Crimean-Congo hemorrhagic fever in Rostov Province: the epidemiological characteristics of an outbreak

The results of the epidemiological analysis of the outbreak of hemorrhagic fever which was caused by Crimean-Congo hemorrhagic fever virus and occurred during the period of July 3-19, 1999, in the Oblivskaya district of Rostov Province are presented. The specific epidemiological features of the outbreak have been determined. The possible versions of the appearance of the focus of infection and the role of Ixodes ticks in the circulation of the infective agent are discussed.     

Draft Genome Sequences of Two Streptococcus pyogenes Strains Involved in Abnormal Sharp Raised Scarlet Fever in China, 2011

A scarlet fever outbreak caused by Streptococcus pyogenes occurred in China in 2011. To determine the genomic features of the outbreak strains, we deciphered genomes of two strains isolated from the regions with the highest incidence rates. The sequences will provide valuable information for comprehensive study of mechanisms related to this outbreak.     

Analysis of Enterovirus 68 Strains from the 2014 North American Outbreak Reveals a New Clade,Indicating Viral Evolution

Enterovirus 68 (EVD68) causes respiratory illness, mostly in children. Despite a reported low-level of transmission, the occurrence of several recent outbreaks worldwide including the 2014 outbreak in North America has raised concerns regarding the pathogenesis and evolution of EVD68. To elucidate the phylogenetic features of EVD68 and possible causes for the 2014 outbreak, 216 EVD68 strain sequences were retrieved from Genbank, including 22 from the 2014 outbreak. Several geographic and genotypic origins were established for these 22 strains, 19 of which were classified as Clade B. Of these 19 strains, 17 exhibited subsequent clustering and variation in protein residues involved in host-receptor interaction and/or viral antigenicity. Approximately 18 inter-clade variations were detected in VP1, which led to the identification of a new Clade D in EVD68 strains. The classification of this new clade was also verified by the re-construction of a Neighbor-Joining tree during the phylogenetic analysis. In addition, our results indicate that members of Clade B containing highly specific alterations in VP1 protein residues were the foremost contributors to the 2014 outbreak in the US. Altered host-receptor interaction and/or host immune recognition may explain the evolution of EVD68 as well as the global emergence and ongoing adaptation of this virus.     

Specific features of the typhoid fever epidemic process in organized collective

During the chronic water epidemic of typhoid fever in Tajikistan in 1996-1997 specific features of the epidemic process dynamics in groups of servicemen were studied in several cities. The infective agent was proved to be transmitted by the alimentary route and through everyday contacts, the water route of transmission playing the most important role. The early clinical and epidemiological signs of the water outbreak of typhoid fever and the risk factors were established. The clinical and epidemiological aspects of vaccination were analyzed.     

新型冠状病毒感染与复制的进展

冠状病毒是一类具有囊膜包裹的线性单股正链RNA病毒,在自然界广泛存在,可引起不同程度的呼吸性传染病。新型冠状病毒是一种新发突发病毒,对各类人群均易感。截止目前,该病已经在世界范围内广泛流行,对公共卫生安全构成极大的威胁。文中从冠状病毒及新型冠状病毒的基因组特征、关键蛋白、对宿主的感染和复制的角度加以综述,旨在为获得病毒侵染宿主细胞致病机制的探究提供理论依据,也为特异的抗病毒药物的研发提供基础支持。     

Outbreak of coagulase negative staphylococcus highly resistant to ciprofloxacin in a leukaemia unit.

OBJECTIVE--To define an outbreak of bacteraemia due to coagulase negative staphylococci highly resistant to ciprofloxacin in a leukaemia unit, investigate the source and mode of spread of the outbreak strain, and assess control measures. DESIGN--The outbreak strain was characterised by five different typing methods. Surveillance of patients, staff, and environment was carried out during the outbreak and five months after control measures were introduced. SETTING--A unit with 10 beds for adults with leukaemia and patients receiving bone marrow transplants. The outbreak occurred during a trial of ciprofloxacin for empirical treatment of neutropenic fevers. INTERVENTIONS--Ciprofloxacin was withdrawn from use in the unit and daily bathing with chlorhexidine gluconate solution started. Main outcome measure--The absence of bacteraemia due to the outbreak strain for five months after control measures. RESULTS--During the study 49 patients developed 21 episodes of bacteraemia due to the outbreak strain, which was ciprofloxacin resistant (minimum inhibitory concentration greater than or equal to 128 mg/l), susceptible to phage 155 A9C, and SII biotype and had characteristic immunoblot and DNA fingerprint features. There was a high amount of colonisation of patients but not staff with this strain, which was also wide spread in the environment. The control measures led to rapid resolution of the outbreak and disappearance of the strain from the unit. CONCLUSIONS--In areas where coagulase negative staphylococcal infections are common doctors must be aware of the possibility of cross infection with single strain, and the availability of more discriminatory methods of typing will facilitate the identification and control of such episodes.     

