I have been closely following the emerging swine flu virus which is being transmitted from human to human in Mexico and Southern California. It has already resulted in more than sixty deaths in Mexico.

Analysis of the virus by the USA’s Centers for Disease control has shown the current virus contains sequences from swine flu, avian flu, and human flu. A CDC press briefing on the 23rd of April 2009 stated:

We know so far that the viruses contain genetic pieces from four different virus sources. This is unusual. The first is our North American swine influenza viruses. North American avian influenza viruses, human influenza viruses and swine influenza viruses found in Asia and Europe.

Three influenza pandemics occurred in the 20th century and killed tens of millions of people *. Humans getting ill from avian flu and swine flu etc. is not unusual in periods between flu pandemics. Causes for concern that a virus which may have pandemic potential has emerged include high rates of human-human transmission and recombination of animal and human flu viruses. What we are now seeing in Mexico and Southern California is in my view much more alarming than any of the avian influenza outbreaks in recent years because we appear to now have these factors in place. There are large numbers people who have not been in direct contact with pigs or birds falling ill, and authoritative reports suggest the virus itsself contains elements of human and animal flu.

The CDC also published a brief report on the USA cases, dated April 21, which states:

Preliminary genetic characterization of the influenza viruses has identified them as swine influenza A (H1N1) viruses. The viruses are similar to each other, and the majority of their genes, including the hemagglutinin (HA) gene, are similar to those of swine influenza viruses that have circulated among U.S. pigs since approximately 1999; however, two genes coding for the neuraminidase (NA) and matrix (M) proteins are similar to corresponding genes of swine influenza viruses of the Eurasian lineage (1). This particular genetic combination of swine influenza virus segments has not been recognized previously among swine or human isolates in the United States, or elsewhere based on analyses of influenza genomic sequences available on GenBank.

There was no mention of a human component to the virus in this report.

In my view the element to watch out for in news coverage over the week or so is clarification on this point of if recombination between human and animal viruses has occurred; if it has then based on previous pandemics, that is something to worry about. The viruses responsible for previous pandemics are those which have resulted from an animal strain of influenza recombining with a human strain. The current information on elements present within the emerging virus will have been based on PCR and immunological tests; only when the newly emerging virus is fully sequenced will it be possible to fully determine what recombinations have taken place. The molecular biology has, of course, to be viewed along side what we are seeing in terms of people’s health and people dying, but it is valuable additional information which can enable better predictions to be made.

The World Health Organisation’s Director-General, Dr Margaret Chan made a statement and took questions during phone based press conference today (25th April). In her statement Dr Chan said:

“This is an animal strain of the H1N1 virus and it has pandemic potential because it is infecting people; however we cannot say on the basis of currently available laboratory epidemiological and clinical evidence whether or not it will indeed cause a pandemic.”

It appears to me that Dr Chan has decided to make a pointed effort to describe the virus as an “animal strain”. Neither the CDC or WHO have stated that recombination between human and animal viruses has occurred to create the new strain. The CDC’s statements are much closer to describing that alarming state of affairs than the WHO’s. That said Dr Chan of the WHO is taking the no-nonsense, say it as it is approach with her clear statement: “it has pandemic potential because it is infecting people”, true, but it highlights that she does not yet have enough information on which to make a more reasoned statement.

Dr Chan also, as the CDC has, confirmed the strain of the virus in Mexico and California was the same. The CDC has published a brief report on the USA cases which states:

Preliminary genetic characterization of the influenza viruses has identified them as swine influenza A (H1N1) viruses. The viruses are similar to each other, and the majority of their genes, including the hemagglutinin (HA) gene, are similar to those of swine influenza viruses that have circulated among U.S. pigs since approximately 1999; however, two genes coding for the neuraminidase (NA) and matrix (M) proteins are similar to corresponding genes of swine influenza viruses of the Eurasian lineage (1). This particular genetic combination of swine influenza virus segments has not been recognized previously among swine or human isolates in the United States, or elsewhere based on analyses of influenza genomic sequences available on GenBank.

