Direct sequencing of SARS-coronavirus S and N genes from clinical specimens shows limited variation

Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) emerged, in November 2002, as a novel agent causing severe respiratory illness. To study sequence variation in the SARS-CoV genome, we determined the nucleic acid sequence of the S and N genes directly from clinical specimens from 10 patients--1 specimen with no matched SARS-CoV isolate, from 2 patients; multiple specimens from 3 patients; and matched clinical-specimen/cell-culture-isolate pairs from 6 patients. We identified 3 nucleotide substitutions that were most likely due to natural variation and 2 substitutions that arose after cell-culture passage of the virus. These data demonstrate the overall stability of the S and N genes of SARS-CoV over 3 months during which a minimum of 4 generations for transmission events occurred. These findings are a part of the expanding investigation of the evolution of how this virus adapts to a new host.

Severe acute respiratory syndrome coronavirus on hospital surfaces

Background. Health care workers continued to contract severe acute respiratory syndrome (SARS), even after barrier precautions were widely implemented.

Methods. We explored the possible contribution of contaminated hospital surfaces to SARS transmission by swabbing surfaces in 2 hospitals and testing the swab samples by reverse-transcriptase polymerase chain reaction (RT-PCR) and viral culture.

Results. Twenty-six of 94 swab samples tested positive for viral RNA. Swab samples of respiratory secretions from each of the 4 patients examined tested positive by RT-PCR, as were 12 of 43 swabs from patient rooms and 10 of 47 swabs from other parts of the hospital, including the computer mouses at 2 nursing stations and the handrail of the public elevator. Specimens from areas with patients with SARS in the most infectious phase of illness (days 5–15 after onset) were more likely to be RNA positive than were swab specimens from elsewhere (24 of 63 samples vs. 2 of 31 samples; P = .001). All cultures showed no growth.

Conclusions. Although the viruses identified may have been noninfectious, health care workers should be aware that SARS coronavirus can contaminate environmental surfaces in the hospital, and fomites should be considered to be a possible mode of transmission of SARS.

Human metapneumovirus infection among children hospitalized with acute respiratory illness

Recent studies have associated human Metapneumovirus (HMPV) infection in children with respiratory disease of similar severity as respiratory syncytial virus (RSV) infection. We studied 668 banked swab specimens (one per admission) collected from a population-based, prospective study of acute respiratory illness among inpatient children from two U.S. cities. Specimens were tested for HMPV, RSV, influenza, and parainfluenza viruses by reverse transcription–polymerase chain reaction assays. Twenty-six (3.9%) were positive for HMPV; 125 (18.7%) for RSV; 45 (6.7%) for parainfluenza 1, 2, or 3; and 23 (3.4%) for influenza. HMPV-positive children were significantly older than RSV-positive children. HMPV-positive children required medical intensive care and received supplemental oxygen in similar frequencies to RSV-positive children. Among children hospitalized with respiratory illness, the incidence of HMPV infection was less than RSV, but clinical disease severity mirrored that of RSV infection. Further investigations to better characterize HMPV infection and its clinical effect are needed.

Pulmonary delivery of respiratory syncytial virus DNA vaccines using macroaggregated albumin particles

At present there is no safe and effective vaccine for respiratory syncytial virus (RSV). DNA vaccines encoding RSV surface glycoproteins are one option being examined. Current methods to deliver DNA vaccines generally require repeated high dose intramuscular or intradermal administration for effectiveness. In this study, we examine the efficacy of pulmonary DNA vaccination using low dose DNA vaccines encoding the RSV F glycoprotein conjugated to macroaggregated albumin (MAA-F). Single vaccination of BALB/c mice with 1 microg MAA-F was ineffective, however mice boosted with an additional 1 microg MAA-F, or vaccinated a single time with 10 microg MAA-F, developed substantially improved immunity associated with reduced viral titers, increased anti-F antibody responses, and enhanced Th1 and Th2 intracellular cytokine responses. This study shows that MAA may be a useful carrier for RSV DNA vaccines.

