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


#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.

IMG_9911 (2)

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.

IMG_9656 (2)

 

 

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.

 

 


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Zika Virus News Events in Jamaica & Elsewhere

The past few days have been significant ones for news about the Zika virus.

who zika press conference 1-2-16

WHO Press briefing re Zika virus Feb 1, 2016

WHO Declares Public Health Emergency of International Concern

On Monday (Feb 1, 2016), the World Health Organization (WHO)  declared “that the recent cluster of microcephaly cases and other neurological disorders reported in Brazil, following a similar cluster in French Polynesia in 2014, constitutes a Public Health Emergency of International Concern.” (WHO Director-General Dr Margaret Chan’s statement) This decision was taken after the first meeting of the Emergency Committee which had been convened by the Director-General to look at these clusters in some areas now experiencing outbreaks of Zika virus. (WHO statement on 1st meeting of International Health Regulations Committee on Zika virus)

A Case of Sexually Transmitted Zika in Texas

zika - Dallas release 2-2-16 with highlightingThen yesterday came the headline-catching news from Dallas that the Centres for Disease Control (CDC) had confirmed a case of Zika virus infection which had been sexually transmitted. The Dallas County Health and Human Services (DCHHS) sent out a press release about the case. DCHHS Press Release re Sexually Transmitted Case of Zika Virus. A case of sexually transmitted Zika virus was recorded in 2008, but no cases during the current epidemic. (Listen to a 2011 CDC podcast about the 2008 case in Colorado.) Though the main mode of infection remains via the Aedes aegypti mosquito, this new case in Dallas does add another dimension to the current epidemic.

Two Briefings in the Wake of Jamaica’s First Confirmed Case of Zika Virus

Yesterday (Feb2, 2016) in Jamaica the Ministry of Health (MOH) held a press briefing, to update the country about the first confirmed case of Zika virus, which it had informed the public of last Saturday. Five Government Ministers addressed the briefing on aspects of the Government’s actions and plans regarding the Zika outbreak. Also in attendance were some Members of Parliament and Mayors, the MOH Permanent Secretary, the new Chief Medical Officer and a number of other government personnel.

Zika - GOJ press briefing 5 ministers - 2-2-16The Ministers (from left to right) were: Minister of Local Government & Community Development, Noel Arscott; Minister of Youth & Culture, Lisa Hanna; Minister of Information, Sandrea Falconer; Minister of Health, Horace Dalley and Minister of Education, Ronald Thwaites.

The video of the press conference is posted online, with the Minister of Health’s comments about the first confirmed case and subsequent actions taken by his Ministry running from 10:37 – 16:46 of the video.

Among the things that Minister Dalley mentioned were that:

  • the child who was the 1st confirmed case of Zika has recovered & no other member of the family is showing symptoms of the disease
  • there is increased fever/rash surveillance in Portmore and the entire island
  • that 1894 households in the particular area have been checked & interviews done with 1355 people
  • that 15 blood samples were taken as a result of the interviews & were sent to the CARPHA lab in Trinidad for Zika testing

The presentations were followed by a question and answer session with journalists.

Last night, zika - PM Simpson Miller 2-2-16Prime Minister Simpson Miller made a national broadcast regarding the preparations to reduce the impact of the Zika virus (video).

Text of National Broadcast re Zika Virus by PM Simpson Miller

At 5:30 that evening, the University of the West Indies (UWI) Faculty of Medical Sciences in collaboration with PAHO/WHO and the MOH held a Public Symposium entitled “Zika Virus Update”. It is a pity that this symposium wasn’t broadcast or recorded, as it was an excellent session, with very informative presentations and a robust question and answer session.UWI Faculty of Med Zika Update 2-2-16 poster with border

The focus of this symposium was obviously different from that of the MOH press briefing in the morning and a great deal of medical and scientific information was given and issues explored. It was particularly useful to have information given about the Jamaican context for the Zika outbreak and the issues arising out of that context. I found Professor Christie’s presentation of particular interest, raising as it did issues about the seriousness of the situation being faced regarding our ability to deal with an increase in cases of children born with possibly severe microcephaly.

