain surveillance among children

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.

An outbreak of novel betacoronavirus, SARS-CoV-2 (formerly named 2019-nCoV), began in Wuhan, China in December 2019 and the COVID-19 disease associated with infection has since spread rapidly to multiple countries. Here we report the development of SARS-CoV-2 DETECTR, a rapid (∼30 min), low-cost, and accurate CRISPR-Cas12 based lateral flow assay for detection of SARS-CoV-2 from respiratory swab RNA extracts. We validated this method using contrived reference samples and clinical samples from infected US patients and demonstrated comparable performance to the US CDC SARS-CoV-2 real-time RT-PCR assay.

An outbreak of betacoronavirus severe acute respiratory syndrome (SARS)-CoV-2 began in Wuhan, China in December 2019. COVID-19, the disease associated with SARS-CoV-2 infection, rapidly spread to produce a global pandemic. We report development of a rapid (

We report the nearly complete genome sequence of a human enterovirus, a strain of echovirus 30, obtained from a cerebrospinal fluid specimen from a teenaged patient with aseptic meningitis in September 2017.

Highlights • We validated genogroup-specific one-step conventional RT-PCR assays (PC assays) for sequence-based dual typing of GI and GII norovirus strains. • The PC assays use a combination of oligonucleotide primers that target a genomic region spanning the 3’-end of ORF1 and 5’end of ORF2 of GI and GII noroviruses. • The PC assays are sensitive (5 to 50 copies/rx) and detect all currently identified norovirus P-types and capsid genotypes from different geographic regions. • The PC assays have been successfully implemented by CaliciNet USA and CaliciNet China., Background Noroviruses are the major cause of acute gastroenteritis (AGE) in people of all ages globally. Standardized genotyping is key for outbreak investigations and surveillance networks. Objective Here we describe the validation of a one-step conventional RT-PCR assay for sequence-based dual typing of GI and GII noroviruses. This polymerase (P) and capsid (C) dual typing assay uses a combination of previously published oligonucleotide primers amplifying a genomic region spanning the 3'-end of ORF1 and 5'end of ORF2 resulting in a 579 bp product for GI and 570 bp product for GII viruses. Results The limit of detection of the assay ranged from 5 to 50 copies of viral RNA per reaction for GI and GII. To validate the assay, we tested 2,663 noroviruspositive stool samples from outbreaks and sporadic cases of AGE in Bangladesh, Guatemala, Peru, and USA collected between 2010–2019, of which 2,392 (90 %) were genotyped successfully. Most of the known genotypes infecting humans (GI (n = 9) and GII (n = 23)) and P types (GI (n = 15), GII, (n = 20)) could be detected. The remaining 270 samples had low viral load (Ct > 30) by real-time RT-PCR. A panel of 166 samples positive for other enteric viruses (rotavirus, astrovirus, sapovirus, adenovirus type 40/41) tested negative. Conclusion The use of broadly reactive genotyping assays greatly strengthens exchange of standardized genotype data globally to monitor trends in genotype diversity which is important for both the development of vaccines and to measure their impact.

On June 22, 2017, the Los Angeles County Department of Public Health (LAC DPH) was notified of seven patients who were seen at an eye care clinic on June 8, 2017, and later developed symptoms of epidemic keratoconjunctivitis (EKC). EKC is a contagious, severe form of viral conjunctivitis that can cause pain and blurred vision for up to 4 weeks (1). LAC DPH conducted an investigation, which identified 17 patients with EKC, including 15 who had visited the optometry clinic and two who were household contacts of clinic patients. Observations in the clinic found deficiencies in disinfection of tonometers (an instrument connected to a slit lamp and used to test for glaucoma by measuring intraocular pressure) and multiuse eye drop administration. Staff member education and revision of disinfection practices interrupted further transmission. Patient specimens tested positive for human adenovirus (HAdV) type D53 (HAdV-53). As the first documented EKC outbreak associated with HAdV-D53 in the United States, this outbreak highlights the need for rigorous implementation of recommended infection prevention practices in eye care settings.