Real-time reverse transcription-polymerase chain reaction assay for SARS-associated coronavirus

A real-time reverse transcription–polymerase chain reaction (RT-PCR) assay was developed to rapidly detect the severe acute respiratory syndrome–associated coronavirus (SARS-CoV). The assay, based on multiple primer and probe sets located in different regions of the SARS-CoV genome, could discriminate SARS-CoV from other human and animal coronaviruses with a potential detection limit of <10 genomic copies per reaction. The real-time RT-PCR assay was more sensitive than a conventional RT-PCR assay or culture isolation and proved suitable to detect SARS-CoV in clinical specimens. Application of this assay will aid in diagnosing SARS-CoV infection.

Sequence polymorphism of the predicted human metapneumovirus G glycoprotein

The putative G glycoprotein genes of 25 human metapneumovirus (hMPV) field isolates obtained during five consecutive epidemic seasons (1997 to 2002) were sequenced. Sequence alignments identified two major genetic groups, designated groups 1 and 2, and two minor genetic clusters within each major group, designated subgroups A and B. Extensive nucleotide and deduced amino acid sequence variability was observed, consisting of high rates of nucleotide substitutions, use of alternative transcription-termination codons and insertions that retained the reading frame. Deduced amino acid sequences showed the greatest variability, with most differences located in the extracellular domain of the protein: nucleotide and amino acid sequence identities for the entire open reading frame ranged from 52 to 58 % and 31 to 35 %, respectively, between the two major groups. Like the closely related avian pneumovirus and human and bovine respiratory syncytial viruses, the predicted G protein of hMPV shared the basic features of a type II mucin-like glycosylated protein. However, differences from these related viruses were also observed, e.g. lack of conserved cysteine clusters as seen in human respiratory syncytial virus and avian pneumovirus. The displacement of genetic groups of hMPV observed during the study period suggests that potential antigenic differences in the G glycoprotein, which have evolved in response to immune-mediated pressure, may influence the circulation patterns of hMPV strains.

Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association

Effective prophylaxis and antiviral therapies are urgently needed in the event of reemergence of the highly contagious and often fatal severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) infection. We have identified eight recombinant human single-chain variable region fragments (scFvs) against the S1 domain of spike (S) protein of the SARS-CoV from two nonimmune human antibody libraries. One scFv 80R efficiently neutralized SARS-CoV and inhibited syncytia formation between cells expressing the S protein and those expressing the SARS-CoV receptor angiotensin-converting enzyme 2 (ACE2). Mapping of the 80R epitope showed it is located within the N-terminal 261-672 amino acids of S protein and is not glycosylation-dependent. 80R scFv competed with soluble ACE2 for association with the S1 domain and bound S1 with high affinity (equilibrium dissociation constant, Kd=32.3 nM). A human IgG1 form of 80R bound S1 with a 20-fold higher affinity of 1.59 nM comparable to that of ACE2 (Kd=1.70 nM), and neutralized virus 20-fold more efficiently than the 80R scFv. These data suggest that the 80R human monoclonal antibody may be a useful viral entry inhibitor for the emergency prophylaxis and treatment of SARS, and that the ACE2-binding site of S1 could be an attractive target for subunit vaccine and drug development.

Guidelines for preventing health-care--associated pneumonia, 2003: recommendations of CDC and the Healthcare Infection Control Practices Advisory Committee

