• Research continues to find cause behind sudden deaths 

By Sarah Hannan As the Covid-19 data platforms managed by the Epidemiology Unit of the Ministry of Health (MoH) reflect the number of Covid-19 cases reported in the country, which is increasing by hundreds per day, the virologists and a dedicated team of scientists have placed all hands on deck to understand the present Covid-19 virus strain in Sri Lanka. It is clear that its virulence has increased severalfold.  Meanwhile, increased sample collection has created somewhat of a backlog in report generation as diagnostic labs have stretched their workforce thin to deliver the PCR test results in a timely manner.  A month following the second Covid-19 wave hitting Sri Lanka, a report on the whole genome sequencing of the virus strain present in the country was issued by the Department of Immunology and Molecular Medicine and Allergy of the Immunology and Cell Biology Unit at the University of Sri Jayewardenepura (USJ).  MoH Secretary (Retd.) Maj. Gen. Dr. Sanjeewa Munasinghe, earlier last week, stated that the virus is said to be spreading rapidly this time around, and also noted that if a person who had contracted the virus in April had 100,000 particles of the virus in a droplet of saliva when they coughed or sneezed, this time (second wave), the number of particles had increased to the millions and perhaps even one billion.  “The viral load is higher this time around and can infect a larger number of people. If people continue to travel a lot, that will accelerate the speed of the virus spreading to the whole country. Therefore, I kindly request all of you to limit your travel to essential duties,” Dr. Munasinghe reiterated.  The scientists at the Department of Immunology and Molecular Medicine and Allergy at USJ carried out whole genome sequencing of the virus to determine if the current outbreak has resulted in the spread of different strains, if there are certain mutations that result in the rapid spread of the virus, and also to investigate the relationship between the currently circulating virus strains and previous strains that circulated in Sri Lanka.    [caption id="attachment_104340" align="aligncenter" width="791"] Phylogenetics of the current strains (circled) compared to previous strains in Sri Lanka (blue dots) and other strains in the world (Source:Nextstrain.org)[/caption] Different from first strain  Key findings of the study outlined that the current strain of the coronavirus in circulation is different to the strains that circulated in the first wave earlier this year. The present virus strain was also found to have higher transmissibility due to its high viral loads.  Furthermore, it was also found that the same virus strain is so far responsible for the infections detected in Minuwangoda, the Colombo Municipality area, and the Peliyagoda Fish Market cluster.  Sixteen virus strains originating from patients of the Minuwangoda apparel factory and in turn the Minuwangoda cluster, the Colombo Municipality, and the Beruwala Fish Market, who were admitted to tertiary care hospitals, were subjected to sequencing.  Whole genome sequencing was successful in 13 strains while partial genome sequencing was successful in three strains.  The findings revealed that 12 out of 13 strains were similar to each other and were of the B.1.42 lineage (clade 20C), suggesting that the virus strains circulating in different places of the country are of common origin. Fifteen out of sixteen strains had the D614G mutation, which is associated with high viral load and higher rates of transmissibility.  The previous strains that circulated in Sri Lanka were of the B.1, B.2, B 1.1, and B.4 lineages (the Kandakadu cluster viruses were of B.1 lineage), and therefore, the current virus strain is slightly different as it belongs to the B.1.42 lineage.    Similar to strains in Europe  Samples of the first Covid-19 cases detected in the country were tested by the laboratory of the Department of Immunology and Molecular Medicine and Allergy of the Immunology and Cell Biology Unit at USJ, and its researchers said the virus strain in circulation in Sri Lanka at present was similar to that of the strain found in Sweden, Denmark, and other European countries at present.  Researchers also say that categorisation of the virus needs to be included in any precautionary measures against it. They say the virus is likely to change in a few weeks – that is, there is a risk of another viral strain spreading.  "The Ministry of Health informed us that this time, the Covid-19 virus is spreading rapidly and asked us to conduct the necessary research to identify the characteristics of this present strain and provide information. That is how our research team began its work. The required biological samples were obtained through the Ministry of Health. That is why we conducted the research and released the report on 31 October,” said USJ Faculty of Medicine senior lecturer Dr. Chandima Jeewandara, who is part of the research team at the university.  Dr. Jeewandara stated that 16 biological samples were taken for testing this time, adding that these were obtained from the Minuwangoda Brandix cluster, Peliyagoda Fish Market cluster, and the Colombo Municipal Council cluster. Of these samples, 12 out of 13 showed a homogeneous state.  “Our research in March, observed changes in samples of this virus. There is no similarity between the Kandakadu cluster virus and the Peliyagoda and Minuwangoda cluster virus,” he said.  “Although the SARS-CoV- 2 virus group that is prevalent in Ukraine these days is not 100% similar to the Covid virus group in Sri Lanka, there is a very close link,” he added.  Researchers also say that there is no data on whether this group was formed from the Kandakadu cluster. But researchers say that there is a possibility that the virus which was introduced to the Kandakadu cluster had later mutated and re-emerged in the Minuwangoda apparel factory cluster.   Studies to continue  “The virulence of the present strain and its aggressive nature can be observed through the symptoms that it generates once it enters our body; it can range from asymptomatic cases to sudden death. Patients can react adversely to this disease.  “Moreover, the DNA construct too can affect the way the virus behaves in each person’s immune system, causing varying symptoms and side effects. If the virus enters a sick person, it is more likely to cause complications. We are conducting continuous research on the mutations of the new strains,” Dr. Jeewandara noted.  It was in 2012 that, as a result of findings in a research paper that stated a virus could affect Sri Lanka in the future, Dr. Jeewandara informed the Central Bank of Sri Lanka (CBSL) of the need for a well-equipped laboratory for the very purpose of handling a deadly virus. Accordingly, in 2019, funds were allocated by the World Health Organisation (WHO) to purchase equipment for this research.  “The quality of our laboratory is at a very high level,” Dr. Jeewandara said.  Dr. Jeewandara emphasised that washing hands with soap, wearing masks, and social distancing are very important to get rid of this virus, and added that the current virus strain may change in a few weeks.  He added that there is no data to say that it originated from the Kandakadu cluster, despite speculation.  Responding to the question of whether conducting PCR tests and isolating patients can actually help in controlling the spread of the virus, the Head of the USJ research team Prof. Neelika Malavige explained: “PCRs detect the presence of nucleic acid, irrespective of whether the organism is alive or not. In the case of Covid-19, due to the highly sensitive nature of a PCR, it picks up on the nucleic acid of non-infectious viruses.”  “Under normal circumstances, the diagnosis will reflect whether someone presents with pneumonia (causative agent), extent of spread of a virus (those who have been infected), etc. But with Covid-19, all those who are PCR-positive are quarantined, whilst sometimes having already passed the infectious period,” she said.  “This becomes a big problem in countries in Europe, the US, Latin America, and many Asian countries, where there is widespread Covid-19 transmission. But in countries such as Sri Lanka, it is important to find those who had the infection (although not infectious anymore), because we are trying to limit community spread. Our aims are very different, because Sri Lanka still has not got into the situation that most countries have,” Prof. Malavige reiterated.  The team of scientists that carried out the sequencing work from the University of Sri Jayewardenepura are: Dr. Chandima Jeewandara, Dr. Deshni Jayathilaka, Dr. Dinuka Ariyaratne, Laksiri Gomes, and Diyanath Ranasinghe, led by Prof. Neelika Malavige.  Dr. Ananda Wijewickrama and Dr. Malika Karunaratne from the National Institute of Infectious Diseases (NIIH) provided the initial samples from the Brandix cluster for genome sequencing. 