Impact of quarantine on the 2003 SARS outbreak: a retrospective modeling study

During the 2003 Severe Acute Respiratory Syndrome (SARS) outbreak, traditional intervention measures such as quarantine and border control were found to be useful in containing the outbreak. We used laboratory verified SARS case data and the detailed quarantine data in Taiwan, where over 150,000 people were quarantined during the 2003 outbreak, to formulate a mathematical model which incorporates Level A quarantine (of potentially exposed contacts of suspected SARS patients) and Level B quarantine (of travelers arriving at borders from SARS affected areas) implemented in Taiwan during the outbreak. We obtain the average case fatality ratio and the daily quarantine rate for the Taiwan outbreak. Model simulations is utilized to show that Level A quarantine prevented approximately 461 additional SARS cases and 62 additional deaths, while the effect of Level B quarantine was comparatively minor, yielding only around 5% reduction of cases and deaths. The combined impact of the two levels of quarantine had reduced the case number and deaths by almost a half. The results demonstrate how modeling can be useful in qualitative evaluation of the impact of traditional intervention measures for newly emerging infectious diseases outbreak when there is inadequate information on the characteristics and clinical features of the new disease-measures which could become particularly important with the looming threat of global flu pandemic possibly caused by a novel mutating flu strain, including that of avian variety.     

Outbreak of Campbell de Morgan Spots

An outbreak of small angiomatous lesions with the same clinical and histological features as Campbell de Morgan spots in adults is described. No infective agent was discovered, but their number was found to increase as the ambient temperature rose.     

Ebolavirus Evolution: Past and Present

The past year has marked the most devastating Ebola outbreak the world has ever witnessed, with over 28,000 cases and over 11,000 deaths. Ebola virus (EBOV) has now been around for almost 50 years. In this review, we discuss past and present outbreaks of EBOV and how those variants evolved over time. We explore and discuss selective pressures that drive the evolution of different Ebola variants, and how they may modify the efficacy of therapeutic treatments and vaccines currently being developed. Finally, given the unprecedented size and spread of the outbreak, as well as the extended period of replication in human hosts, specific attention is given to the 2014–2015 West African outbreak variant (Makona).     

Molecular pathogenesis of severe acute respiratory syndrome

The global outbreak in 2002-2003 of severe acute respiratory syndrome (SARS) posed a serious threat to public health and had a significant impact on socioeconomic stability. Although the global outbreak of SARS has been contained, there are serious concerns over its re-emergence and bioterrorism potential, and up to date, no specific treatment exists for this disease. Here we review the progress of studies on the pathogenesis of the disease, in particular, studies on the molecular level.     

Relationships between change in fire frequency and mortality due to spruce budworm outbreak in the southeastern Canadian boreal forest

Abstract. We present a simple empirical model that allows an estimation of mortality due to spruce budworm (Choristoneura fumiferana) outbreak in relation to fire frequency and site characteristics. The occurrence of a recent spruce budworm outbreak around Lake Duparquet (48° 30’N, 79° 20’W, ca. 300 m a.s.l.) in northwestern Québec permitted a reconstruction of the stand composition before the outbreak, and also of the mortality of Abies balsamea due to the outbreak. The basal area of A. balsamea increases with time since fire in all site types but with increasing values for (1) rock and shallow till, via (2) till and mesic clay up to (3) hydric clay. Mortality (measured as percentage loss of basal area due to the outbreak) increases with time since fire but did not vary with site type. The increasing abundance of A. balsamea with time since fire is mainly responsible for this increase in mortality. Mortality for a specific basal area is, however, lower for the more recently burned stands suggesting a significant residual effect of time since fire. A landscape model integrating mortality due to the outbreak for stands of different age is developed. Both absolute and relative losses of basal area increased with the length of the fire cycles. According to this model, changes in fire cycle could explain a large portion of the spatio-temporal variations observed in outbreak mortality in the southeastern boreal forest of Canada.     