This report updates, expands, and replaces the previously published CDC "Guideline for Prevention of Nosocomial Pneumonia". The new guidelines are designed to reduce the incidence of pneumonia and other severe, acute lower respiratory tract infections in acute-care hospitals and in other health-care settings (e.g., ambulatory and long-term care institutions) and other facilities where health care is provided. Among the changes in the recommendations to prevent bacterial pneumonia, especially ventilator-associated pneumonia, are the preferential use of oro-tracheal rather than naso-tracheal tubes in patients who receive mechanically assisted ventilation, the use of noninvasive ventilation to reduce the need for and duration of endotracheal intubation, changing the breathing circuits of ventilators when they malfunction or are visibly contaminated, and (when feasible) the use of an endotracheal tube with a dorsal lumen to allow drainage of respiratory secretions; no recommendations were made about the use of sucralfate, histamine-2 receptor antagonists, or antacids for stress-bleeding prophylaxis. For prevention of health-care--associated Legionnaires disease, the changes include maintaining potable hot water at temperatures not suitable for amplification of Legionella spp., considering routine culturing of water samples from the potable water system of a facility's organ-transplant unit when it is done as part of the facility's comprehensive program to prevent and control health-care--associated Legionnaires disease, and initiating an investigation for the source of Legionella spp. when one definite or one possible case of laboratory-confirmed health-care--associated Legionnaires disease is identified in an inpatient hemopoietic stem-cell transplant (HSCT) recipient or in two or more HSCT recipients who had visited an outpatient HSCT unit during all or part of the 2-10 day period before illness onset. In the section on aspergillosis, the revised recommendations include the use of a room with high-efficiency particulate air filters rather than laminar airflow as the protective environment for allogeneic HSCT recipients and the use of high-efficiency respiratory-protection devices (e.g., N95 respirators) by severely immunocompromised patients when they leave their rooms when dust-generating activities are ongoing in the facility. In the respiratory syncytial virus (RSV) section, the new recommendation is to determine, on a case-by-case basis, whether to administer monoclonal antibody (palivizumab) to certain infants and children aged <24 months who were born prematurely and are at high risk for RSV infection. In the section on influenza, the new recommendations include the addition of oseltamivir (to amantadine and rimantadine) for prophylaxis of all patients without influenza illness and oseltamivir and zanamivir (to amantadine and rimantadine) as treatment for patients who are acutely ill with influenza in a unit where an influenza outbreak is recognized. In addition to the revised recommendations, the guideline contains new sections on pertussis and lower respiratory tract infections caused by adenovirus and human parainfluenza viruses and refers readers to the source of updated information about prevention and control of severe acute respiratory syndrome.

Persistent Parvovirus B19 Infection without the Development of Chronic Anemia in HIV‐Infected and ‐Uninfected Children: The Women and Infants Transmission Study

We evaluated the prevalence of persistent parvovirus B19 (B19) infection and associated anemia in human immunodeficiency virus (HIV)-infected and HIV-uninfected children. B19 persistence was defined as B19 DNA detected in specimens collected >16 weeks apart. Of 182 children, 3 HIV-infected children and two HIV-uninfected children had evidence of persistent B19 infection. Of the 5 children, none had evidence of B19-associated anemia. Our data suggest that B19 infections can persist in children without the development of symptomatic anemia.

SARS surveillance during emergency public health response, United States, March-July 2003

In response to the emergence of severe acute respiratory syndrome (SARS), the United States established national surveillance using a sensitive case definition incorporating clinical, epidemiologic, and laboratory criteria. Of 1,460 unexplained respiratory illnesses reported by state and local health departments to the Centers for Disease Control and Prevention from March 17 to July 30, 2003, a total of 398 (27%) met clinical and epidemiologic SARS case criteria. Of these, 72 (18%) were probable cases with radiographic evidence of pneumonia. Eight (2%) were laboratory-confirmed SARS-coronavirus (SARS-CoV) infections, 206 (52%) were SARS-CoV negative, and 184 (46%) had undetermined SARS-CoV status because of missing convalescent-phase serum specimens. Thirty-one percent (124/398) of case-patients were hospitalized; none died. Travel was the most common epidemiologic link (329/398, 83%), and mainland China was the affected area most commonly visited. One case of possible household transmission was reported, and no laboratory-confirmed infections occurred among healthcare workers. Successes and limitations of this emergency surveillance can guide preparations for future outbreaks of SARS or respiratory diseases of unknown etiology.

SARS-associated coronavirus transmission, United States

To better assess the risk for transmission of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV), we obtained serial specimens and clinical and exposure data from seven confirmed U.S. SARS patients and their 10 household contacts. SARS-CoV was detected in a day-14 sputum specimen from one case-patient and in five stool specimens from two case-patients. In one case-patient, SARS-CoV persisted in stool for at least 26 days after symptom onset. The highest amounts of virus were in the day-14 sputum sample and a day-14 stool sample. Residual respiratory symptoms were still present in recovered SARS case-patients 2 months after illness onset. Possible transmission of SARS-CoV occurred in one household contact, but this person had also traveled to a SARS-affected area. The data suggest that SARS-CoV is not always transmitted efficiently. Routine collection and testing of stool and sputum specimens of probable SARS case-patients may help the early detection of SARS-CoV infection.

