virology blog

About viruses and viral disease

bat

Hepatitis B viruses in bats

by

hepadnaviridae virionHepatitis B virus (HBV, illustrated) is a substantial human pathogen. WHO estimates that there are now 240,000,000 individuals chronically infected with HBV worldwide, of which 25% will die from chronic liver disease or hepatocellular carcinoma. The hepatitis B virus vaccine is highly effective at preventing infection. Because there are no known animal reservoirs of the virus, it is believed that HBV could be globally eradicated. The recent finding of HBV in bats raises the possibility of zoonotic introduction of the virus.

Serum and liver samples from 3,080 bats from Panama, Brazil, Gabon, Ghana, Germany, Papua New Guinea, and Australia were screened for HBV-like sequences by polymerase chain reaction (PCR). Ten positive specimens were found from three bat species: Uroderma bilobatum from Panama, and Hipposideros cf. ruber and Rhinolophus alcyone from Gabon. The complete viral genome sequence was determined for 9 of the positive specimens. Phylogenetic analysis revealed that the bat viruses form three different lineages, and that each virus differs by at least 35% from known hepadnaviruses.

The virus from Hipposideros cf. ruber has been named roundleaf bat HBV, while those from Rhinolophus and Uroderma have been named horshoe bat HBV, and tent-making bat HBV.

Viral DNA in the liver of Hipposideros bats was found to be higher than in other organs or serum. Some lymphocyte infiltration was observed in the liver of these animals, as well as deposits of viral DNA within hepatocytes. These observations indicate that the bat HBV viruses likely replicate in the bat liver and cause hepatitis.

Serological studies revealed that hepadnaviruses are widespread in Old World bats: antibodies against bat hepadnaviruses were detected in 18% of hipposiderid bats and 6.3% of rhinolophid bats.

An important question is whether these three bat hepadnaviruses can infect human cells. Only tent-making bat HBV could infect primary human hepatocytes, which occurred via the human HBV cell receptor, sodium taurocholate cotransporting polypeptide. However serum from humans that had been immunized with HBV vaccine did not block infection of human hepatocytes with this virus.

These observations show that viruses related to human HBV are replicating in the liver of bats. Earlier this year another hepadnavirus was identified in long-fingered bats (Miniopterus fuliginosus) in Myanmar. The complete genome sequence was obtained and virus particles were observed in bat liver tissues.

The finding of hepadnaviruses in bats raise many interesting questions. The first is whether human HBV originated by infection with bat HBV, either by consumption of bat meat or another mode of transmission. How long ago this occurred is not known. It has been suggested that HBV has been in humans for at least 15,000 years. Some avian species contain avihepadnaviral sequences integrated into their genome, indicating that these viruses originated at least 19 million years ago.

These findings also raise many questions about the pathogenesis of hepadnaviral infection in bats, including the mode of transmission (in humans, the virus is transmitted by exposure to blood, e.g. by injection or during childbirth), and whether chronic infections can occur as they do in humans.

Finally it is interesting to consider the zoonotic potential of tent-making bat HBV, which can infect human cells. Because bat hepadnaviruses are genetically distinct from HBV, current serological and nucleic acid screening programs would not detect human infections. The authors suggest that human and non-human primate sera from areas in which these bat viruses were isolated should be screened using assays that detect the bat hepadnaviruses. Without such information we do not know if these viruses currently infect humans.

How many viruses on Earth?

by

EarthHow many different viruses are there on planet Earth? Twenty years ago Stephen Morse suggested that there were about one million viruses of vertebrates (he arrived at this calculation by assuming ~20 different viruses in each of the 50,000 vertebrates on the planet). The results of a new study suggest that at least 320,000 different viruses infect mammals.

To estimate unknown viral diversity in mammals, 1,897 samples (urine, throat swabs, feces, roost urine) were collected from the Indian flying fox, Pteropus giganteus, and analyzed for viral sequences by consensus polymerase chain reaction. This bat species was selected for the study because it is known to harbor zoonotic pathogens such as Nipah virus. PCR assays were designed to detect viruses from nine viral families. A total of 985 viral sequences from members of 7 viral families were obtained. These included 11 paramyxoviruses (including Nipah virus and 10 new viruses), 14 adenoviruses (13 novel), 8 novel astroviruses, 4 distinct coronaviruses, 3 novel polyomaviruses, 2 bocaviruses, and many new herpesviruses.

Statistical methods were then used to estimate that P. giganteus likely harbor 58 different viruses, of which 55 were identified in this study. If the 5,486 known mammalian species each harbor 58 viruses, there would be ~320,000 unknown viruses that infect mammals. This is likely to be un under-estimate as only 9 viral families were targeted by the study. In addition, the PCR approach only detects viruses similar to those that we already know. Unbiased approaches, such as deep DNA sequencing, would likely detect more.

