Bats and their virome: an important source of emerging viruses capable of infecting humans

Bats are being increasingly recognized as an important reservoir of zoonotic viruses of different families, including SARS coronavirus, Nipah virus, Hendra virus and Ebola virus. Several recent studies hypothesized that bats, an ancient group of flying mammals, are the major reservoir of several important RNA virus families from which other mammalian viruses of livestock and humans were derived. Although this hypothesis needs further investigation, the premise that bats carry a large number of viruses is commonly accepted. The question of whether bats have unique biological features making them ideal reservoir hosts has been the subject of several recent reviews. In this review, we will focus on the public health implications of bat derived zoonotic viral disease outbreaks, examine the drivers and risk factors of past disease outbreaks and outline research directions for better control of future disease events.

Severe acute respiratory syndrome (SARS) and the rhetorical construction of "bad" scientific work

How are secondary accounts of "bad" scientific practice constructed? How do they engage with the primary data produced by "bad" scientists? And what happens to those primary data as generations of secondary accounts purporting to describe them accumulate? This paper addresses such questions via a case study of Dr. Hong, a microbiologist accused of "bad" scientific practice by numerous secondary accounts of the 2003 SARS outbreak. Bringing Hong's own account of his own actions into dialogue with one of the most influential secondary accounts of his actions, the paper highlights the gross disparity between the two. Having argued that the rhetorical structuring of the secondary account is, ultimately, responsible for Hong's characterisation as a "bad" scientist, it then moves to explore how subsequent accounts developed their own characterisations. What becomes clear is that as secondary accounts began feeding off one another, references to Hong's account disappeared. Aided by the concepts of the "vanishing" and the "phantasm", the paper concludes with a consideration of how this process left Hong's work with a very peculiar form of existence.

Wild animal surveillance for coronavirus HKU1 and potential variants of other coronaviruses

1. Although CoV-HKU1 was not identified in any of the studied animals, a coronavirus closely related to SARS-CoV (bat-SARS-CoV) was identified in 23 (19%) of 118 wild Chinese horseshoe bats by reverse transcriptase polymerase chain reaction (RT-PCR). 2. Complete genome sequencing and phylogenetic analysis showed that bat-SARS-CoV formed a distinct cluster with SARS-CoV as group 2b coronaviruses, distantly related to known group 2 coronaviruses. 3. Most differences between the bat-SARS-CoV and SARS-CoV genomes were observed in the spike gene. The presence of a29-bp insertion in ORF 8 of bat-SARS-CoV genome, not in most human SARS-CoV genomes, suggests that it has a common ancestor with civet SARS-CoV. 4. Antibody against recombinant bat-SARS-CoV nucleocapsid protein was detected in 84% of Chinese horseshoe bats using an enzyme immunoassay.Neutralising antibody to human SARS-CoV was also detected in those with lower viral loads.5. This study also revealed a previously unknown diversity of coronaviruses in bats, which are important natural reservoir for coronaviruses including SARS-CoV-like viruses.

Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review

Aerosol generating procedures (AGPs) may expose health care workers (HCWs) to pathogens causing acute respiratory infections (ARIs), but the risk of transmission of ARIs from AGPs is not fully known. We sought to determine the clinical evidence for the risk of transmission of ARIs to HCWs caring for patients undergoing AGPs compared with the risk of transmission to HCWs caring for patients not undergoing AGPs. We searched PubMed, EMBASE, MEDLINE, CINAHL, the Cochrane Library, University of York CRD databases, EuroScan, LILACS, Indian Medlars, Index Medicus for SE Asia, international health technology agencies and the Internet in all languages for articles from 01/01/1990 to 22/10/2010. Independent reviewers screened abstracts using pre-defined criteria, obtained full-text articles, selected relevant studies, and abstracted data. Disagreements were resolved by consensus. The outcome of interest was risk of ARI transmission. The quality of evidence was rated using the GRADE system. We identified 5 case-control and 5 retrospective cohort studies which evaluated transmission of SARS to HCWs. Procedures reported to present an increased risk of transmission included [n; pooled OR(95%CI)] tracheal intubation [n = 4 cohort; 6.6 (2.3, 18.9), and n = 4 case-control; 6.6 (4.1, 10.6)], non-invasive ventilation [n = 2 cohort; OR 3.1(1.4, 6.8)], tracheotomy [n = 1 case-control; 4.2 (1.5, 11.5)] and manual ventilation before intubation [n = 1 cohort; OR 2.8 (1.3, 6.4)]. Other intubation associated procedures, endotracheal aspiration, suction of body fluids, bronchoscopy, nebulizer treatment, administration of O2, high flow O2, manipulation of O2 mask or BiPAP mask, defibrillation, chest compressions, insertion of nasogastric tube, and collection of sputum were not significant. Our findings suggest that some procedures potentially capable of generating aerosols have been associated with increased risk of SARS transmission to HCWs or were a risk factor for transmission, with the most consistent association across multiple studies identified with tracheal intubation.

