COVID-19: Prelude to a Pandemic

COVID-19 has traveled far and wide from the original outbreak zone in Wuhan China.  Currently, the outbreak has spread to 68 countries (+ 1 cruise ship).  As of March 1st, 2020, there are a total of 89,081 cases with 3,057 deaths.  The rate of new cases in China has steadily dropped, likely due to containment efforts. Last week, the trajectory of the COVID-19 outbreak suddently changed, when local spread began to be reported in South Korea (4,212 cases), Italy (1,701 cases) and Iran (978 cases).  With higher caseloads in these countries, it is only a matter of time that the outbreak will become a global pandemic.
It is possible that transmission will smolder in some countries, while it is surges in other countries.  The surges will increase the likelihood of further spread.  Thereafter, it could be introduced and lead to outbreak spikes in other countries.  There is some suspicion that the disease may already have penetrated into sites, while rigid case definitions and persons under investigation were used.  What is also incredible is the degree of measures that countries are taking to protect themselves from localized spread or introduced infections.
A few local, unconnected COVID-19 cases have already been confirmed in the United States.  Currently, the US has 87 confirmed cases, with several recent cases identified in Washington State, including within a care facility, with two deaths reported.  A recent case of a high school student in Snohomish County was found to have virus with a geneitc link to the first US case, that of a man in his 30s who had traveled to Wuhan and returned to Washington state several weeks prior – potentially six weeks of local spread.  On Friday February 28th, a case was confirmed in Oregon.  On Sunday, a second case was confirmed, who was a contact of the other.  Neither of them fit the original definition of a person at risk.  A surge in cases, particularly those unconnected to the original outbreak, raises the high likelihood that occult community spread is already occurring.  
Key Points:
  • The case fatality rate is likely lower than original estimates and varies with at-risk groups, including age and underlying chronic disease
  • It is likely that occult transmission of COVID-19 has already occurred in a few areas (e.g. Washington State) in the United States
  • Masks are unlikely to be useful in preventing COVID-19 disease beyond the usual prevention measures, such as handwashing, hand sanitizers, social distancing and not touching hands to the mouth, eyes and nose.
  • Although person-to-person contact of COVID-19 is the usual mode of transmission, inanimate objects or surfaces could pose a risk.  The virus may survive on surfaces possibly for several days but are easily addressed with dilute bleach or alcohol solutions.
  • Rapid diagnostic tests, particularly at the point-of-care, are necessary and useful tools to mitigate risk and concentrate resources and containment efforts.
  • As a means of capturing all at-risk patients, the CDC recommends COVID-19 screening of any patient with severe respiratory disease and no other identifiable cause.
The Case fatality rate
The case fatality rate is one way of determining the severity of a disease.  It is specifically the total number of people who die from a disease over the number of those diagnosed with the disease.  This number is not always accurate because of assumptions on the reliability on the denominator.
Case fatality rate (%):       Number who die from disease
                                             ————————————————–                      X 100
                                              Number confirmed with disease
In epidemiology, a case definition often relies on syndrome lists, when tests to confirm diagnosis are not readily available.  Whereas death from a disease is usually more accurate, the number of people with a certain disease may be misrepresented.  Many people do not come to be assessed if they have mild disease.  Moreover, as with COVID-19, there was no readily available test in the beginning of the outbreak.  So, in an active epidemic, as more cases are determined with widespread, reliable diagnostic tests, the denominator becomes more accurate.  As is often the case, the case fatality rate tends to drift downward and closer to a reliable metric.
Based on the February 24th, 2020 JAMA article, of the 72,314 cases records, 44,672 were diagnosed with the viral nucleic acid test that was available (62%);  22% were suspected based on symptoms and exposures without testing; 15% were clinically diagnosed cases without testing; 1% were asymptomatic cases diagnosed with the nucleic acid testing.  This means that about 37% of the cases that go into the denominator were not confirmed with diagnostic testing.  Not to mention, how many more persons were not included, who didn’t seek care for likely milder disease and possibly, who died and the infection wasn’t considered.
Those with COVID-19 presented with mild (81% of cases), severe (14%) or critical disease (5%), of which almost 50% died.  The total case fatality rate (CFR) of confirmed cases was 2.3%.  Adjusting the CFR to age provides a more accurate picture of the impact of age.  From this, you can see that the infection is disproportionately more severe in the elderly.
AGE                                                                                                                 DEATH RATE (all cases)
80+ years old                                                                                                                14.8%
70-79 years old                                                                                                              8.0%
60-69 years old                                                                                                              3.6%
50-59 years old                                                                                                              1.3%
40-49 years old                                                                                                              0.4%
10-39 years old                                                                                                              0.2%
Less than 10 years old                                                                                                no fatalities
About 35% of those who died from COVID-19 in this study had a known chronic disease:  10.5% had cardiovascular disease, 7.3% had diabetes, 6.3% had respiratory illness, 6% had hypertension and 5.6% had cancer.
Outside of Wuhan, case fatality rate is lower (0.7%).  It is expected that with the secondary outbreak sites, we will have a better understanding of both numerator and denominator, as well as other demographic information to better inform us on the impact of thise disease.
More on Masks:  Save them for Healthcare Workers
Behaviors have surfaced over the fears of COVID-19 “coming to a city near you,” some proactive and some not always thought out as well.  In one survey in Taiwan, 79.9% of the people questioned said that they were using masks to protect themselves from COVID-19.  The CDC currently does not recommend the use of facemasks or respiratorys (e.g. N-95) for the general public.  Masks or respirators likely do not provide any protection from general precautions such as handwashing or hand sanitizer use and avoiding touching your mouth, nose or eyes.
For the purpose of definition of “close contact spread”, this is when a person is in contact within 6 feet from an infected person for at least 1 hours of exposure.  The greatest at risk for infection with close contact spread are healthcare workers.  Like SARS and Ebola in the past, front-line healthcare workers face the biggest risk of becoming infected.  The sickening of healthcare workers would represent a strong blow toward our treatment capacity, and should be prevented.
At present good handwashing technique or the use of alcohol hand sanitizer and social distancing are probable the most helpful measures to protect the general population from infection.  If you are ill, please sneeze in your arm – not in your hands.

