Right Steps & Poui Trees


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Covid Reflections: What has happened to genome sequencing test results?

A few months ago, as the media reported on the surge of Covid cases caused by the Delta variant in first the UK and then the USA, some of us in Jamaica began asking whether the variant was present in Jamaica. There is a great deal of travel to Jamaica from these two countries – residents, members of the diaspora, tourists – and it seemed only a matter of time before we got cases of the Delta variant here. Was testing being done for the variant by the Ministry of Health and Wellness (MOHW) and, if so, what had been found?

Responding to a question at the MOHW Covid-19 press conference on July 1, 2021, Chief Medical Officer Dr Jacquiline Bisasor-McKenzie said the following:

“The Delta variant is something that we really are watchful for. We certainly don’t want to have that in country because we recognise that there is an increased transmissible rate and also that there is an increased chance of admission. And so in our population that is vastly not vaccinated, it does put us at risk. 


In terms of the testing for the variant, we did, we sent off 200 samples to PAHO testing laboratory in Brazil last week. We have another 92 samples that we have sent off to the CDC. I’m not absolutely sure that that went off this week, but that was the plan, to send off another 92 samples to the CDC and another hundred samples to PAHO to be tested in Panama. 


So we have three arrangements in place now. We really have had some problems in terms of getting the genomic sequencing done. And a lot of that delay has been because of transportation, not because we have not had willing partners to do the testing. But the transportation problems have delayed us getting the samples out, even to the extent that transportation routes, because they have to be longwinded, have resulted in damage to the samples that made not all of them at some times suitable for testing. So we believe that we have worked out something now, a more reliable transport method to get these samples out and we have three partners – the PAHO, CDC and CARPHA – to do the testing. So we do expect that at least every two weeks we should be getting out at least a hundred samples for testing.


The turnaround time once they receive the sample for PAHO, we have been told, is two weeks. The samples last batch went out last week. They are in receipt of the samples, so we are hopeful. We know that sometimes we get times and it may not turn out to be exactly that but we are hopeful that in another two weeks we will have that first set of results. And thereafter we should have results coming after.


We also have started to do some in house testing using kits that are donated by PAHO that enable us to choose the samples better for testing. So we have now a method in place where we can pick up whether or not there are mutations. So mutations can be quite varied and can sometimes not be of any significance at all. But we can now pick up if there are any variations from the normal wild type and those are the samples that we have been sending for testing for genomic sequencing to see if those mutations show any variants of interest or variants of concern.”

(Transcribed from PBCJ recording of July 1, 2021 MOHW press briefing)

This left me hopeful that, despite previous problems that had affected testing for variants, there was now a new system in place that would mean faster results that could help to inform government decisions and responses and help the public to better understand what we were facing. The time lag was still not optimal, but seemed better until we had the equipment needed to do genomic sequencing here.

However, there seemed to be a delay in the hoped for two week turnaround time for the results from PAHO and in a presentation on July 20, 2021, at the Joint Select Committee of Parliament dealing with Covid-19 and related matters, National Epidemiologist Dr Karen Webster-Kerr included this slide:

It showed that results had been received for samples sent to the CDC, but that no results had at that time been received for the samples sent to PAHO.

(I wrote about that presentation in Parliament in a post I made on July 22, 2021 – On the Verge of a Third Wave? – Jamaica’s Current Covid-19 Situation.)

And to date we have not had any clear update on what has happened regarding those and any other subsequent samples sent to any of the three labs for genomic sequencing. The most we have heard is comments during various media interviews or at press briefings that we are still awaiting results from overseas partners. And that there is no confirmation through testing that the Delta variant is here, but that from other indicators we can assume that it is.

