Re: Vietnam: New virus isolated from patients with severe brain infections
Re: Vietnam: New virus isolated from patients with severe brain infections
Wow.
Published Date: 2013-06-24 13:52:47
Subject: PRO/AH/EDR> Circovirus - Viet Nam, Malawi: human, cerebrospinal fluid
Archive Number: 20130624.1789227
CIRCOVIRUS - VIET NAM MALAWI: HUMAN, CEREBROSPINAL FLUID
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In this posting:
[1] Viet Nam, Malawi: Science journal
[2] Malawi: Emerging Infectious Diseases journal
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[1] Viet Nam, Malawi: Science journal
Date: Thu 20 Jun 2013
Source: Science Now, American Association for the Advancement of Science (AAAS) [edited]
http://news.sciencemag.org/sciencenow/2013/06/new-viruses-found-in-asia-and-af.html
New viruses found in Asia and Africa tentatively linked to neurological disease
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[Authors: Mara Hvistendahl, Martin Enserink]
A mysterious group of viruses known for their circular genome [the family _Circoviridae_] has been detected in patients with severe disease on 2 continents. In papers published independently this week [week of 20 Jun 2013], researchers report the discovery of agents called cycloviruses in Viet Nam and in Malawi. The studies suggest that the viruses -- one of which also widely circulates in animals in Viet Nam -- could be involved in brain inflammation and paraplegia, but further studies are needed to confirm a causative link.
The discovery in Viet Nam grew out of a frustrating lack of information about the causes of some central nervous system (CNS) infections such as encephalitis and meningitis, which can be fatal or leave lasting damage. "There are a lot of severe cases in the hospitals here, and very often we can't come to a diagnosis," says H Rogier van Doorn, a clinical virologist with the Oxford University Clinical Research Unit in the Hospital for Tropical Diseases, Ho Chi Minh City. Extensive diagnostic tests turn up pathogens in only about half of patients with such infections, he says. Van Doorn and colleagues in Viet Nam and at the University of Amsterdam's Academic Medical Center hoped that they might uncover new pathogens using a powerful new technique called next-generation sequencing. The group sequenced all the genetic material in cerebrospinal fluid (CSF) samples taken from more than 100 patients with undiagnosed CNS infections. One sample batch returned a promising lead: a viral sequence belonging to the family _Circoviridae_.
Probing the original patient samples, the scientists ferreted out the sequence in 2 of the samples-one from an adult and one from a child. Next, they expanded their search, testing samples from an additional 642 patients with CNS infections using a sensitive polymerase chain reaction (PCR) test developed to specifically target the detected sequence. Roughly 4 percent of the samples tested positive, the team reported in mBio on Tuesday [18 Jun 2013; see ProMED-post Circovirus - Viet Nam: acute CNS infection 20130618.1780170]. Whole-genome sequencing confirmed that the virus, which the scientists have dubbed CyCV-VN, for cyclovirus-Viet Nam, is novel; it belongs to a genus within the family _Circoviridae_, the guns _Cyclovirus_.
Meanwhile, a team at Erasmus MC in Rotterdam, the Netherlands, had been trying to determine what causes paraplegia in some patients in Malawi, in southeast Africa. It's well known that trauma and some infections can cause people to lose control over their legs, but in many cases, doctors can't find a cause. The Dutch team hunted for viruses in blood serum and CSF samples from 12 patients who had suddenly become paraplegic in 2010 and 2011. They found a new cyclovirus as well; when they tested for the virus in a broader group of 58 paraplegia patients, they found it in 15 percent of 54 serum samples and 10 percent of 40 CSF samples, the team reports in a paper published online this week in Emerging Infectious Diseases [see part [2] below].
Cycloviruses were 1st discovered in 2009-along with a host of other viruses-in fecal samples from South-Asian children suffering from acute flaccid paralysis, by a team led by Eric Delwart of the Blood Systems Research Institute in San Francisco. Since then, they have also been found in human fecal samples from Nigeria and Tunisia, as well as in farm animals, chimpanzees, bats, cockroaches, and dragonflies. While the new viruses are related, says Le Van Tan, a researcher at the Oxford University Clinical Research Unit and the 1st author on the Viet Nam paper, initial comparisons of the genomes suggest that they form 2 new [virus] species. Neither of the studies proves that the viruses cause disease, however, says Delwart, who was not involved in the new papers. In the Malawi study, researchers did not include a control group, so they don't know if healthy people carry the virus as well; in the Viet Nam study, samples taken from a control group of 122 patients with noninfectious CNS conditions tested negative for the new virus. Still, other factors might explain that, Delwart says. It's possible, Delwart says, that these viruses aggravate existing disease; 16 of the 26 people who carried the cyclovirus in the Viet Nam study also had a lab-confirmed infection with another pathogen, such as Japanese encephalitis or dengue. "It may be: one virus, bad; 2 viruses, worse," he says.
