Human's gut virus composition is as unique as a fingerprint: Study
What is the gut microbiome?
How the food you eat affects your gut - Shilpa Ravella
How the food you eat affects your brain - Mia Nacamulli
Lee’s work titled “The gut virome in two indigenous populations from Malaysia” has been published in the prestigious Nature publication, Scientific Reports.
“The sole purpose of a virus’s life is to multiply, but the irony is that it cannot multiply on its own.”
VIRUSES have been in our lives and newsfeeds almost incessantly in the last two years. We have been double-jabbed and masked for much of this time in an effort to avoid the SARS-CoV-2 virus. As we have learnt, these steps can help limit the spread of Covid-19 and help us avoid infection.
But can we avoid viruses entirely? The simple answer is no.
The sole purpose of a virus’s life is to multiply, but the irony is that it cannot multiply on its own.
Instead, viruses must rely on the cellular machinery from more advanced forms of life – bacteria, plants or animals.
How many viruses in total are there in the world at any time? An estimated ten nonillion (1031) is the figure that has been bandied about – a number so enormous that we cannot truly appreciate what it means.
There are so many types of viruses occupying so many different hosts and ecosystems that we have no idea of how many categories of viruses there are.
Humans carry an astronomical number of viruses all the time. These viruses do not kill us because their targets are the billions of bacteria that reside in our bodies, principally in the gut.
A recent paper from Chuen Zhang Lee, an Honours student at Monash University Malaysia, reports progress in identifying bacterial viruses in our guts by using human faeces as the starting material. Lee used faecal matter from two Malaysian Orang Asli groups, the Jehai and the Jakun, to show that the viruses they contain are different from viruses in more frequently studied groups, such as Europeans or Chinese.
Lee enriched the viruses in the faeces (as an indicator, of what is actually in the gut) away from all the yucky material, bacterial cells and human cells and extracted the genetic material from this virus enriched material.
The viral DNA was then sequenced at the Monash University Malaysia Genomics Facility using a technique that allows one to read long stretches of DNA.
Muhammad Zarul Hanifah, who works at the Genomics Facility, assisted Lee in analysing his data.
Using this method, Lee recognised approximately half the DNA as coming from known viruses. Based on the viruses he found, he could identify what some of the sample-givers had consumed and their lifestyle and environment.He also identified some of the bacteria in our guts these viruses could attack and therefore, get a partial picture of what types of bacteria could be in our guts.
These results start to build up a picture of how our gut health is determined, which can significantly determine our overall health. It is clear that viruses may also have a role in determining gut health – a complex topic.
Lee was supervised by a group of researchers including Prof Maude Phipps from the Jeffrey Cheah School of Medicine and Health Sciences, Dr Jeremy Barr from Monash University School of Biological Sciences and Prof Qasim Ayub, Prof Sunil Lal and Prof Sadequr Rahman from the School of Science.
Lee’s work titled “The gut virome in two indigenous populations from Malaysia” has been published in the prestigious Nature publication, Scientific Reports.
Viruses are clearly ‘cool’ and ‘hot’ right now, and are likely to remain that way for a long time. We look forward to furthering discoveries on viruses and insights into how they can be used to our benefit.
To know more about the programmes offered by the School of Science, Monash University Malaysia, visit www.monash.edu. my/science. Alternatively, visit www.monash.edu.my for more information.
If you really need to do online bank transactions in your hotel room or any public space, use your own mobile data or a VPN.
Eight things you should not do while travelling abroad.
WATCH your wallet, don’t buy fake designer goods and skip the ice cubes if you’re in the tropics – most people are aware of these “issues” when going abroad.
But there are more travel taboos than you may know. Bear these eight tips in mind on what not to do in order to be safe, and enjoy your trip.
1. Trusting the hotel safe
You may be used to stowing your passport, money, tickets and other valuable items in the hotel room safe, to avoid losing them when you are out and about, or getting robbed.
How safe are hotel safes, though? Not particularly – some very old models can be opened if the power supply is cut. Other safes can be opened if they are returned to their factory setting. Then there are those that spring open if you punch the lid.
Safes in hotel rooms often present little obstacle for thieves as they are only mounted in the wardrobe or on the wall with screws so they can easily be removed from the site, a German consumer advice centre warned in 2019.
It is safer to use the safe at hotel reception, where you can drop off your valuables. You’ll get a receipt and your items will be fully insured – unlike if you use the room safe.
