Bats are the major reservoir of coronaviruses worldwide


Results of a five-year study in 20 countries on three continents have found that bats harbour a large diversity of coronaviruses (CoV). Findings from the study – led by scientists in the USAID-funded PREDICT project at the Center for Infection and Immunity (CII) at Columbia University’s Mailman School of Public Health and the University of California, Davis’ One Health Institute in the School of Veterinary Medicine – are published in the journal Virus Evolution. PREDICT is a globally coordinated effort to detect and discover viruses of pandemic potential and reduce risk for future epidemics.

With the cooperation of local governments, researchers sampled and tested 19,192 bats, rodents, non-human primates, and humans in areas where the risk of animal-to-human transmission is greatest, including sites of deforestation, ecotourism, and animal sanctuaries. The researchers identified 100 different CoVs and found that more than 98 percent of the animals harbouring these viruses were bats, representing 282 bat species from 12 taxonomic families. Extrapolating to all 1,200 bat species, they estimate a total of 3,204 CoV are carried by bats worldwide, most of which have yet to be detected and described. They also found that CoV diversity correlated with bat diversity with high numbers of CoVs concentrated in areas where there are the most bat species, suggesting CoVs coevolved with or adapted to preferred families of bats.

“This study fills in a huge gap in what we know about the diversity of coronaviruses in animal hosts,” says first author Simon Anthony, assistant professor of Epidemiology in CII. “Charting the geographic and genetic diversity of coronaviruses in animals is a critical first step towards understanding and anticipating which specific viruses could pose a threat to human health.”

The researchers used consensus PCR, a cost-effective technique that targets a small section of the viral genome – sufficient to locate the position of each virus in the family tree of all CoVs. To go a step further, researchers are using more powerful genome-wide sequencing to take a detailed look at those viruses that resemble known threats to humans. In a study published in April, they reported that a MERS CoV-like virus did not have the genetic prerequisites to jump to humans – a sign that MERS-CoV had evolved to become more capable of transmission. A similar effort is now underway to sequence viruses similar to SARS-CoV.

Researchers report preliminary evidence that CoVs in bats in Latin America were less likely than CoVs in Africa and Asia to “jump” outside their genus or family, potentially a sign of relatively lower risk of bat-to-human transmission on that continent. However, the authors caution that these regional differences may reflect variation in the ecology of bats in the various areas, and more work needs to be done to understand this.

The researchers say their findings should not be interpreted as a call to cull bats. Bats play an important role in the ecosystem, and most of the coronaviruses they carry are harmless to humans. Additionally, culling may have unintended consequences: destabilizing host ecology can actually increase risk for disease transmission, as seen in studies of Marburg and rabies viruses.

“Our goal is to shed light on the ecology of virus-host interactions to better understand and address the conditions that give rise to outbreaks like SARS and MERS,” says senior author Tracey Goldstein, associate professor at the One Health Institute at the University of California, Davis.

Article: Global patterns in coronavirus diversity by Simon J. Anthony, Christine K. Johnson, Denise J. Greig, Sarah Kramer, Xiaoyu Che, Heather Wells, Allison L. Hicks, Damien O. Joly, Nathan D. Wolfe, Peter Daszak, William Karesh, W. I. Lipkin, Stephen S. Morse, PREDICT Consortium, Jonna A. K. Mazet, Tracey Goldstein, published in Virus Evolution (2017) 3 (1): vex012, doi: 10.1093/ve/vex012

[SOURCE: Columbia University's Mailman School of Public Health]

Pandemic potential of H9N2 avian influenza viruses studied


Researchers have identified the molecular mechanisms that enable H9N2 viruses – the most common type of avian influenza virus – to infect humans, helping improve risk assessments for its potential to cause pandemic.

Although H9N2 viruses are considered less pathogenic than some types of avian influenza virus, they still cause significant losses for the poultry industry in many countries throughout Asia, the Middle East and North Africa – sometimes with death rates as high as 60%.

Over the past 20 years there have also been a growing number of (generally mild) human infections of H9N2 in Hong Kong, mainland China, Bangladesh and Egypt, especially amongst poultry workers. Concerns increased however when other experiments demonstrated the potential for human-to-human airborne transmission; a property normally associated with the potential to cause pandemic.

Despite the widespread global distribution and diversity of H9N2 viruses and their potential threat to human health, they have not been extensively characterised until now. A study of the specific properties that enable some lineages of H9N2 to adapt for successful human infection is published in Emerging Microbes and Infections.

Led by Dr Munir Iqbal, head of the avian influenza virus group at The Pirbright Institute, researchers specifically focussed on the surface protein haemagglutinin, which enables the virus to bind and fuse with host cells for entry and infection. In particular scientists investigated two properties that facilitate adaption for human infection: its preference for binding to different host receptors that allow cell entry and the pH level at which the virus can fuse with the host cells (pH of fusion) and therefore begin infection.

Dr Iqbal’s team aimed to explore the potential relevance of these biomarkers for zoonotic risk assessments. They characterised which host cell receptors the H9N2 haemagglutinin prefers to bind to, which is important as human and bird receptors are slightly different, which usually means that bird flu strains bind to ‘bird-like’ receptors and human strains bind to ‘human-like’ receptors. Bird flu strains can infect humans when a mutation occurs that enables a preference for binding receptors that are ‘human-like’. This has been partially or entirely attributed to a single amino-acid change in the haemagglutinin.