SARS-Coronavirus ancestor's foot-prints in South-East Asian bat colonies and the refuge theory

One of the great challenges in the ecology of infectious diseases is to understand what drives the emergence of new pathogens including the relationship between viruses and their hosts. In the case of the emergence of SevereAcute Respiratory Syndrome Coronavirus (SARS-CoV), several studies have shown coronavirus diversity in bats as well as the existence of SARS-CoV infection in apparently healthy bats, suggesting that bats may be a crucial host in the genesis of this disease. To elucidate the biogeographic origin of SARS-CoV and investigate the role that bats played in its emergence, we amplified coronavirus sequences from bat species captured throughout Thailand and assessed the phylogenetic relationships to each other and to other published coronavirus sequences. To this end, RdRp sequence of Coronavirinae was targeted by RT-PCR in non-invasive samples from bats collected in Thailand. Two new coronaviruses were detected in two bat species: one Betacoronavirus in Hipposideros larvatus and one Alphacoronavirus in Hipposiderosarmiger. Interestingly, these viruses from South-East Asia are related to those previously detected in Africa (Betacoronavirus-b) or in Europe (Alphacoronavirus & Betacoronavirus-b). These findings illuminate the origin and the evolutionary history of the SARS-CoV group found in bats by pushing forward the hypothesis of a Betacoronavirus spill-over from Hipposideridae to Rhinolophidae and then from Rhinolophidae to civets and Human. All reported Betacoronaviruses-b (SARS-CoV group) of Hipposideridae and Rhinolophidae respectively cluster in two groups despite their broad geographic distribution and the sympatry of their hosts, which is in favor of an ancient and genetically independent evolution of Betacoronavirus-b clusters in these families. Moreover, despite its probable pathogenicity, we found that a Betacoronavirus-b can persistently infect a medium-sized hipposiderid bat colony. These findings illustrate the importance of the host phylogeny and the host/pathogen ecological interactions in the description and the understanding of pathogen emergence. The host's phylogeny, biogeography and behaviour, combined with already described roles of pathogen plasticity and anthropic changes are likely to be co-factors of disease emergence. Elucidating the common ancestor of Hipposideridae and Rhinolophidae is key to understanding the evolutionary history of actual betacoronaviruses and therefore to get an insight of the deep origin of SARS-CoV.

A cost-based comparison of quarantine strategies for new emerging diseases

A classical epidemiological framework is used to provide a preliminary cost analysis of the effects of quarantine and isolation on the dynamics of infectious diseases for which no treatment or immediate diagnosis tools are available. Within this framework we consider the cost incurred from the implementation of three types of dynamic control strategies. Taking the context of the 2003 SARS outbreak in Hong Kong as an example, we use a simple cost function to compare the total cost of each mixed (quarantine and isolation) control strategy from a public health resource allocation perspective. The goal is to extend existing epi-economics methodology by developing a theoretical framework of dynamic quarantine strategies aimed at emerging diseases, by drawing upon the large body of literature on the dynamics of infectious diseases. We find that the total cost decreases with increases in the quarantine rates past a critical value, regardless of the resource allocation strategy. In the case of a manageable outbreak resources must be used early to achieve the best results whereas in case of an unmanageable outbreak, a constant-effort strategy seems the best among our limited plausible sets.

Epidemiology of SARS in the 2003 Hong Kong epidemic

1. The temporal and spatial evolution of the SARS epidemic in Hong Kong is described. 2. Estimates of key epidemiological distributions and their stability over the course of the epidemic are derived. 3. The characteristics of those who contracted the disease are determined including factors associated with the likelihood of mortality as a result of SARS coronavirus infection.