At the press briefing on Monday, August 9, 2021, held to announce the latest changes to the Covid restriction measures, Minister Tufton said, in response to a question from Jamila Maitland about test results and the Delta variant:

“As it relates to the test for the variant strain, I think we are on record of saying that we do believe that it is here based on the movement between countries where it is the dominant strain. We have not yet confirmed its presence based on the test results that we have gotten to date. However, those results up to this point were results that were a little dated because it takes a while to get back the results from where we send them. We are anxiously anticipating the results of tests that would hopefully reflect more what is present in the population. But we continue to advise caution.”

Minister Chris Tufton, at OPM press briefing, August 9, 2021 (transcribed from PBCJ recording)

It is now nearly six weeks since Dr Bisasor-McKenzie outlined the new arrangements for genomic sequencing testing and it is three weeks since the presentation and discussion at the Covid Joint Select Committee in Parliament. We really need a clear update on what has happened with the new arrangements and why it is that we haven’t seen any further results other than the CDC results shown on July 20.

I assume that the MOHW will be holding a press briefing on Thursday and that would be an appropriate opportunity for a full update. Some questions I would hope to hear answered would be:

  • Since the list shared shared on July 20, 2021, have the results of any samples sent for genomic sequencing been received from PAHO, CDC and CARPHA?
  • If so, when were these results received and what did they show?
  • If any results were received, what were the dates on which those samples were collected?
  • What samples have been sent for which results are still outstanding?
  • What has been the cause of the delay in receiving the results for samples sent? What has been or is being done to remedy this?
  • What impact do delays such as this have on the Ministry’s ability to make plans and decisions?
  • Specifically, is it still the case that there is no confirmation by testing that the Delta variant is present in Jamaica?
  • What is the current status of plans to be able to do genomic sequencing here?

Let’s see.

PBCJ Recording of MOHW press conference held on July 1, 2021

PBCJ Recording of OPM press conference held on August 9, 2021

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#ZikaVirus Update: Jamaica, Caribbean & Beyond

The news regarding the Zika virus is being updated all the time. Underlying the updates is an acute awareness of how much is not yet known about the virus and its effects, how much there is still to learn. Almost on a daily basis, new information about the virus’ spread is reported. In this post, I’ll touch on a few of these updates.

Jamaica: 7 weeks after 1st confirmed case of Zika, 4 new cases confirmed

Up until Thursday, March 17, 2016, Jamaica had one confirmed case of Zika virus, a case which had been confirmed on January 29. The 4-year-old child had started to show symptoms on January 17. This was the first confirmed case and remained the only confirmed case for the following 7 weeks.

As I was driving to a Technical Update on Zika, Gillain-Barre & Microcephaly being held on the evening of March 17 at the Faculty of Medical Sciences at the University of the West Indies (UWI) Mona, this was the foremost question in my mind: Why hadn’t there been any further cases of Zika reported? I wondered what explanations the experts might have for this.

The Technical Update was a collaboration by UWI, the Ministry of Health and PAHO/WHO. A PAHO/WHO technical team was in Jamaica for consultations and the opportunity was seized to have an update which was open to the public.

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Dr Winston De La Haye, Chief Medical Officer, was chairing the proceedings and after the opening remarks, the first presentation began. Dr Stephane Hugonnet of WHO presented on Zika and arbovirus surveillance, microcephaly and other neurological disorders – recent evidence & implications for health systems. IMG_9648 (2)

At the end of his update regarding the global situation, Dr Hugonnet made some comments about the situation regarding the Zika virus in Jamaica. He said that for Jamaica, the epidemic curve of about 95 suspected cases showed a sharp increase, with a peak in week 5, which corresponded with the week in which there was the first confirmed case at the end of January.  This was then followed by a decrease in suspected cases.

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Dr Hugonnet said it was very surprising that there hadn’t been any other cases and it was hard to understand having only one case. He said that the surveillance system was working well, and there were suspected cases of dengue, chikungunya or fever and rash that were being picked up and sampled.

He said that it was a priority to assess whether or not the Zika virus was circulating in the country and that it was necessary to strengthen the investigation around the index case, including retesting to check if it was indeed positive. He also advised sampling of the negative tests to see if they were really negative.