Prior airway exposure to allergen increases virus-induced airway hyperresponsiveness

BACKGROUND

Respiratory syncytial virus (RSV) bronchiolitis in early life can lead to changes in airway function, but there are likely additional predisposing factors, such as prior allergen exposure, determining which children develop wheezing and asthma.

OBJECTIVE

To define the effects of prior airway exposure to sensitizing allergen on the development of airway inflammation and hyperresponsiveness (AHR) to subsequent RSV infection.

METHODS

BALB/c mice were exposed to ovalbumin or PBS exclusively through the airways and subsequently infected with RSV or sham-inoculated. AHR, lung inflammation, and the frequency of cytokine-producing T lymphocytes in the lung were determined.

RESULTS

In PBS-exposed mice, RSV infection induced AHR and an increased proportion of TH1-type (IFN-gamma and IL-12) cytokine-producing cells in the lungs. However, in mice previously exposed to ovalbumin through the airways and subsequently infected with RSV, the degree of AHR was significantly increased and was associated with an increased proportion of TH2 (IL-4, IL-5) cytokine-producing T lymphocytes. This response was also associated with an increased accumulation of eosinophils, neutrophils, and CD8+ T cells in the lungs.

CONCLUSIONS

These data suggest that prior airway exposure to allergen may predispose sensitized hosts to a greater degree of altered airway function upon subsequent respiratory viral infection.

Viral meningitis-associated hospitalizations in the United States, 1988-1999

We used the National Hospital Discharge Survey and the Nationwide Inpatient Sample of the Health Care Cost and Utilization Project to estimate disease burden associated with viral meningitis hospitalizations in the United States. During 1988-1999, viral meningitis accounted for an estimated 434,000 hospitalizations (annual average, 36,000; average annual hospitalization rate, 14/100,000), and 2.1 million hospital days (annual average, 175,000). The estimated mean charge for viral meningitis-associated hospitalization during 1993-1997 varied between USD 6,562 and 8,313, resulting in annual estimated hospitalization costs between USD 234 and 310 million and a total estimated cost of nearly USD 1.3 billion for the 5-year period. In summary, viral meningitis remains an important cause of morbidity and financial burden and merits efforts to improve diagnostic, treatment, and prevention options.

Active surveillance for respiratory virus infections in adults who have undergone bone marrow and peripheral blood stem cell transplantation

Community-acquired respiratory virus (RV) infections are an important cause of disease in immunocompromised adults with cancer. To investigate the viral etiology, incidence, clinical presentation, and outcome of RV infections in an outpatient cohort of adult bone marrow or peripheral blood stem cell transplant (SCT) recipients, we monitored 62 outpatient volunteers from January 1 to April 30, 2001. A nasopharyngeal aspirate was collected from subjects when they reported new respiratory symptoms and tested for RV (influenza A, influenza B, human parainfluenza 1-3, adenovirus, and respiratory syncytial virus) by culture and reverse transcription polymerase chain reaction (RT-PCR) assay. Of 62 subjects enrolled, 27% had received allogeneic SCT and 45% were within 1 year of their transplant. In all, 35 participants (56%) reported 37 episodes of respiratory symptoms. Of the 37 specimens tested, five (14%) were positive for RV by culture and 20 (54%) were positive by RT-PCR. Only six patients with RV infections developed lower respiratory tract illnesses; these patients had received either autologous or allogeneic transplants and developed illnesses between 41 and 2666 days post transplant. Although RV infections were common in SCT outpatients during the RV season, most participants had upper respiratory tract infections, which resolved without the need for hospitalization.