An epidemiological model for West Nile virus: invasion analysis and control applications

Infectious diseases present ecological and public health challenges that can be addressed with mathematical models. Certain pathogens, however, including the emerging West Nile virus (WN) in North America, exhibit a complex seasonal ecology that is not readily analysed with standard epidemiological methods. We develop a single-season susceptible-infectious-removed (SIR) model of WN cross-infection between birds and mosquitoes, incorporating specific features unique to WN ecology. We obtain the disease reproduction number, R0, and show that mosquito control decreases, but bird control increases, the chance of an outbreak. We provide a simple new analytical and graphical method for determining, from standard public health indicators, necessary mosquito control levels. We extend this method to a seasonally variable mosquito population and outline a multi-year model framework. The model's numerical simulations predict disease levels that are consistent with independent data.     

Early onset of neurological features differentiates two outbreaks of Lassa fever in Ebonyi state,Nigeria during 2017–2018

Lassa fever (LF) is an acute viral haemorrhagic illness with various non-specific clinical manifestations. Neurological symptoms are rare at the early stage of the disease, but may be seen in late stages, in severely ill patients.The aim of this study was to describe the epidemiological evolution, socio-demographic profiles, clinical characteristics, and outcomes of patients seen during two Lassa fever outbreaks in Ebonyi State, between December 2017 and December 2018.Routinely collected clinical data from all patients admitted to the Virology Centre of the hospital during the period were analysed retrospectively. Out of a total of 83 cases, 70(84.3%) were RT-PCR confirmed while 13 (15.7%) were probable cases. Sixty-nine (83.1%) patients were seen in outbreak 1 of whom 53.6% were urban residents, while 19%, 15%, and 10% were farmers, students and health workers respectively. There were 14 (16.8%) patients, seen in second outbreak with 92.9% rural residents. There were differences in clinical symptoms, signs and laboratory findings between the two outbreaks. The case fatality rates were 29.9% in outbreak 1 and 85.7% for outbreak 2. Neurological features and abnormal laboratory test results were associated with higher mortality rate, seen in outbreak 2. This study revealed significant differences between the two outbreaks. Of particular concern was the higher case fatality during the outbreak 2 which may be from a more virulent strain of the Lassa virus. This has important public health implications and further molecular studies are needed to better define its characteristics.     

Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2

Human angiotensin-converting enzyme 2 (ACE2) is a functional receptor for SARS coronavirus (SARS-CoV). Here we identify the SARS-CoV spike (S)-protein-binding site on ACE2. We also compare S proteins of SARS-CoV isolated during the 2002-2003 SARS outbreak and during the much less severe 2003-2004 outbreak, and from palm civets, a possible source of SARS-CoV found in humans. All three S proteins bound to and utilized palm-civet ACE2 efficiently, but the latter two S proteins utilized human ACE2 markedly less efficiently than did the S protein obtained during the earlier human outbreak. The lower affinity of these S proteins could be complemented by altering specific residues within the S-protein-binding site of human ACE2 to those of civet ACE2, or by altering S-protein residues 479 and 487 to residues conserved during the 2002-2003 outbreak. Collectively, these data describe molecular interactions important to the adaptation of SARS-CoV to human cells, and provide insight into the severity of the 2002-2003 SARS epidemic.     

Advances in diagnostics,vaccines and therapeutics for Nipah virus

Nipah virus is an emerging zoonotic paramyxovirus that causes severe and often fatal respiratory and neurological disease in humans. The virus was first discovered after an outbreak of encephalitis in pig farmers in Malaysia and Singapore with subsequent outbreaks in Bangladesh or India occurring almost annually. Due to the highly pathogenic nature of NiV, its pandemic potential, and the lack of licensed vaccines or therapeutics, there is a requirement for research and development into highly sensitive and specific diagnostic tools as well as antivirals and vaccines to help prevent and control future outbreak situations.     

Genomic Characterization of Listeria monocytogenes Strains Involved in a Multistate Listeriosis Outbreak Associated with Cantaloupe in US

A multistate listeriosis outbreak associated with cantaloupe consumption was reported in the United States in September, 2011. The outbreak investigation recorded a total of 146 invasive illnesses, 30 deaths and one miscarriage. Subtyping of the outbreak associated clinical, food and environmental isolates revealed two serotypes (1/2a and 1/2b) and four pulsed-field gel electrophoresis two-enzyme pattern combinations I, II, III, and IV, including one rarely seen before this outbreak. A DNA-microarray, Listeria GeneChip®, developed by FDA from 24 Listeria monocytogenes genome sequences, was used to further characterize a representative sample of the outbreak isolates. The microarray data (in the form of present or absent calls of specific DNA sequences) separated the isolates into two distinct groups as per their serotypes. The gene content of the outbreak-associated isolates was distinct from that of the previously-reported outbreak strains belonging to the same serotypes. Although the 1/2b outbreak associated isolates are closely related to each other, the 1/2a isolates could be further divided into two distinct genomic groups, one represented by pattern combination I strains and the other represented by highly similar pattern combinations III and IV strains. Gene content analysis of these groups revealed unique genomic sequences associated with these two 1/2a genovars. This work underscores the utility of multiple approaches, such as serotyping, PFGE and DNA microarray analysis to characterize the composition of complex polyclonal listeriosis outbreaks.     