2. Making phone calls or downloading a video onboard a ship
If you’re on a ferry, say from Germany to Sweden or Norway in Europe, you might not think twice about reaching for your smartphone, after roaming charges in the European Union and some other countries were dropped back in 2017.
But that only applies to landbased networks. As passengers would not have a mobile phone connection at sea, major ferries often have an onboard mobile phone network, connected to a satellite network.
Sadly these onboard networks are very expensive and the costs are not capped at a certain level. A brief call in Europe costs between €3 (RM14) and €7 (RM33) per minute.
You can also expect to pay up to €2.50 (RM12) per 100KB of data – and bear in mind that a brief Whatsapp video of less than a minute has a volume of around 1MB to 3MB. This means that playing it back could cost €25 (RM117) to €75 (RM352).
The cost of letting the kids watch a Youtube film would be eye-watering, so you are safest if you switch the phone to flight mode until you reach dry land.
3. Packing everything in your check-in bag
Another piece of vital travel advice is to put your necessities in your hand luggage. In 2019, airlines worldwide lost around 25.4 million luggage items, or just over 5.5 suitcases per thousand passengers, according to IT service provider Sita.
That is not necessarily a cause for concern, as 99.5% of all missing luggage eventually turn up, according to the International Air Transport Association (IATA). But if you want to avoid being among the remaining 0.5%, make sure your bag doesn’t have loose straps dangling off it, and ensure your suitcase is not excessively worn.
A further issue to bear in mind is the minimum connecting time at a transfer airport. If you have less than the minimum specified, time might get tight and your suitcase will probably only reach your destination on the airline’s next flight at the earliest, to be sent onwards by taxi or courier.
So if you want to avoid being stranded without fresh underwear and a toothbrush, carry the bare minimum in your hand luggage.
4. Being unprepared in case of an emergency
Have you ever checked out where the hotel’s emergency exit is? No matter how good the sprinkler system, you want to know the way out if something catches fire, particularly if you’re on an upper storey as fire brigade ladders only reach up to the seventh or eighth floor.
While we’re at it, make sure you know what emergency number to dial in the country you’re in – and whether it is worth calling there at all. Just over 70 countries (two-thirds of them in Europe) have a nationwide emergency service that’s always available. Elsewhere, you need to make your own way to the nearest hospital.
5. Skipping a leg of a flight
It seems odd that a flight ticket from Oslo (Norway) to New York via Berlin (Germany) costs less than a ticket from Berlin to New York, without the first leg. You might wonder, do I really have to board the plane in Oslo?
Yes, you do.
If you skip a leg of the journey on your ticket, the airline may charge you the difference compared to the regular route price. Legally, that may be a grey area, but it could be an expensive headache afterwards.
6. Being unaware of local laws
Most travellers make an effort to be sure they abide by local laws but sometimes that requires some extra research. Be aware that if you are in Thailand for example, you don’t want to place your foot on a banknote, as there’s a picture of the king on it, so you could get into trouble.
Meanwhile in Buddhist countries, some people don’t like to see tourists posing playfully by Buddha statues. If you’re in the native islands of the Maldives, that aren’t part of tourist resorts, bikinis are banned.
In Bhutan, you may not smoke in public. And if you are in Singapore, you may not transport the musty-smelling durian fruit on the train. (In Malaysia, you can’t bring durian into any hotel premises.)
Taking pictures using drones may cause you problems in several places – special permits are required in many countries, while the practise is banned completely in Morocco, Iran, Kenya and Egypt, for example. Flying a drone without the right paperwork close to a military zone could land you in jail.
7. Being careless with your medication
There are pills for everything from tension to fear of flying but think twice about whether to pack them when travelling.
Many countries have strict drug laws such as the United Arab Emirates, Singapore, Malaysia and many others, so while a drug might be commonplace in Europe, for example, even a small quantity could land you in jail abroad. Check embassy websites before you travel and a letter from your doctor confirming that the medication is necessary is also advisable.
8. Checking your bank balance at the hotel
It’s a bad idea to do online banking at the hotel particularly if the Wifi is not password-protected. You might wind up in the wrong network, if you see something like “Guest” on the list of free networks and assume that is the one for you. It could be a scam set up close to the hotel and if you are unlucky, thieves can find your email log-ins and bank passwords, track all your activities, install malware or redirect the connection to phishing sites.
Beware of similar issues at airports and in restaurants. For safer browsing, you can also use your own mobile data or VPN tunnel software.
