A Kenyan Scientist Accurately Predicts COVID-19 Surges

A Kenyan scientist has developed a COVID-19 predictive mathematical model which successfully predicted all the four Kenyan surges with accuracy. Dr. Shem Otoi Sam is now working closely with the Lake Region Economic Bloc Committee of Eminent Persons to mitigate any future surge in the region. RoGGKenya talked to him and he shared about the brilliant concept.

Dr. Shem Sam, a Researcher, and Infectious Disease Modelling Expert from the University of Nairobi’s School of Mathematics, has developed a mathematical model to help predict COVID-19 waves.

The researcher told RoGGKenya that the new model can help governments to control the spread of COVID-19 if they implement the recommendations.

“The model was first shared with the Commission of Science Technology and Innovations (NACOSTI) with advice from Dr. Edwardina Ndhine and piloted in Homabay county where it successfully predicted the second wave from October 28, 2020 to January 4, 2021 .The Committee of Eminent Persons chaired by Prof Khama Rogo then got wind of it and invited me to work with them,“ said Sam.

It was then recommended to the leaders of the Lake Region Economic Block (LREB) counties. The 14 counties comprises of Bungoma, Busia, Homa Bay, Kakamega,Kisii, Kisumu, Migori, Nyamira, Siaya,Trans Nzoia, Kericho,Bomet, Nandi and Vihiga.

Interestingly, the model predicts waves months before they occur. Kenya has experienced four COVID-19 waves since March 13, 2020. Each wave has had higher peak intensity and longer than the previous one.

Dr. Shem Sam, a Researcher, and Infectious Disease Modelling Expert. Picture : Courtesy

What triggers the waves?

A short while after the first case of COVID-19 was reported in Kenya in March 13, 2020, the Government of Kenya imposed a three months cessation of movement. When it was lifted, people relocated to various parts of the country for economic easy and convenience.

That movement caused the first wave of COVID-19 infections from July 23, 2020, to September 4, 2020.

During the cessation period, learning institutions were also closed. Then the government partially opened schools in October 12, 2020 for candidates.

On that Day Dr. Sam was piloting the model in Homa Bay County, courtesy of Prof. Richard Muga the County Executive Committee Member for Health. In response, people moved to where their children went to school. There was increased movement of learners, teachers, and families.

This resulted to the second wave which struck on October 28, 2020, and lasted until January 4, 2021.

The LREB was mostly affected by the third wave. The surge began after February 25, 2021, had a short lull between April 23 and May 15 and experienced peak intensity on June 26, 2021.

The LREB Committee of Eminent Persons appointed by the region’s Governors decided to approach the infections mitigation in a scientific way. They sought to understand the spread and underlying socioeconomic, clinical, and biomedical issues.

The fourth wave is expected to peak after October 4, 2021. The third wave ran into 4th wave with multiplicity of variants.

Through the model, Dr. Sam predicted that the LREB cases would begin to decline after July 10, 2021, if all public health measures were observed, otherwise after August 15, 2021. It did decline exactly from July 10, 2021.

The use of the model which included successful predictions of multi-variant infections in the LREB necessitated rapid assessment of how prepared the counties are and establishment an integrated online data system.

Scarcity of oxygen

Scarcity of oxygen in Kenya has led to death of many critically ill COVID-19 patients. Picture :Dr Shem Sam

With advice from Prof Khama Rogo’s committee, Dr. Sam and his team visited all the 14 counties as a matter of urgency and presented summary findings on June 25, 2021 during the governors’ summit in Kisumu.

A report was submitted. It included county specific needs and recommendations, general findings and conclusions.

The findings included insufficient oxygen for critical care, low testing capacity, and inadequate medical staff. There were also few isolation beds with piped oxygen gas. However, counties were not ready to share their resources and data to implement integrated online data system.

“The only counties with sufficient oxygen were kisii, Siaya and Kisumu, out of 14 counties,” said Sam.

Also, the region had low testing capacity and urgently needed rapid diagnostic kits. The report recommended rapid testing that gives instant results and can be used decide if a patient needs to be isolated instead of being released to  mingle with other people. Some of test reagents were however missing in some counties.

Healthcare providers were also demotivated and fatigued. They have to undergo a 14-days-quarantine before being released to meet their families after attending to COVID-19 patients. They therefore needed psychological support.

Governors’ resolution 

The LREB Eminent persons committee chair by Prof Khama Rogo and deputized by Ms Catherine Muma is happy that governors from the LBEB are co-operating. During their last meeting, they resolved to:

  1. Budget for oxygen, purchase and install oxygen plants in the next financial budget.
  2. Seek approval from the national government to import rapid testing kits, which are cost effective and support quick decision making on whether to isolate a patient or not.
  3. Counties to collaborate with county commissioners to implement and enforce stringent public health measures.
  4. Counties to cooperate on data sharing for establishment of integrated online data system.

He said that a herd immunity is the final solution but is not happening soon enough. “We need at least 51% vaccination of eligible Kenyan adults to avoid future high peak intensities.”

He however explained that the vaccination exercise has to be in large numbers within a short period so as to reduce the number of people who can infect others. “Vaccine equality is a necessity”, Dr. Sam observed.

“We recommend a combination of public health observation and vaccination. Our vaccination is taking too long and restriction fatigue is also getting in,” said Sam.

He gave an example of Israel that vaccinated 71 per cent of its population yet they are experiencing a third wave and are taking third jabs or booster shots.

Strict public health protocol should also the adhered to because the vaccinated people can still be infected or re-infected.

Low vaccination rate

According to a daily online update by the Ministry of Health, 2.8 per cent out of a population of approximately 53 million people, had received full doses by August 17, 2021.

Kenya is already experiencing vaccine shortages. Kenya’s vaccine supply chain relies exclusively on donor goodwill, under motivated health workforce (a significant percentage of antivaxers and vaccine hesitants) and lack of trust hangs heavily in the air.

Kenyan scientists are now calling on African governments to support medical research so that they are not forced to rely on developed countries to donate vaccines.

“Systems management requires significant overhaul to change the foregoing negative factors. We do not have enough medical oxygen in our institutions across the land so we cannot give good care to very sick patients. The limited oxygen available is not affordable,” said. Dr Shem Sam.

Access to oxygen is the new definition of access to healthcare for common Kenyans. Elite private urban hospitals that have oxygen can charge anything they want because there is no price control for this life saving commodity.

“Historical efforts to promote oxygen production in public hospitals have been frustrated by torturous procurement processes and tender preneurship ,” said Governor Wycliffe Oparanya,  LREB chair in one of their reports.

Dr.Sam suffered severe COVID-19 infection and stayed in ICU between  March 17 to 23, 2021. He finally recovered and continued researching even harder.

He is urging the national government to embrace the model and implement their recommendations across the country. “COVID-19 is a very predictive virus and if all necessary measures are put in place and adhered to then we should have very few infection cases or none.”

What journalists should do:

  1. Read the periodic advisories by the LREB Committee of Eminent Persons and follow up if they are being implemented.
  1. Warn your audience about the waves whenever they are predicted.
  1. Talk to the team of scientists working with Dr Shem Sam to understand the predictive model better.
  1. Follow up with your county government officials and find out how far they have implemented the recommendations presented to them and the resolutions they made.
  1. Find out how much has been spent by county governments to fight COVID-19 and how much they plan to budget in the next budget year.
  1. Report on how future waves come about. What are their causes? Can they be prevented? Were there warnings?









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