PM IAS EDITORIAL ANALYSIS AUGUST 14

Editorial 1: Metagenome sequencing technology is transforming pathogen surveillance

Introduction

One of the initial breakthroughs in the definitive identification of SARS-CoV-2 as the causative agent of COVID-19 came from the application of unbiased genome sequencing technologies to infected patient samples. This new approach – called metagenomics. The technique and its adoption also drastically changed the way pathogen identification would be undertaken thereafter.

Metagenomics

Metagenomics is the study of the structure and function of entire nucleotide sequences isolated and analyzed from all the organisms (typically microbes) in a bulk sample.
Metagenomics is often used to study a specific community of microorganisms, such as those residing on human skin, in the soil or in a water sample.
The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.

Genomic tech to the frontline

Scientists in countries worldwide have since developed scores of technologies based on genome-sequencing – including the very popular CovidSeq assay – spawning several national and international SARS-CoV-2 genome surveillance activities.
GISAID, a popular repository on the Internet to which SARS-Co-V-2 genome-sequence data could be submitted, is a testimony to such high-throughput genome surveillance activities.
India also initiated a national SARS-CoV-2 genome-sequencing and surveillance programme supplemented by several State government and private initiatives.
The success has provided a template for applying sophisticated genomic technologies as frontline tools to surveil known and unknown organisms and to tracking emerging pathogens in an unbiased and high-throughput manner.

The Nigerian study

In paper of Nature Communications, scientists from the Nigerian Centre for Disease Control applied metagenomic sequencing for pathogen surveillance and detection in three cohorts of patients.
The first cohort represented population-level surveillance of individuals presenting with symptoms consistent with Lassa fever, a viral haemorrhagic fever caused by the Lassa virus endemic to West African countries.
The second cohort consisted of people from outbreaks with suspected infectious aetiologies.
The third cohort consisted of people with clinically challenging but undiagnosed conditions.
The scientists were able to identify 13 distinct viruses afflicting the individuals. The genomic approach also helped them pinpoint the second and third documented cases of human blood-associated dicistrovirus among the cohorts.
The scientists also identified pegivirus C as a common co-infection in patients with Lassa fever as well as that the presence of pegivirus C was associated with a lower viral load in patients.
Further investigations revealed the presence of yellow fever virus and mpox virus in patients.
As it happened, the metagenome-sequencing approach also allowed the scientists to rule out viral infections in some individuals and link their symptoms to pesticide poisoning instead.
The study demonstrated the power of metagenomic sequencing investigations for pathogen detection and disease diagnosis, and to inform public health outbreak responses.

Key to early response

More recently, experts have used genome sequencing technologies as frontline tools to motivate the detection and surveillance of lumpy skin disease in cattle and the emergence of drug-resistant tuberculosis, among the use-cases.
It is heartening that several initiatives worldwide are taking advantage of the speed, accuracy, and high-throughput nature of advanced genome sequencing technologies to detect pathogens from diverse environmental sources, such as wastewater, air, soil, and animals.

Conclusion

Since genome surveillance provides the sort of information that experts can use to devise an early response strategy, identify emerging viral strains, and undertake risk-based surveillance of key animal species, genomic technologies are likely to become mainstays of our arsenal against pathogens of the future.

Context

India’s Defence Ministry has decided to replace the Microsoft Operating System (OS) in all its computers that can connect to the Internet with Maya, an Ubuntu-based OS built locally.

Maya, the new OS

The new OS is currently being rolled out only in the Defence Ministry computers, and not the three Services.
While the Navy is said to have cleared Maya for use in its systems, the Army and the Air Force are still evaluating the software.
Maya has been developed by Indian government agencies within six months, and it is aimed at preventing malware attacks by cybercriminals who are increasingly targeting critical infrastructure and government agencies.
The new OS will be backed by a protection system called Chakravyuh.

Maya va Microsoft OS

While the two operating systems provide a platform for the user to interact with computer hardware, Maya and Windows differ significantly, both in terms of cost and build.
Windows is a commercial software sold by Microsoft for a license fee. It is the most widely used OS, and is easy to install and run.
Devices powered by Microsoft’s OS run on the Windows NT kernel.
A kernel is the core of an operating system. It runs on a computer’s Random Access Memory (RAM) and gives the device instructions on how to perform specific tasks.
Prior to building the kernel architecture, progammers used to run codes directly on the processor.
In the 1970s, Danish computer scientist Per Brinch Hansen pioneered the approach of splitting what needs to be done by a processor from how it executes that task, thus introducing the kernel architecture in the RC 4000 multiprogramming system.

Difference in the core

This design was monolithic, meaning a single programme contained all necessary codes to perform kernel-related tasks.
This architecture provided rich and powerful abstraction for the underlying hardware. But it was also large and difficult to maintain as the lines of codes ran in the millions.
Limitations in the traditional architecture led to a new kernel design called the microkernel.
This design broke down the monolithic system into multiple small servers that communicate through a smaller kernel while giving more space for user customisations.
This change allowed developers to run patches easily without rebooting the entire kernel. It did have some drawbacks like larger running memory space and more software interactions that reduced the computer’s performance.
Windows runs on a hybrid kernel architecture which is a microkernel design coupled with additional codes that help enhance performance.
Apple’s MacOS also uses a hybrid kernel called XNU. And Ubuntu, a Linux OS that was used to build Maya, runs on monolithic architecture.
Linux versions are called “distributions” or “distro”, and they comprise free and open-source software. In fact, Android is also based on the Linux kernel.

Conclusion

India’s switch to the Ubuntu-based Maya OS comes at a time when cyberspace is increasingly becoming vulnerable to malware and ransomware attacks.
Such cyber threats arising from proprietary software are once again making global governments look to free and open-source software (FOSS) to develop their own OS.
Apart from cybersecurity, the reason behind this move is to assist IT modernisation efforts that are underway — like digitising government services and making them interoperable.