Van Doorn says that the team is wary of speculating until more is known about CyCV-VN; the team is sharing its results "with the public and the scientific world so that more research can be initiated," he says. To find out if the new viruses actually cause disease, researchers can try to grow them in cell culture and infect animals with them. Another critical task is to cast a wider net using a PCR test that can pick up related cycloviruses as well as CyCV-VN, Van Doorn says-which could help determine how entrenched cycloviruses are in the population. The Rotterdam group is also planning to look for the virus more broadly, says Saskia Smits, the 1st author on the paper.
The Viet Nam study shed some light on how people may pick up the virus. Because other [members of the family] _Circoviridae _ are known animal pathogens, testing chickens, ducks, and pigs for CyCV-VN was the "obvious next step," Van Doorn says. The scientists checked fecal swabs taken from dozens of animals in Dong Thap province and found what the virologist calls "remarkably high" incidence of the virus: Nearly 60 percent of the animal samples tested positive. Moreover, the animal strains of CyCV-VN showed a 98 percent similarity to those isolated from humans. Because chickens, ducks, and pigs are "commonly held in Viet Nam in backyards and on small farms," Van Doorn says, "there is a lot of possible contact between these viruses and humans."
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[2] Malawi: Emerging Infectious Diseases journal
Date: Mon 24 Jun 2013
Source: Emerging Infectious Diseases journal [summ., edited]
http://wwwnc.cdc.gov/eid/article/19/9/13-0404_article.htm
[Ref: Smits SL, Zijlstra EE, van Hellemond JJ, et al: Novel cyclovirus in human cerebrospinal fluid, Malawi, 2010-2011. Emerg Infect Dis 2013, 19(9) DOI: 10.3201/eid1909.130404]
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Abstract
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To identify unknown human viruses, we analyzed serum and cerebrospinal fluid samples from patients with unexplained paraplegia from Malawi by using viral metagenomics. A novel cyclovirus species was identified and subsequently found in 15 percent and 10 percent of serum and cerebrospinal fluid samples, respectively. These data expand our knowledge of cyclovirus diversity and tropism.
The list of diseases caused by viral pathogens is ever changing and growing. Breakthroughs in the field of metagenomics had far-reaching effects on the identification of emerging viral pathogens and on the recognition that an increasing number of diseases that were once attributed to unknown causes are actually caused by infectious agents. Paraplegia is an impairment of motor or sensory functions of the lower extremities. Although it can be caused by spinal cord injury, nontraumatic paraplegia also should be considered, particularly in a tropical environment; tuberculosis and schistosomiasis may play a role, but in many cases, no firm diagnosis can be made. In this study, cerebrospinal fluid (CSF) and serum samples were obtained from 58 patients from Malawi who had paraplegia of unknown etiology and were studied for the presence of known or unknown viruses by using a metagenomics approach.
The Study
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During 2010-2011, we enrolled 58 adults who sought care at Queen Elizabeth Central Hospital in Blantyre, Malawi, for unexplained paraplegia in this study. All procedures were performed in compliance with relevant laws and institutional guidelines. The study was approved by the College of Medicine Research and Ethics Committee.
[Interested readers should access the original text at the URL above to obtain a comprehensive account of the methods, the data generated and the references sited. - Mod.CP]
A cyclovirus genome was obtained by Roche 454-sequencing from serum of patient VS5700009. Cycloviruses (family _Circoviridae_, genus _Cyclovirus_) have been detected in human and chimpanzee feces and tissues of farm animals, bats, and dragonflies. They are non-enveloped viruses with a single-stranded circular DNA genome of approximately 2 kb. The genome contains 2 major inversely arranged open reading frames (ORFs) encoding the putative replication-associated protein (Rep) and capsid protein (Cap). A potential stem-loop structure with a conserved nonanucleotide motif located between the 5'-ends of these 2 ORFs is required to initiate the replication of the viral genome. The genome organization of human cyclovirus VS5700009 (GenBank accession no. KC771281) resembles that of human cycloviruses TN18 and TN25. The Rep ORF of human cyclovirus VS5700009 was interrupted by a 96-bp intron with a splice donor site (GT) and splice acceptor site (AG). The 3' intergenic region between the Rep and Cap ORFs was only 7 bp long. The cyclovirus stem-loop structure with the conserved nonamer sequence (5'-TAATACTAT-3') in the 5' intergenic region was observed, as were 3 other potential ORFs. These latter ORFs are not conserved among cycloviruses and show low partial homology to bacterial enzymes, Phylogenetic analyses were conducted with MEGA5 [molecular evolutionary genetics analysis version 5]. The human cyclovirus VS5700009 Rep protein was most closely related to the Rep proteins of human cycloviruses TN18 and TN25 (approximately 75 percent aa identity). Similar relations, but with much lower amino acid identities, were observed in Cap proteins (approximately 37 percent identity; data not shown). Cycloviruses belong to the same species when sharing more than 85 percent aa identity in the Rep region.