Stay Safe Sri Lanka digital project  The Information and Communication Technology Agency of Sri Lanka (ICTA) last Wednesday (4) proposed a digital project to streamline the contact tracing process in the backdrop of the present Covid-19 outbreak, The Sunday Morning learnt.  During a meeting with President Gotabaya Rajapaksa, the developers and officials of ICTA Sri Lanka, headed by Chairman Jayantha De Silva, demonstrated the mechanism of the “Stay Safe Sri Lanka” digital project, after which approval was granted for the project to be launched yesterday (7).  Speaking to The Sunday Morning, the project’s Lead Developer and data scientist Shanaka Perera explained that this project will ease the burden of having to manually collect data from the public.  “Over the past few weeks, people had to write down their details such as the name, contact number, and national identity card (NIC) number in contact tracing forms or books maintained by service providers, retail outlets, supermarkets, and so on. However, there was a question about how effective that would be when having to actually contact trace, which got me thinking of an effective platform for data collection.”  Perera then reached out to Nuzhi Meyen, Christopher Adikaram, and Kanishka Bandara for assistance in developing a data collection platform, which they then presented to ICTA Sri Lanka.  The platform developed for the Stay Safe Sri Lanka digital project would be made available to retailers, supermarkets, state and private institutions that are constantly accessed by the public, and even transport sector personnel, Perera explained.  “Data collection will be done through QR code scanning, SMS, and direct entry, and the public can choose either of these options. The public will not need to install any apps to be able to enter their details to the platform,” Perera added.  Details on the process follow: 

1. QR code: The merchant will be assigned a unique QR code they could print and display at the entrance to their store or institution, which the public will have to scan using a smartphone. 
2. SMS: For those who do not use smartphones, they could enter their details using SMS, for which, at the first instance, they will have to register by sending the following command via SMS to 1919 to register: SS<space>user’s NIC number. After that, when they access any place which has the Stay Safe Sri Lanka unique ID, they will only have to send an SMS with the unique ID of the outlet to 1919. 
3. Direct entry: The merchant will be given a user interface to which they only have to enter a person’s NIC number/mobile phone number. 