A few other issues that came up during the symposium:

  • the impact of the advice for women to postpone pregnancies, given the fact that 50-60% of pregnancies in Jamaica are unplanned
  • whether in Jamaica women will have the option of an abortion in cases of Zika infection
  • the complexities surrounding testing for Zika virus & Jamaica’s current and planned capability for doing such testing
  • whether the current levels of fever/rash surveillance are adequate or should be greatly increased during the early stages of the outbreak

Repeatedly the point was made regarding how much is not yet known about the Zika virus and the possible complications associated with this generally mild to moderate disease. The need for further and ongoing research was stressed, but as Professor Figueroa said, in public health, you need to take the best of what you know and act on it; you can’t tell patients to wait on the results of a study.

There is a need for more opportunities for professionals to share information of this kind regarding Zika, and to be able to answer questions and engage in discussions with members of the public. These opportunities mustn’t be scripted and limited, but must allow for the open exchange of information and for frank discussion. A wide range of options exists for sharing such information and they must be used.

 


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For Jamaica, #BeAwareZikaIsNear Becomes #BeAwareZikaIsHere

On Saturday, the Ministry of Health (MOH) in Jamaica issued a release saying that Jamaica has now recorded its first confirmed case of Zika virus.

The patient is a 4-year-old child from Portmore, St Catherine who has now recovered from the illness. The child first showed symptoms on January 17, the sample was sent to the Caribbean Public Health Agency (CARPHA) lab in Trinidad for testing on January 26 and the positive test result was received from CARPHA on January 29.

zika - MOH release re 1st confirmed case - 30-1-16(The press release is posted on the MOH website.)

 

In its tweets on Saturday, the MOH indicated the change in the country’s status by changing its Zika campaign hashtag from #BeAwareZikaIsNearzika - MOH hashtag 1

to #BeAwareZikaIsHerezika - moh hashtag 2

A press conference is scheduled for Monday, February 1, 2016, to update the country on this new (but not unexpected) development.

It is essential that the Ministry of Health, along with other Government agencies, develop and maintain clear, regular, reliable, responsive and trustworthy lines of communication with the general public, as well as with specific stakeholders & organizations. This is necessary at all times, but increases in importance during public health crises. People need up-to-date information and opportunities to ask questions and get answers, and they need to know where to go for reliable, official information.

The communication with the public during the ChikV epidemic in 2014 and the major fire at the Riverton Dump in 2015  was exceptionally poor, and left the public ill-informed, frustrated, angry and vulnerable. The experience so far with the Zika virus has been an improvement, and the Ministry must continue to build on this and not drop the ball.

And if I were going to be attending the press conference, these are some of the questions I would want to ask:

zika MOH press conference questions 30-1-16

 

 

 

 

 

 


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Zika Virus: Caribbean Public Health Agency (CARPHA) Shares a Regional Perspective at Jan 25 Media Conference

In Port of Spain, Trinidad, yesterday, the Caribbean Public Health Agency (CARPHA) held a media conference to give an update regarding the Zika virus in the region. Ms Carlon Kirton, Communications Manager, who chaired the briefing, explained the reason for it being held:

“As you may know, CARPHA is the sole public health agency for the Caribbean and our functions include the coordination of effective responses to public health crises in the Caribbean, as well as the provision of accurate, reliable, timely and relevant public health information. It is therefore important that we clear the air on issues pertaining to the Zika virus.”

Five presentations followed:

carpha Hospedales 25-1-16Dr C. James Hospedales, Executive Director, gave a regional perspective on Zika in the Caribbean (text).

“Zika, like Chikungunya in 2014/15, is historic as only rarely does a new disease emerge and spread through a population. And CARPHA, like CAREC before, has a major part of its mission as the discovery and monitoring of the spread of new diseases, with the support of health workers who are on the front line, the laboratories, and regional airlines which cooperate in transporting diagnostic specimens from our 24 member states….

As a new disease in this population, it’s not completely clear how it will behave. The situation is rapidly evolving as new information comes to light. In terms of context, we already have Dengue fever — for generations, and ChikV. We also have Leptospirosis and Malaria, in some countries, which can have similar symptoms to Zika. Doctors and health workers need to consider these possibilities when seeing patients with Zika-like disease.

Dr Karen Polson-Edwards, Senior Technical Officer, Vector-Borne & Neglected Tropical Diseases, presented on Zika – the disease (text).