Substantial variability in community respiratory syncytial virus season timing

BACKGROUND

Respiratory syncytial virus (RSV) is the major cause of bronchiolitis and pneumonia in young children. Prevention of RSV disease in children in certain high risk groups through use of immunoglobulin preparations has been recommended by the American Academy of Pediatrics since 1998. A more precise understanding of the timing of annual RSV epidemics should assist providers in maximizing the benefit of these preventive therapies. The objective of this study was to determine whether current national RSV surveillance data could be used to define the timing of seasonal outbreaks

METHODS

Weekly RSV testing data from the National Respiratory and Enteric Viruses Surveillance System for the period July 1990 through June 2000 were analyzed. RSV season onset week, peak week and duration were calculated for the entire United States, Census regions and select local laboratories. Season variability was estimated by comparing calculations for individual RSV seasons to median measurements for the entire surveillance period

RESULTS

RSV seasons in the South region began significantly earlier (P < 0.05) and lasted longer (P < 0.05) than seasons for the rest of the nation. RSV seasons in the Midwest region began significantly later (P < 0.01) and were shorter (P < 0.05) than those for the rest of the nation. Local RSV seasons varied substantially by year and by laboratory. The variability between laboratories generally increased with distance between laboratories

CONCLUSIONS

Onset weeks and durations of RSV seasons vary substantially by year and location. Local RSV data are needed to accurately define the onset and offset of RSV seasons and to refine timing of passive immune prophylaxis therapy recommendations.

GeneScan reverse transcription-PCR assay for detection of six common respiratory viruses in young children hospitalized with acute respiratory illness

A reverse transcription-PCR (RT-PCR) assay based on automated fluorescent capillary electrophoresis and GeneScan software analysis was developed to detect six common respiratory viruses in clinical specimens from young children. Assays for human respiratory syncytial virus (HRSV); human parainfluenza viruses 1, 2, and 3 (HPIV1, -2, and -3, respectively); and influenza A and B viruses were incorporated into a single standard assay format. The optimized assay panel was used to test 470 respiratory specimens obtained from 462 children hospitalized with acute respiratory illness that had been previously tested by viral culture (405 specimens) or direct immunofluorescence staining (DIF) (65 specimens). Of 93 specimens positive for respiratory viruses by culture or DIF, 86 (92%) were positive by RT-PCR, including 66 HRSV, 2 HPIV2, 5 HPIV3, 3 influenza A virus, and 10 influenza B virus specimens. An additional 119 respiratory viruses were identified by RT-PCR in 116 patients for whom results were negative by viral isolation or DIF. We conclude that the GeneScan RT-PCR panel can markedly improve detection of acute respiratory virus infections in young children.

Enhanced disease and pulmonary eosinophilia associated with formalin-inactivated respiratory syncytial virus vaccination are linked to G glycoprotein CX3C-CX3CR1 interaction and expression of substance P

Vaccination with formalin-inactivated respiratory syncytial virus (FI-RSV) vaccine or RSV G glycoprotein results in enhanced pulmonary disease after live RSV infection. Enhanced pulmonary disease is characterized by pulmonary eosinophilia and is associated with a substantial inflammatory response. We show that the absence of the G glycoprotein or G glycoprotein CX3C motif during FI-RSV vaccination or RSV challenge of FI-RSV-vaccinated mice, or treatment with anti-substance P or anti-CX3CR1 antibodies, reduces or eliminates enhanced pulmonary disease, modifies T-cell receptor Vbeta usage, and alters CC and CXC chemokine expression. These data suggest that the G glycoprotein, and in particular the G glycoprotein CX3C motif, is key in the enhanced inflammatory response to FI-RSV vaccination, possibly through the induction of substance P.

CD40 ligand (CD154) improves the durability of respiratory syncytial virus DNA vaccination in BALB/c mice

Respiratory syncytial virus (RSV) infection is the single most important cause of serious acute respiratory illness in children <1 year of age worldwide, and is associated with life-threatening pneumonia or bronchiolitis in the elderly. Current vaccine strategies include live, attenuated virus, subunit and DNA vaccines, however, none have been sufficiently safe, or shown to induce satisfactory long-term immunity, thus immune modulators are being considered to enhance the effectiveness of RSV vaccines. In this study, we examine CD40 ligand (CD40L) as an immune modulator to enhance the durability of DNA vaccines encoding RSV F and/or G glycoproteins in BALB/c mice. The addition of CD40L to DNA vaccines encoding the F glycoprotein enhanced virus clearance and some aspects of the immune response to RSV challenge, suggesting that CD40L may enhance the durability of RSV DNA vaccines.