Alert Phases

The WHO, CDC and others use a system of six levels of alert relating to the potential of a pandemic. The world is currently at level 3 which is described as:

Human infection(s) with a new subtype but no human-to-human spread, or at most rare instances of spread to a close contact.

Phase 4, the next highest phase of alert is:

Small cluster(s) with limited human-to-human transmission but spread is highly localized, suggesting that the virus is not well adapted to humans.

Clearly events in Mexico and California will result in the WHO looking at if an increase in the likelihood of a pandemic has occurred. An increase in the alert phase will result in action being taken around the world, including in the UK.

From alert phase 4 elements of the UK Department of Health’s Plan entitled Pandemic flu: A national framework for responding to an influenza pandemic start to come into effect. While most government actions will wait until there are outbreaks in the UK some things are planned to start happening as soon as the WHO declares “alert phase 4”:

• From WHO Phase 4, the FCO will recommend that British nationals in affected and neighboring countries consider returning to the UK.
• The possible health benefits that may accrue from international travel restrictions/Border restrictions or border closures need to be considered in the context of closures the practicality, proportionality and potential effectiveness of imposing them, and balanced against their wider social and economic consequences.
• Initial allocations (two-week supply) [of drugs] from national stockpiles pre-distributed to PCT level.
• The Government will consider the relaxation of medicines and NHS regulations where necessary to ensure ease and speed of access.
• The Ministerial Committee on Civil Contingencies (CCC) will meet as required to agree early policy decisions and to oversee completion of planning. Regional Civil Contingencies Committees (RCCCs) will meet as required to promulgate policy decisions/advice and maintain overview of response.
• Emergency regulations under the Civil Contingencies Act may be made

It is notable that unlike other countries the UK does not plan to step up health surveillance of people returning from affected areas. Many countries have already started monitoring those returning from Mexico and the affected areas of the USA.

The UK’s Health Protection Agency’s Influenza Pandemic Contingency Plan does call for some screening within the UK if the WHO alert phase is increased to phase 4:

In communities with travel/family-related contact with countries affected by the novel virus, implement enhanced virological sampling or routine respiratory specimens, regardless of timing in relation to normal “influenza season”

UK Preparedness

No experts on pandemics or virology or other area of the life sciences on the UK’s National Security Forum despite a pandemic being identified as a leading threat in the national security strategy. I would expect Gordon Brown to correct this omission rapidly.

No doubt we will regardless be introduced over the next few days to figures such as Professor Lindsey Davies, National Director of Pandemic Influenza Preparedness along with local and national Health Protection Agency spokespeople.

Various UK agencies will be considering whether to activate the next stages of their pandemic flu plans; democratically elected leaders will be being briefed and asked to make decisions on what action to take and when.

An influenza pandemic will be very expensive, to the NHS as well as Local and National Government and the country more broadly. I see one of the main roles of government as to keep us all as safe as possible from threats such as pandemic flu. We have to find ways of decoupling the current financial crisis from anything which needs to be done to protect the health of those in the UK. (If there are further collapses in the derivates markets then such a “decoupling” of day to day life and the financial sector might need to be more widespread and revolutionary).

In terms of a technological approach this ought be an opportunity for the UK’s life-science base. I would like to see efforts made to develop a DNA vaccine, in parallel with conventional vaccine production, along with support for other research and development activity. Just as the second world war resulted in a massive technological jump, our life-sciences are now in a position where a meeting a challenge like this pandemic might push them forward. I am concerned that we do not have the best people we could working as clinicians or medical researchers in the UK; our selection criteria for both is not based on merit, if we are lucky and have an opportunity to correct this before the next pandemic it is one I think we ought take.

As I am writing this Sky News is reporting a member of British Airways cabin crew is in hospital in Northwick Park, London with flu like symptoms which emerged on a flight from Mexico City.

Here in Cambridge we are a city which is traditionally full of colds and illness as we have so many people, tourists and academics, visiting from around the world. That will surely put us at greater risk than other, more remote, parts of the UK. One possible victim is already only about 65 miles away in North London.

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