Let’s extend this analysis to additional species, even though it might not be correct to do so. If we assume that the 62,305 known vertebrate species each harbor 58 viruses, the number of unknown viruses rises to 3,613,690 – over three times more than Dr. Morse’s estimate. The number rises to 100,939,140 viruses if we include the 1,740,330 known species of vertebrates, invertebrates, plants, lichens, mushrooms, and brown algae. This number does not include viruses of bacteria, archaea, and other single-celled organisms. Considering that there are 1031 virus particles in the oceans – mostly bacteriophages – the number is likely to be substantially higher.

Based on the cost to study viruses in P. giganteus ($1.2 million), it would require $6.4 billion to discover all mammalian viruses, or $1.4 billion to discover 85% of them. I believe this would be money well spent, as the information would allow unprecedented study on the diversity and origins of viruses and their evolution. The authors justify this expenditure solely in terms of human health; they note that the cost “would represent a small fraction of the cost of many pandemic zoonoses”. However it is not at all clear that knowing all the viruses that could potentially infect humans would have an impact on our ability to prevent disease. Even the authors note that “these programs will not themselves prevent the emergence of new zoonotic viruses”. We have known for some time that P. giganteus harbors Nipah virus, yet outbreaks of infection continue to occur each year. While it is not inconceivable that such information could be useful in responding to zoonotic outbreaks, the knowledge of all the viruses on Earth would likely impact human health in ways that cannot be currently imagined.

Update 1: I neglected to point out an assumption made in this study, that detection of a PCR product in a bat indicates that the virus is replicating in that animal. As discussed for MERS-CoV, conclusive evidence that a virus is present in a given host requires isolation of infectious virus, or if that is not possible, isolation of full length viral genomes from multiple hosts, together with detection of anti-viral antibodies. Obviously these measures cannot be taken for a study such as the one described above whose aim is to estimate the number of unknown viruses.

Update 2: We discussed this estimate of mammalian viruses on TWiV #249.

TWiV 247: Today’s weather in virology

by

On episode #247 of the science show This Week in Virology, Ian Lipkin joins Vincent, Alan, Rich, and Kathy to describe how his laboratory is searching for the origin of MERS-coronavirus.

You can find TWiV #247 at www.microbe.tv/twiv.

Part of MERS-CoV nucleotide sequence found in a bat

by

What is wrong with this paragraph from today’s New York Times that describes the origin of the Middle East Respiratory Syndrome (MERS) coronavirus:

Health officials confirmed Wednesday that bats in Saudi Arabia were the source of the mysterious virus that has sickened 96 people in the Middle East, killing 47 of them.

Here is the science behind that statement, which has been published in Emerging Infectious Diseases. Samples (fecal, fecal swab, throat swab, blood) were collected from bats in an area of Saudi Arabia where human infections with MERS-CoV have been identified. Total nucleic acids were extracted and analyzed for the presence of coronavirus sequences by polymerase chain reaction. Coronavirus sequences were amplified from 220 of 732 fecal samples and 7 of 91 rectal swab samples or fecal pellets. One PCR product obtained from a single bat sample (fecal pellet of a T. perforatus bat captured in October 2012 in Bisha) had 100% nucleotide identity to a human MERS-CoV isolate.

A single PCR product 190 nucleotides in length from one bat was a perfect match with the genome sequence of a MERS-CoV isolate.

No infectious MERS-CoV has yet been isolated from this single bat. Therefore it is not yet possible to say that bats are the source of virus causing the MERS-CoV outbreak. As I have written previously, a virus is very different from a viral sequence.

It is certainly possible that MERS-CoV originated in a bat. Bats are known to harbor many viruses, and of course the SARS coronavirus originated in bats. But there is more than one explanation for the presence of this short viral sequence in bats. Perhaps the virus (or viral sequence) was obtained when the bat ingested a meal. Perhaps the 190 nucleotides are from a recombinant virus that is not MERS-CoV. I can think of other reasons why bats might not be the source of MERS-CoV.

For these reasons I believe that it is inaccurate for ‘health officials’ and the New York Times to confirm that bats are the source of MERS-CoV. Additional work is clearly needed to show that T. perforatus is the source of MERS-CoV, including isolation of infectious virus from bats and demonstrating infection of bats by the presence of antibodies to the virus. The work is in clearly progress; indeed the results might even be known, but they are not included in the Emerging Infectious Diseases article on which the NY Times piece was based.

Update 1: The term ‘frag-virus’ was proposed in 2008 to indicate viruses known only from sequence data. Although the term never caught on, the short article points out the problems that arise when genomic fragments are used to identify new viruses :

Although unintentional, these reports may mislead the readership of scientific journals and the general press. Having no distinction between preliminary genome-based evidence and conclusive proof by biological isolation and characterization of a replication-competent virus blurs the meaning of new virus.

Update 2: A phylogenetic analysis of the DNA fragment amplified from T. perforatus has been carried out. The author writes that “although this fragment means a very close relative of the human MERS-CoV is found in a bat geographically close to the first case, the fact it is identical in this short region doesn’t mean that these bats are the direct source of the human case.”  I would add even more uncertainty because we have no evidence that the virus was replicating in this single bat.