The G glycoprotein of respiratory syncytial virus depresses respiratory rates through the CX3C motif and substance P

Respiratory syncytial virus (RSV) infection in the neonate can alter respiratory rates, i.e., lead to episodes of apnea. We show that RSV G glycoprotein reduces respiratory rates associated with the induction of substance P (SP) and G glycoprotein-CX3CR1 interaction, an effect that is inhibited by treatment with anti-G glycoprotein, anti-SP, or anti-CX3CR1 monoclonal antibodies. These data suggest new approaches for treating some aspects of RSV disease.

Multiple risk factors in root survivorship: a 4-year study in Concord grape

• Minirhizotron techniques were used to examine root lifespan in Vitis labruscana (Concord grape) for roots born in four different years that varied in rainfall. • Experimental vines were given irrigation (irrigated or not) and canopy pruning treatments (minimal or balanced). Root survival was assessed from 1997 through 2000 and analysed using Cox proportional hazards regression. Model covariates included pruning, irrigation, vine yield, soil depth, root diameter, time of root birth, and numbers of neighboring roots. • Soil depth, root diameter and time of birth consistently influenced root lifespan in all years (P < 0.05). Deeper and coarser roots had longer lifespans. Roots born near bloom were shorter-lived than roots born later in the season. Pruning and irrigation influenced root lifespan in some years but their effects seemed to vary with growing-season environmental conditions. • These data underscore the value of long-term studies in distinguishing factors that consistently affect root lifespan from those that change annually with environmental conditions, and emphasize the diversity in life histories of fine roots within a species.

Risk factors for bronchiolitis-associated deaths among infants in the United States

BACKGROUND

Risk factors for bronchiolitis deaths have not been described on a national level. We examined the epidemiology of and identified risk factors for bronchiolitis-associated deaths among infants in the United States.

METHODS

Multiple cause-of-death and linked birth/infant death data for 1996 through 1998 were used to examine bronchiolitis-associated infant deaths. Risk factors were assessed by comparing infants who died with bronchiolitis and surviving infants.

RESULTS

During 1996 through 1998 there were 229 bronchiolitis infant deaths, resulting in an average annual infant mortality rate of 2.0 per 100 000 live births. The majority (55%) of infant deaths occurred among infants ages 1 through 3 months. The bronchiolitis mortality rate was highest among infants weighing <1500 g at birth (VLBW) as compared with infants weighing 1500 to 2499 g (LBW) and > or =2500 g at birth (29.8, 6.4 and 1.3 per 100 000 live births, respectively). Sixty-three percent of bronchiolitis deaths were among infants weighing > or =2500 g. VLBW and LBW infants remained at an increased risk of dying with bronchiolitis after controlling for other risk factors. Other risk factors included increasing birth order, low 5-min Apgar score, young maternal age, unmarried mother and tobacco use during pregnancy.

CONCLUSIONS

VLBW and LBW infants are at increased risk of dying with bronchiolitis, even when taking into account other risk factors. Although infants weighing <2500 g at birth are at increased risk for dying with bronchiolitis, the majority of bronchiolitis deaths occur among infants of normal birth weight.

Characterization of a novel coronavirus associated with severe acute respiratory syndrome

In March 2003, a novel coronavirus (SARS-CoV) was discovered in association with cases of severe acute respiratory syndrome (SARS). The sequence of the complete genome of SARS-CoV was determined, and the initial characterization of the viral genome is presented in this report. The genome of SARS-CoV is 29,727 nucleotides in length and has 11 open reading frames, and its genome organization is similar to that of other coronaviruses. Phylogenetic analyses and sequence comparisons showed that SARS-CoV is not closely related to any of the previously characterized coronaviruses.