WHEN US President Joe Biden asked the United States Intelligence Community (IC) to determine the origin of Covid-19, its conclusion was remarkably understated but nonetheless shocking. In a one-page summary, the IC made clear that it could not rule out the possibility that SARS-CoV-2 (the virus that causes Covid-19) emerged from a laboratory.
But even more shocking for Americans and the world is an additional point on which the IC remained mum: If the virus did indeed result from laboratory research and experimentation, it was almost certainly created with US biotechnology and know-how that had been made available to researchers in China.
To learn the complete truth about the origins of Covid-19, we need a full, independent investigation not only into the outbreak in Wuhan, China, but also into the relevant US scientific research, international outreach, and technology licensing in the lead-up to the pandemic.
We recently called for such an investigation in the Proceedings of the National Academy of Sciences. Some might dismiss our reasons for doing so as a “conspiracy theory.” But let us be crystal clear: If the virus did emerge from a laboratory, it almost surely did so accidentally in the normal course of research, possibly going undetected via asymptomatic infection.
It is of course also still possible that the virus had a natural origin. The bottom line is that nobody knows. That is why it is so important to investigate all the relevant information contained in databases available in the US.
Missed opportunities
Since the start of the pandemic in early 2020, the US government has pointed an accusatory finger at China. But while it is true that the first observed Covid-19 cases were in Wuhan, the full story of the outbreak could involve America’s role in researching coronaviruses and in sharing its biotechnology with others around the world, including China.
US scientists who work with SARS-like coronaviruses regularly create and test dangerous novel variants with the aim of developing drugs and vaccines against them. Such “gain-of-function” research has been conducted for decades, but it has always been controversial, owing to concerns that it could result in an accidental outbreak, or that the techniques and technologies for creating new viruses could end up in the wrong hands. It is reasonable to ask whether SARS-CoV-2 owes its remarkable infectivity to this broader research effort.
Unfortunately, US authorities have sought to suppress this very question. Early in the epidemic, a small group of virologists queried by the US National Institutes of Health told the NIH leadership that SARS-CoV-2 might have arisen from laboratory research, noting that the virus has unusual features that virologists in the US have been using in experiments for years – often with support from the NIH.
How do we know what NIH officials were told, and when? Because we now have publicly available information released by the NIH in response to a Freedom of Information Act (FOIA) request. We know that on Feb 1, 2020, the NIH held a conference call with a group of top virologists to discuss the possible origin of the virus. On that call, several of the researchers pointed out that laboratory manipulation of the virus was not only possible, but according to some, even likely. At that point, the NIH should have called for an urgent independent investigation. Instead, the NIH has sought to dismiss and discredit this line of inquiry.Heads in the sand
Within days of the Feb 1 call, a group of virologists, including some who were on it, prepared the first draft of a paper on the “Proximal Origin of SARS-CoV-2.” The final draft was published a month later, in March 2020. Despite the initial observations on Feb 1 that the virus showed signs of possible laboratory manipulation, the March paper concluded that there was overwhelming evidence that it had emerged from nature.
The authors claimed that the virus could not possibly have come from a laboratory because “the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone.” Yet the single footnote (number 20) backing up that key claim refers to a paper from 2014, which means that the authors’ supposedly “irrefutable evidence” was at least five years out of date.
Owing to their refusal to support an independent investigation of the lab-leak hypothesis, the NIH and other US federal government agencies have been subjected to a wave of FOIA requests from a range of organisations, including US Right to Know and The Intercept. These FOIA disclosures, as well as internet searches and “whistleblower” leaks, have revealed some startling information.
Consider, for example, a March 2018 grant proposal submitted to the US Defense Advanced Research Projects Agency (DARPA) by EcoHealth Alliance (EHA) and researchers at the Wuhan Institute of Virology (WIV) and the University of North Carolina (UNC). On page 11, the applicants explain in detail how they intend to alter the genetic code of bat coronaviruses to insert precisely the feature that is the most unusual part of the SARS-CoV-2 virus.
Although DARPA did not approve this grant, the work may have proceeded anyway. We just don’t know. But, thanks to another FOIA request, we do know that this group carried out similar gain-of-function experiments on another coronavirus, the one that causes Middle East respiratory syndrome (MERS).
In yet other cases, FOIA disclosures have been heavily redacted, including a remarkable effort to obscure 290 pages of documents going back to February 2020, including the Strategic Plan for Covid-19 Research drafted that April by the US National Institute of Allergy and Infectious Diseases. Such extensive redactions deeply undermine public trust in science, and have only served to invite additional urgent questions from researchers and independent investigators.