We report here two genome sequences of a newly designated rhinovirus genotype, RV-C56, which were obtained from respiratory specimens of three patients with acute respiratory illness in 2016 and 2017. To our knowledge, these sequences represent the first near-complete genomes for RV-C56 strains.

Before the introduction of rotavirus vaccine in 2006, rotavirus was the most common cause of severe diarrhea among U.S. children (1). Currently, two rotavirus vaccines are licensed for use in the United States, both of which have demonstrated good field effectiveness (78%-89%) against moderate to severe rotavirus illness (2), and the use of these vaccines has substantially reduced the prevalence of rotavirus in the United States (3). However, the most recent national vaccine coverage estimates indicate lower full rotavirus vaccine-series completion (73%) compared with receipt of at least 3 doses of vaccines containing diphtheria, tetanus, and pertussis antigens (95%), given on a similar schedule to rotavirus vaccines (4). In the postvaccine era in the United States, rotavirus activity persists in a biennial pattern (3). This report describes three rotavirus outbreaks that occurred in California in 2017. One death was reported; however, the majority of cases were associated with mild to moderate illness, and illness occurred across the age spectrum as well as among vaccinated children. Rotavirus vaccines are designed to mimic the protective effects of natural infection and are most effective against severe rotavirus illness (2). Even in populations with high vaccination coverage, some rotavirus infections and mild to moderate illnesses will occur. Rotavirus vaccination should continue to be emphasized as the best means of reducing disease prevalence in the United States.

Here, we report the full coding sequence of rhinovirus C47 (RV-C47), obtained from a patient respiratory sample collected during an acute respiratory illness investigation in Butte County, California, in January 2017. This is the first whole-genome sequence of RV-C47 to be reported.

Background Sapoviruses are responsible for sporadic and epidemic acute gastroenteritis worldwide. Sapovirus typing protocols have a success rate as low as 43% and relatively few complete sapovirus genome sequences are available to improve current typing protocols. Objective/study design To increase the number of complete sapovirus genomes to better understand the molecular epidemiology of human sapovirus and to improve the success rate of current sapovirus typing methods, we used deep metagenomics shotgun sequencing to obtain the complete genomes of 68 sapovirus samples from four different countries across the Americas (Guatemala, Nicaragua, Peru and the US). Results VP1 genotyping showed that all sapovirus sequences could be grouped in the four established genogroups (GI (n = 13), GII (n = 30), GIV (n = 23), GV (n = 2)) that infect humans. They include the near-complete genome of a GI.6 virus and a recently reported novel GII.8 virus. Sequences of the complete RNA-dependent RNA polymerase gene could be grouped into three major genetic clusters or polymerase (P) types (GI.P, GII.P and GV.P) with all GIV viruses harboring a GII polymerase. One (GII.P-GII.4) of the new 68 sequences was a recombinant virus with the hotspot between the NS7 and VP1 regions. Conclusions Analyses of this expanded database of near-complete sapovirus sequences showed several mismatches in the genotyping primers, suggesting opportunities to revisit and update current sapovirus typing methods.

Human metapneumovirus (hMPV), a recently discovered paramyxovirus, is thought to be primarily a winter-spring pathogen affecting young children with a clinical presentation similar to that of respiratory syncytial virus. In June-July 2006, a respiratory outbreak in a long-term-care facility was reported to the local health department and investigated. Surveillance identified 26 residents and 13 staff with acute respiratory illness; 8 residents (31%) developed radiographically confirmed pneumonia, and 2 (5%) were hospitalized. Five of 14 respiratory specimens were positive by polymerase chain reaction assay for hMPV; sequencing identified genotype A. In institutionalized elderly persons, hMPV may be an important cause of respiratory outbreaks year-round.