Once it was established that the virus was circulating in Jamaica, there would be no need to keep testing all cases. It would then be necessary to monitor the trend of the epidemic and the geographical spread. It would also be necessary to monitor pregnant women and cases of Guillain-Barre Syndrome (GBS), and to establish baseline data for microcephaly and GBS.

At the end of Dr Hugonnet’s presentation, Dr De La Haye resumed the podium to continue his duties as Chairperson. In a rather dramatic turn of events, he told the gathering that on his way to the symposium, he had actually received information that 2 new cases of Zika had been confirmed. This meant that the country now had a total of 3 confirmed cases. He noted that the 2 cases had been confirmed by the recently upgraded Virology Lab at UWI, saying that it was an advantage to have a shorter turn around time for getting test results. (See JIS report regarding UWI Virology Lab upgrade)

MOH zika virus press conference 18-3-16

Ministry of Health press briefing on Zika virus, March 18, 2016 (Far left: Dr De La Haye. 2nd from left Minister Tufton.)

By the time the Ministry of Health held a press briefing the following afternoon (Friday, March 18), the number of confirmed cases had increased to 4. Remarks by Minister of Health Dr Christopher Tufton at Zika press briefing – 18-3-16 By the post-Cabinet press briefing on Tuesday, March 22, another case had been confirmed, bringing the total to 5. Four of the cases were in Portmore, St Catherine and one was in Lyssons, St Thomas. And it is expected that the number of cases will increase.

moh zika tufton more cases 18-3-16

Representatives of the Ministry of Health have been doing many media interviews, outlining the steps being taken by the Ministry regarding the increased number of cases and reiterating the ongoing public health messages about reducing the risks of being infected by the Zika virus.

Caribbean Public Health Agency Update on Zika in the Caribbean

On March 23, 2016, the Caribbean Public Health Agency (CARPHA) posted a short video in which Executive Director, Dr. C. James Hospedales provided an update on the Zika virus in the Caribbean region. (Click here for video.)carpha zika virus video update 23-3-16Some points made by Dr Hospedales:

  • 15 countries in the region have reported cases of Zika virus transmission in their countries/territories.
  • Microcephaly & Guillain-Barre are rare conditions and are not required to be reported in the Caribbean region, so there is little baseline data on these conditions.
  • CARPHA is now in the process of setting up collection of baseline data.
  • The Caribbean is vulnerable to Zika virus for a number of reasons: a susceptible population which has not met the virus before, wide spread Aedes aegypti mosquitoes & a lot of travel in and out of the region.
  • In another 2 months, many of the countries will see the start of the rainy season, which will increase possibilities for increased mosquito breeding.
  • The two most important messages for stopping the spread of Zika are stopping the mosquito breeding & stopping the mosquitoes biting.

CDC Issues Updated Zika Recommendations to do with Pregnancy and with Sexual Transmission

On March 25, 2016, the US Centres for Disease Control & Prevention (CDC), issued an update of its recommendations regarding aspects of Zika Virus. (Click here for full update.)

cdc update re zika 25-3-16

The updated recommendations, which are worth reading in full, are given under 3 headings:

Article 1: Updated interim guidance for pregnant and reproductive age women

Includes the following:

cdc zika 25-3-16 coloured page A

Article 2: Updated interim guidance for preventing sexual transmission of Zika

Includes the following:

cdc zika 25-3-16 coloured page B

Article 3: Increasing access to contraception in areas with active Zika transmission

Includes the following:

cdc zika 25-3-16 coloured page C

(It is significant to note that more than 50% of pregnancies in Jamaica are unintended, which impacts the public health education regarding Zika and pregnancy here also.)

As the spread and impact of the Zika virus continues in the region, we in Jamaica need to keep informed and act on the information to best protect ourselves from this new personal and public health challenge.