Interested merchants, businesses, institutions can obtain their unique QR code or outlet code through the www.staysafe.gov.lk/ website, which was activated yesterday.  Perera also noted that the platform was designed with the consideration of data protection, and not even the merchants will have access to the information of a customer accessing their services.  “The full information will be saved in the Government of Sri Lanka cloud and access will be granted to the task force appointed to prevent the Covid-19 outbreak, the Ministry of Defence, and the Ministry of Health,” he assured.  The Stay Safe Sri Lanka data platform will also provide ease the process of alerting people if they have been exposed to a Covid-19-positive patient during their activities. Furthermore, if a person becomes a close contact of a Covid-19-positive person while they are accessing services, the moment they scan the QR code, send the SMS, or the merchant enters the details into the platform, they are alerted and asked not to enter/permit entry to the premises.  “The app is currently undergoing the preliminary stages of implementing a database that records all employees’ locations of all companies, which can be accessed by anyone, regardless of whether they have a smartphone or not. The database will be implemented by Sunday (today), and the app will be launched officially on Monday (tomorrow),” ICTA Sri Lanka Chairman De Silva stated.  The team commissioned by ICTA Sri Lanka to design the Stay Safe Sri Lanka digital project comprises Shanaka Perera (BSc – University of Colombo, AMCA – UK, MSc – UK, at present is pursuing PhD in Data Science – UK), Nuzhi Meyen (consultant in the tech space, BSc – University of Colombo, MSc – University of Moratuwa, CIMA-passed finalist), Christopher Adikaram (BSc in IT – University of Moratuwa), and Kanishka Bandara (BSc in Software Engineering – Cardiff Metropolitan University). 

Suggestions to control and mitigate current Covid-19 outbreak   The Government Medical Officers’ Association (GMOA) wrote to President Gotabaya Rajapaksa highlighting areas of concern they believed to be of paramount importance in controlling and mitigating the current outbreak. Below were the areas highlighted:   

1. We observe that a failure in the implementation of “border crossing governance” resulted in Covid-19 spreading across the country through supply chains. A similar situation can be expected from home delivery services and especially trading vehicles which operate in areas with restrictions/curfew. As such, to reinforce border crossing governance as mentioned in the “GMOA Covid-19 Exit Strategy” presented to Your Excellency on 4 April 2020 and incorporated into the guidelines prepared jointly by the Ministry of Health and the GMOA, herewith we attach the draft guidelines for your notice. 
2. We highlight the importance of GPS mapping of Covid-19 data to make decisions timely and efficiently. The GMOA together with the Ministry of Health has developed a GPS mapping system which will enable health authorities to recognise potential “red zones” rapidly with increased accuracy. We believe this system will ultimately be helpful in implementing an efficient and successful zonal management strategy. 
3. Accurate, timely, and effective zonal lockdown/restriction procedures will prevent further spread of Covid-19 in Sri Lanka and help contact tracing and control the pandemic. 
4. “Lock-out” parameters need to be formulated in a transparent manner and communicated properly to build public confidence, pubic contribution, and accountability for safeguarding their zones. 
5. We recently observed that a leading private hospital in Colombo managed to achieve a daily PCR capacity of 2,000 tests, with only two functioning PCR machines, within a very short period of time. In this context, it is disappointing to note that the Ministry of Health, with 20 allocated PCR testing centres, is yet to achieve the daily minimum PCR requirement which is essential to effectively manage the current outbreak in the country. 
6. We highlight the necessity of an audit to monitor the capacity, capability, and efficiency of PCR testing which provides the basis of Covid-19 public health decision-making. Therefore, we propose to categorise results under three headings, as below:   

Test result issued		Category in relation to public health decision-making
A	Within 24 hours	Timely PCR reports
B	Between 24 hours and 48 hours	Delayed PCR reports
C	More than 48 hours	Outdated PCR reports

We expect that this audit format will result in maintaining A and B categories over 90% of results. Since PCR sensitivity falls around 70%, “Test, Test, Test” strategy should be considered under the above audit. 

7. Random community testing formal guidance should be issued in relation to the high-risk category and routine surveillance. 
8. We wish to inform you that the Epidemiology Unit recommended maintaining a minimum PCR capacity of over 10,000 per day with a buffer capacity of over 100,000 testing physical elements, at the meeting chaired by the Minister of Health.