“Zika is transmitted primarily by the Aedes aegypti mosquito, the same mosquito which transmits Aedes_aegypti_during_blood_meal (1)chikungunya, dengue and yellow fever and which is present in every country of the Caribbean. Mosquitoes become infected when they feed on a person during the first week of infection with the virus and in turn these infected mosquitoes can then spread the virus to other people through bites.

The symptoms of Zika are similar to other mosquito-borne infections such as dengue and chikungunya, and include fever, skin rashes, conjunctivitis, headache, muscle and joint pain, and a general feeling of being unwell. Only 1 in 4 persons infected with Zika virus may develop symptoms which are usually mild and last for 2-7 days. However, serious complications can sometimes occur in persons who are infected.”

Dr Lisa Indar, Programme Manager for the Tourism and Health Programme, spoke about Zika and Tourism (text).

Caribbean_general_map“The Caribbean is the one of the most tourism dependent regions in the world, thus travel related diseases like Zika have the huge potential to negatively affect the economies and tourism destination reputation of Caribbean countries. In fact, according to our partners, the Caribbean Tourism Organization (CTO) and Caribbean Hotel and Tourism association (CHTA), there are already reports of travel cancellations in the Caribbean due Zika….

CARPHA, through its integrated regional Tourism and Health program, and in collaboration with its partners, CTO and CHTA, is taking a holistic aggressive approach to travel-related Zika (and other mosquito borne infections) through prevention and control….”

Dr Derrick Aarons, Ethicist, made a brief statement on Ethical Issues – Zika virus in the Caribbean (text) carpha Dr Aarons

“To limit the effects of any possible epidemic, good early communication, and adequate community engagement and collaboration are required. Our communication must therefore outline sufficient details for persons to realize its relevance to them individually before the onset of the illness within their country or community. And so – at the governmental level, good, helpful information about the zika virus and effective measures to minimize infection through eliminating mosquito breeding sites and measures to avoid being bitten by a mosquito – should occur. This helps to avoid confusion, mis-communication, and misunderstanding.

Further, as in every infectious disease, our relevant authorities should not downplay the risks – as this could lead to higher rates of preventable infections. Neither should we overstate the risks, as we would not want any panic or any lack of public trust occurring subsequently, as this can be long-lasting. It is always good to provide timely, adequate and appropriate information, as we are now doing. And so we are telling you of the nature of the disease, the types of interventions to be implemented, and the reasons for these interventions.”

Dr Joy St John, Director, Surveillance, Disease Prevention & Control, reported on Strengthening the Health Sector Response to Zika (text).carpha dr st john

“It is important to note that the laboratory testing for ZIKV is not geared toward identifying EVERY SINGLE case of ZIKV which may occur in a country, as many persons may have mild disease and may not come to clinical care or require a test, at all. The numbers of clinically confirmed cases are therefore not intended to reflect the actual number of cases in any given country; rather, lab confirmation of ZIKV circulation is meant to keep track of the appearance of ZIKV in new areas and provide updates on the spread of the virus. In most cases, physicians will need to use clinical criteria (patients’ signs and symptoms) as well as epidemiologic data on the circulation of ZIKV in the areas from which their patients present, in order to come to a diagnosis of suspected ZIKV.

Special attention is warranted in the follow-up of patients for varying types of neurological sequelae after ZIKV infection and particular attention should be paid to follow up of pregnant patients who present with febrile illness compatible with ZIKV, and their offspring, in light of current concerns regarding a potential connection between ZIKV infection in pregnancy and the development of microcephaly in infants of affected mothers. CARPHA is currently in the process of piloting systems to facilitate the documentation of such cases, should they occur, so as to detect any similar patterns of association, in the Caribbean region, as early as possible. Barbados has been chosen as a pilot site for this activity.

It is important that we follow the course of this disease in the Caribbean very closely from more than one perspective. The first is that it is new to this region and its potential impact is still largely unknown.”

After the presentations, there was a question and answer session. A video of the media conference is posted online.

carpha agenda 25-1-16

As the Zika virus continues to spread throughout the Caribbean, CARPHA is one source of information for the region. Their website is carpha.orgCARPHA objectives