The First Outbreak of Eastern Equine Encephalitis in Vermont: Outbreak Description and Phylogenetic Relationships of the Virus Isolate

The first known outbreak of eastern equine encephalitis (EEE) in Vermont occurred on an emu farm in Rutland County in 2011. The first isolation of EEE virus (EEEV) in Vermont (VT11) was during this outbreak. Phylogenetic analysis revealed that VT11 was most closely related to FL01, a strain from Florida isolated in 2001, which is both geographically and temporally distinct from VT11. EEEV RNA was not detected in any of the 3,905 mosquito specimens tested, and the specific vectors associated with this outbreak are undetermined.     

鹅圆环病毒浙江永康株全基因组的克隆及序列分析

为研究水禽流感大规模爆发的机理,进行了水禽流感病例中并发病原,特别是免疫抑制性病原的检测研究。根据已发表的鹅圆环病毒(Goosecircovirus,GoCV)序列,设计了一对检测引物,对浙江永康禽流感病死鹅样品进行PCR扩增,获得与预期552bp大小相符的DNA片段,经测序确认为GoCV特异序列,推测样品中存在GoCV。根据测定的序列进一步设计反向扩增引物,经扩增、测序、拼接后获得GoCV全长基因组序列。基因组序列分析表明,浙江永康株GoCV_yk01全长1821bp,具有圆环病毒共同的与病毒复制相关的茎环结构和Rep蛋白保守基序等特征,它与德国、中国台湾发表的序列在全基因组水平有91%～93%的同源性,在Rep和外壳蛋白的氨基酸水平有94%～97%的同源性。应用ClustalW方法作进化树分析显示,GoCV_yk01序列与德国株及中国台湾株均不在同一分支。圆环病毒可以感染淋巴细胞等增殖快的细胞,引起免疫抑制,从而造成其他病原的并发和继发感染,怀疑GoCV可能在2004年初永康爆发的鹅流感中起到了一定的协同作用。该GoCV_yk01是中国内地首次检测确认并测定全基因组序列的鹅圆环病毒。     

Zika virus infection: an update

Since the ZIKV outbreak in Brazil in 2015, the scientific community has joined efforts to gather more information on the epidemiology, clinical features and pathogenicity of the virus. Here, we summarize the most important advances made recently and discuss promising, innovative approaches to understand and control ZIKV infection.     

Comparative Genomic Analysis of Two Novel Sporadic Shiga Toxin-Producing Escherichia coli O104:H4 Strains Isolated 2011 in Germany

A large outbreak of gastrointestinal disease occurred in 2011 in Germany which resulted in almost 4000 patients with acute gastroenteritis or hemorrhagic colitis, 855 cases of a hemolytic uremic syndrome and 53 deaths. The pathogen was an uncommon, multiresistant Escherichia coli strain of serotype O104:H4 which expressed a Shiga toxin characteristic of enterohemorrhagic E. coli and in addition virulence factors common to enteroaggregative E. coli. During post-epidemic surveillance of Shiga toxin-producing E. coli (STEC) all but two of O104:H4 isolates were indistinguishable from the epidemic strain. Here we describe two novel STEC O104:H4 strains isolated in close spatiotemporal proximity to the outbreak which show a virulence gene panel, a Shiga toxin-mediated cytotoxicity towards Vero cells and aggregative adherence to Hep-2 cells comparable to the outbreak strain. They differ however both from the epidemic strain and from each other, by their antibiotic resistance phenotypes and some other features as determined by routine epidemiological subtyping methods. Whole genome sequencing of these two strains, of ten outbreak strain isolates originating from different time points of the outbreak and of one historical sporadic EHEC O104:H4 isolate was performed. Sequence analysis revealed a clear phylogenetic distance between the two variant strains and the outbreak strain finally identifying them as epidemiologically unrelated isolates from sporadic cases. These findings add to the knowledge about this emerging pathogen, illustrating a certain diversity within the bacterial core genome as well as loss and gain of accessory elements. Our results do also support the view that distinct new variants of STEC O104:H4 repeatedly might originate from yet unknown reservoirs, rather than that there would be a continuous diversification of a single epidemic strain established and circulating in Germany after the large outbreak in 2011.