BACKGROUND. Encephalitis is a complex, debilitating, and sometimes fatal neurologic condition to which children are especially prone. Mycoplasma pneumoniae, a common respiratory pathogen, has been implicated as an etiology of encephalitis. Evidence for recent or acute M pneumoniae infection has been demonstrated in limited studies of both pediatric and adult patients with encephalitis. PATIENTS AND METHODS. Unexplained encephalitis cases are referred to the California Encephalitis Project for diagnostic testing. Serum, cerebrospinal fluid, and respiratory specimens are tested by polymerase chain reaction and serology methods for the presence of multiple pathogens, including M pneumoniae. M pneumonia–associated cases of encephalitis were compared with other bacterial agents, herpes simplex virus 1, and enterovirus. RESULTS. Of 1988 patients referred to the California Encephalitis Project, evidence of acute M pneumoniae infection was found in 111 patients, of which 84 (76%) were pediatric patients. Eighty percent of the 84 patients were positive for M pneumoniae by serology alone. Cerebrospinal fluid polymerase chain reaction for M pneumoniae was rarely positive (2%). Patients with M pneumoniae–associated pediatric encephalitis were a median of 11 years old, progressed rapidly (median: 2 days from onset to hospitalization), and were often in the ICU (55%). Symptoms included fever (70%), lethargy (68%), and altered consciousness (58%). Gastrointestinal (45%) and respiratory (44%) symptoms were less common. Compared with patients with other bacterial as well as viral agents, patients with M pneumoniae–associated encephalitis had fewer seizures and less-severe hospital courses. CONCLUSIONS. M pneumoniae is the most common agent implicated in the California Encephalitis Project. Patients with M pneumoniae–associated encephalitis are predominantly pediatric, and their presentations are clinically similar to enterovirus encephalitis, although they frequently require intensive care with prolonged hospitalizations. Given that M pneumoniae infection is found more than any other pathogen, increased emphasis should be placed on elucidating the role and mechanism of M pneumoniae in encephalitis.

During April 2009–June 2010, thirty-seven (0.5%) of 6,740 pandemic (H1N1) 2009 viruses submitted to a US surveillance system were oseltamivir resistant. Most patients with oseltamivir-resistant infections were severely immunocompromised (76%) and had received oseltamivir before specimen collection (89%). No evidence was found for community circulation of resistant viruses; only 4 (unlinked) patients had no oseltamivir exposure.

BACKGROUND The purpose of the current study was to evaluate the tolerance and efficacy of hypofractionated three-dimensional conformal radiotherapy (3DCRT) with or without transarterial chemoembolization (TACE) for technically unresectable or medically inoperable primary liver carcinoma (PLC). METHODS Between April 1999 and August 2003, 128 patients with a clinical diagnosis of PLC received hypofractionated 3DCRT at Cancer Hospital, Guangxi Medical University. Both hypofractionated 3DCRT and TACE were used to treat 48 of these 128 patients. Liver cirrhosis of Child–Pugh Grade A was found in 108 patients, and Grade B was found in 20 patients. The mean gross tumor volume (GTV) was 459 ± 430 cm3. A mean total irradiation dose of 53.6 ± 6.6Gy was delivered at an average fraction of 4.88 ± 0.47Gy, 3 times a week using 8-MV photons. RESULTS The median follow-up time after 3DCRT was 12 months (range, 2–56 mos.). The immediate response rate was 55%. The overall survival rates at 1, 2, and 3 years were 65%, 43%, and 33%, respectively, with a median survival of 20 months (range, 7–31 mos.). Radiation Therapy Oncology Group (RTOG) Grade 2 acute gastrointestinal complications developed in 8 patients, whereas 4 patients developed Grade 3 late gastrointestinal complications. Radiation-induced liver disease (RILD) developed in 19 (15%) patients, of which 12 had Child–Pugh Grade B liver cirrhosis, and 7 had Grade A. GTV and associated liver cirrhosis were identified by Cox regression analysis as independent predictors for survival (P = 0.044 and 0.015). CONCLUSIONS Hypofractionated 3DCRT is effective in carefully selected patients with PLC. Gastrointestinal complications and RILD were the most distinct complications. Cancer 2005. © 2005 American Cancer Society.