In a one-page summary, the IC made clear that it could not rule out the possibility that SARS-CoV-2 (the virus that causes Covid-19) emerged from a laboratory. – AFP
The facts of the case
Here are ten things that we do know.
First, the SARS-CoV-2 genome is distinguished by a particular 12-nucleotide sequence (the genetic code) that serves to increase its infectivity. The specific amino acid sequence directed by this insertion has been much discussed and is known as a furin cleavage site (FCS).
Second, the FCS has been a target of cutting-edge research since 2006, following the original SARS outbreak of 2003-04. Scientists have long understood that the FCS holds the key to these viruses’ infectivity and pathophysiology.
Third, SARS-CoV-2 is the only virus in the family of SARS-like viruses (sarbecoviruses) known to have an FCS. Interestingly, the specific form of the FCS that is present in SARS-CoV-2 (eight amino acids encoded by 24 nucleotides) is shared with a human sodium channel that has been studied in US labs.
Fourth, the FCS was already so well known as a driver of transmissibility and virulence that a group of US scientists submitted a proposal to the US government in 2018 to study the effect of inserting an FCS into SARS-like viruses found in bats. Although the dangers of this kind of work have been highlighted for some time, these bat viruses were somehow considered to be in a lower-risk category. This exempted them from NIH gain-of-function guidelines, thereby enabling NIH-funded experiments to be carried out at the inadequate BSL-2 safety level.
Fifth, the NIH was a strong supporter of such gain-of-function research, much of which was performed using US-developed biotechnology and executed within an NIH-funded three-way partnership between the EHA, the WIV, and UNC.
Sixth, in 2018, a leading US scientist pursuing this research argued that laboratory manipulation was vital for drug and vaccine discovery, but that increased regulation could stymie progress. Many within the virology community continue to resist sensible calls for enhanced regulation of the most high-risk virus manipulation, including the establishment of a national regulatory body independent of the NIH.
Seventh, the virus was very likely circulating a lot earlier than the standard narrative that dates awareness of the outbreak to late December 2019. We still do not know when parts of the US government became aware of the outbreak, but some scientists were aware of the outbreak as of mid-December.
Eighth, the NIH knew as early as Feb 1, 2020, that the virus could have emerged as a consequence of NIH-funded laboratory research, but it did not disclose that fundamental fact to the public or to the US Congress.
Ninth, extensive sampling by Chinese authorities of animals in Wuhan wet markets and in the wild has found not a single wild animal harboring the SARS-CoV-2 virus. Despite this, there is no indication that the NIH has requested the laboratory records of US agencies, academic centers, and biotech companies involved in researching and manipulating SARS-like coronaviruses.
Tenth, the IC has not explained why at least some of the US intelligence agencies do in fact believe that a laboratory release was either the most likely or at least a possible origin of the virus.
Time for transparency
Given the questions that remain unanswered, we are calling on the US government to conduct a bipartisan investigation. We may never understand the origin of SARS-CoV-2 without opening the books of the relevant federal agencies (including the NIH and the Department of Defense), the laboratories they support, academic institutions that store and archive viral sequence data, and biotechnology companies.
A key objective of the investigation would be to shed light on a basic question: Did US researchers undertake research or help their Chinese counterparts to undertake research to insert an FCS into a SARS-like virus, thereby playing a possible role in the creation of novel pathogens like the one that led to the current pandemic?
Investigations into Covid-19’s origins should no longer be secretive ventures led by the IC. The process must be transparent, with all relevant information being released publicly for use by independent scientific researchers. It seems clear to us that there has been a concerted effort to suppress information regarding the earliest events in the outbreak, and to hinder the search for additional evidence that is clearly available within the US. We suggest that a panel of independent researchers in relevant disciplines be created and granted access to all pertinent data in order to advise the US Congress and the public.
There is a good chance that we can learn more about the origins of this virus without waiting on China or any other country, simply by looking in the US. We believe such an inquiry is long overdue. – Project Syndicate
Neil L. Harrison is a professor at Columbia University. Jeffrey D. Sachs, university professor at Columbia University, is director of the Center for Sustainable Development at Columbia University and president of the UN Sustainable Development Solutions Network. This article was first published on Project Syndicate.
Overdue inquiry: There is a good chance that we can learn more about the
origins of this virus simply by looking in the US, say the writers. –
123rf.com