It was concluded that human cyclovirus VS5700009 represents a new cyclovirus species. Most of the closest relatives of human cyclovirus VS5700009 (which include TN18 and TN25) detected in feces from children with non polio acute flaccid paralysis, a condition related to paraplegia, which may indicate that TN25/VS5700009-like viruses may be more pathogenic than other cycloviruses
To determine the prevalence of human cyclovirus VS5700009 in the serum and CSF samples of the 58 patients, a VS5700009-specific PCR was performed. 8 (15 percent) of 54 serum samples and 4 (10 percent) of 40 CSF samples from paraplegia patients were human cyclovirus positive. For several amplicons, the cyclovirus nature was confirmed by Sanger sequencing, and the amplicons showed 75 percent-99 percent identity to human cyclovirus VS5700009. Only in patient VS5700009 were both CSF and serum samples positive for human cyclovirus.
Conclusions
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Our results indicate that cycloviruses are commonly found in serum and CSF of paraplegia patients from Malawi. Diverse cycloviruses have been discovered in human and chimpanzee fecal samples and in muscle tissue of farm animals, such as cows, sheep, goats, and chickens. Cycloviruses have been suggested to cause human enteric infections and were not derived from consumed food because the human and animal cycloviruses showed limited genetic overlap.
Our data indicate that cycloviruses may cause systemic infections and are present in multiple organ compartments in humans. Whether cycloviruses play a role in development of paraplegia remains to be determined; this study lacks a control group of healthy persons, and the relatively high virus prevalence in persons with paraplegia may also reflect high overall prevalence in healthy persons. In addition, the apparent interleaved evolution of human and animal cycloviruses suggests the potential for frequent cross-species exposure and zoonotic transmission.
Our observations expand the knowledge of cycloviruses in humans and show how epidemiologic baseline information on virus host range and tropism in animals may indicate the presence of similar viruses in different organ systems of humans. To clarify the epidemiology and pathogenicity of cycloviruses in humans, additional surveillance should be conducted, especially because the prevalence and diversity of human cycloviruses is relatively high. Cross-species transmission of cycloviruses seems plausible , and closely related cyclovirus species may be pathogenic.
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[The cycloviruses are a genus of viruses of un-enveloped single-stranded DNA viruses with ambisense encoding of their genome content, classified as members the family _Circoviridae_. They are widespread and predominantly infect avian species. Recently virologists in Viet Nam discovered a novel cyclovirus in spinal fluid from 4 percent of 642 patients with central nervous system infections of unknown cause and in an average of 58 percent of fecal samples from pigs and poultry, suggesting animals may serve as reservoirs for transmission to humans.
Now scientists in Rotterdam and Malawi describe another novel cyclovirus which they have detected in 15 percent and 10 percent of serum and cerebrospinal fluid samples, respectively. These findings expand our knowledge of cyclovirus diversity and tropism and possible involvement in human disease.
Together these findings suggest roles for cycloviruses in causation of human disease, specifically neurological rises in accordance with the categories of patients studied.
The Science Now commentary, no [1] above, reveals that in fact cycloviruses were first discovered in 2009 -- along with a host of other viruses -- in fecal samples from South-Asian children suffering from acute flaccid paralysis, by a team led by Eric Delwart of the Blood Systems Research Institute in San Francisco. Since then, they have also been found in human fecal samples from Nigeria and Tunisia, as well as in farm animals, chimpanzees, bats, cockroaches, and dragonflies. Consequently the relationship of specific cycloviruses to human disease remains uncertain, as both the Viet Nam and Rotterdam/Malawi groups recognise. - Mod.CP]