Viral loads in clinical specimens and SARS manifestations

1. A high viral load in nasopharyngeal aspirate (with or without a high viral load in serum) is a useful prognostic indicator of respiratory failure or mortality. The presence of viral RNA in multiple body sites is also indicative of poor prognosis. 2. Early treatment with an effective antiviral agent before day 10 may decrease the peak viral load, and thus ameliorate the clinical symptoms and mortality, and reduce viral shedding and the risk of transmission

Label-free, electrical detection of the SARS virus N-protein with nanowire biosensors utilizing antibody mimics as capture probes

Antibody mimic proteins (AMPs) are polypeptides that bind to their target analytes with high affinity and specificity, just like conventional antibodies, but are much smaller in size (2-5 nm, less than 10 kDa). In this report, we describe the first application of AMP in the field of nanobiosensors. In(2)O(3) nanowire based biosensors have been configured with an AMP (Fibronectin, Fn) to detect nucleocapsid (N) protein, a biomarker for severe acute respiratory syndrome (SARS). Using these devices, N protein was detected at subnanomolar concentration in the presence of 44 microM bovine serum albumin as a background. Furthermore, the binding constant of the AMP to Fn was determined from the concentration dependence of the response of our biosensors.

Polymorphism of SARS-CoV genomes

In this work, severe acute respiratory syndrome associated coronavirus (SARS-CoV) genome BJ202 (AY864806) was completely sequenced. The genome was directly accessed from the stool sample of a patient in Beijing. Comparative genomics methods were used to analyze the sequence variations of 116 SARS-CoV genomes (including BJ202) available in the NCBI Gen-Bank. With the genome sequence of GZ02 as the reference, there were 41 polymorphic sites identified in BJ202 and a total of 278 polymorphic sites present in at least two of the 116 genomes. The distribution of the polymorphic sites was biased over the whole genome. Nearly half of the variations (50.4%, 140/278) clustered in the one third of the whole genome at the 3′ end (19.0 kb-29.7 kb). Regions encoding Orf10–11, Orf3/4, E, M and S protein had the highest mutation rates. A total of 15 PCR products (about 6.0 kb of the genome) including 11 fragments containing 12 known polymorphic sites and 4 fragments without identified polymorphic sites were cloned and sequenced. Results showed that 3 unique polymorphic sites of BJ202 (positions 13 804, 15 031 and 20 792) along with 3 other polymorphic sites (26 428, 26 477 and 27 243) all contained 2 kinds of nucleotides. It is interesting to find that position 18379 which has not been identified to be polymorphic in any of the other 115 published SARS-CoV genomes is actually a polymorphic site. The nucleotide composition of this site is A (8) to G (6). Among 116 SARS-CoV genomes, 18 types of deletions and 2 insertions were identified. Most of them were related to a 300 bp region (27 700–28 000) which encodes parts of the putative ORF9 and ORF10–11. A phylogenetic tree illustrating the divergence of whole BJ202 genome from 115 other completely sequenced SARS-CoVs was also constructed. BJ202 was phylogeneticly closer to BJ01 and LLJ-2004.

Public health implications of using various case definitions in The Netherlands during the worldwide SARS outbreak

This study analysed the consequences of deviation from the WHO case definition for the assessment of patients with suspected severe acute respiratory syndrome (SARS) in The Netherlands during 2003. Between 17 March and 7 July 2003, as a result of dilemmas in balancing sensitivity and specificity, five different case definitions were used. The patients referred for SARS assessment were analysed from a public health perspective. None of the patients referred had SARS, based on serological and virological criteria. Nevertheless, all 72 patients required thorough assessment and, depending on the results of the assessment, institution of appropriate prevention and control measures. Changing case definitions caused confusion in classifying cases. A centralised assessment of the reported cases by a team with clinical and public health expertise (epidemiological and geographical risk assessment) is a practical solution for addressing differences in applying case definitions. The burden of managing non‐cases is an important issue when allocating public health resources, and should be taken into account during the preparation phase, rather than during an outbreak. This applies not only to SARS, but also to other public health threats, such as pandemic influenza or a bioterrorist episode.