The team also assessed how the stability of H9N2 haemagglutinins affects the pH of fusion. In order to infect humans, the haemagglutinin must be stable enough to survive in respiratory droplets for airborne transmission and in the mammalian nasal tract, which is mildly acidic (less than a pH of 7). Haemaggluttinins of human flu strains have adapted to be stable and fuse at an acidic pH that is typically less than 5.5, whereas avian flu strain haemagglutinins are generally more stable above this level and are therefore unable to fuse in the acidic conditions of the human nasal tract.

The H9N2 strains being investigated were found to possess haemagglutinins which were stable at lower pH levels, something which was mirrored in other bird flu strains which have adapted to infect humans in the past. It was established that the stability at a lower pH was a more important factor for virus fusion than the preference for binding to different receptors.

Dr Iqbal said: “Based on the two properties we tested, our results indicate that the lineages with the highest zoonotic potential may be those currently circulating in southern China and Vietnam (G1 ‘Eastern’ sub-lineage). However, evaluations in this study of the lineages prevalent in China and Vietnam (BJ94) and from Bangladesh to Morocco (‘Western’ G1 sub-lineage), suggest these viruses could also adapt to humans with relatively few additional mutations and merit further research.

“This study has provided us with some important new insights which are helping us develop our understanding of these influenza viruses from molecular, biophysical and virological perspectives. We hope this will inform risk assessments of their zoonotic and pandemic potential and help improve global vaccine strategies”.

Article: Variability in H9N2 haemagglutinin receptor-binding preference and the pH of fusion by Thomas P Peacock, Donald J Benton, Jean-Remy Sadeyen, Pengxiang Chang, Joshua E Sealy, Juliet E Bryant, Stephen R Martin, Holly Shelton, John W McCauley, Wendy S Barclay and Munir Iqbal, published in Emerging Microbes and Infections (2017) 6, e11; doi:10.1038/emi.2016.139

[SOURCE: The Pirbright Institute]

Novel antibiotic resistance gene in milk


Researchers at the University of Bern have identified a new antibiotic resistance gene in Macrococcus caseolyticus strains from dairy cows. This gene confers resistance to all beta-lactam antibiotics including the last generation of cephalosporins used against methicillin-resistant Staphylococcus aureus (MRSA). A transfer to S. aureus (which is possible according to the researchers) would jeopardize the use of reserve antibiotics to treat human infections caused by multidrug-resistant bacteria in hospitals.

Macrococcus caseolyticus is a harmless bacterium naturally found on the skin of dairy cows which can spread to milk during the milking process. It can also be present in dairy products made from raw milk.

The researchers investigated M. caseolyticus present in milk of dairy cows suffering from mastitis. These strains showed an unusual resistance pattern to beta-lactam antibiotics with a resistance profile resembling that of MRSA, but the known genes responsible for resistance (mecA, mecB and mecC) were missing. Using Next Generation Sequencing (NGS), the researchers rapidly found that the M. caseolyticus isolates acquired a novel antibiotic resistance island which contains a new methicillin resistance gene designated mecD. This discovery is published in Scientific Reports.

The researchers demonstrated that the novel methicillin resistance gene mecD confers resistance to all classes of β-lactams including anti-MRSA cephalosporins. It was located on a resistance island which has been acquired by M. caseolyticus. Further experimental investigations of the resistance island showed that it also has the potential for integration into the chromosome of S. aureus.

M. caseolyticus containing the novel mecD gene has been so far mainly found in cattle, but in one case it has been isolated from skin infection in a dog indicating that this bacterium has the potential to colonize different animal species.

Read article: Novel methicillin resistance gene mecD in clinical Macrococcus caseolyticus strains from bovine and canine sources by Sybille Schwendener, Kerstin Cotting and Vincent Perreten, published in Scientific Reports (2017) 7, article number: 43797, doi:10.1038/srep43797

[SOURCE: University of Bern]

Unique structure of ASFV enzyme may allow drug development


A DNA-copying protein from African swine fever virus (ASFV) has a unique structure that may offer a target for drugs, according to a study published in PLoS Biology by Yiqing Chen and colleagues at Fudan University in Shanghai, China.

Viral replication depends in part on a polymerase enzyme, AsfvPolX, that repairs breaks in the DNA, but the structure of this enzyme has not been determined in detail. The authors used X-ray diffraction and nuclear magnetic resonance to solve the structure at atomic resolution.

The team found that the enzyme contained a unique binding pocket for the building blocks of DNA (nucleotides), not seen in related enzymes in other organisms. They also found several other unique structural features, including a pair of hydrophobic amino acids that interact with incoming nucleotides, and a “platform” created by two basic amino acids that stabilizes a mismatched nucleotide pair, increasing the rate of incorporation of erroneous nucleotides into the DNA chain during the repair process. Together, these features give the polymerase its unique character of a high rate of DNA replication combined with a high copying error rate.

Blocking the binding pocket with a drug may be a valuable strategy to treat ASFV infection, the authors suggest. “Exploiting this unique structural feature to attack the virus may offer a rapid route to develop treatments for this important agricultural virus,” says Chen, although he noted one caveat; the high error rate of the AsfvPolX polymerase enzyme means that the virus mutates rapidly, and therefore may evolve resistance to drugs designed to block it.

Read article: Unique 5′-P recognition and basis for dG:dGTP misincorporation of ASFV DNA polymerase X by Yiqing Chen, Jing Zhang, Hehua Liu, Yanqing Gao, Xuhang Li, Lina Zheng, Ruixue Cui, Qingqing Yao, Liang Rong, Jixi Li, Zhen Huang, Jinbiao Ma and Jianhua Gan, published in PLoS Biology (2017)15(2): e1002599, doi:10.1371/journal.pbio.1002599