sneeze in hands

Surface Transmission of disease
Spread of COVID-19 is mainly spread from person to person, when respiratory droplets containing virus come into contact with a mucus surface, such as the mouth, eyes or nose.  They can also spread on fomites, inanimate objects such as keys, doorknobs, money or phones, or on contaminated surfaces.  According to the CDC, “because of poor survivability of these coronaviruses on surfaces, there is likely very low risk of spread from products or packaging that are shipped over a period of days or weeks at ambient temperatures.
What do we know about COVID-19 and survival on surfaces?
It is generally believed that viruses are relatively fragile and susceptible to desiccation (drying), if they are not in the host.  Smaller respiratory droplets evaporate and likely the virus particles on those droplets are not able to re-infect.  It is not clear whether COVID-19 virus particles on larger droplets would thrive longer.
A recent study in the Journal of Hospital Infection suggested that SARS, MERS and endemic (HCoV) coronaviruses could remain infectious on surfaces, including metal, glass or plastic, for up to nine days – at room temperature.  At a temperature of  30 degrees Celsius (86F) or greater, it is likely to survive a shorter duration.  The CDC is presently studying this concern for COVID-19.  The researchers commented that surface disinfectants such as 0.1% sodium hypochlorite or 62-71% ethanol readily decontaminated surfaces.
The Need for Readily Available Diagnostics
A speedy diagnosis has a lot of benefits.  While taking into account the timing to a positive test, symptomatic patients can be triaged into “confirmed” versus “possible” or “unlikely” groups, while other tests are employed (e.g. influenza and Respiratory virus panel PCR).  Those confirmed groups can be appropriately informed to stay home and avoid contact with others, bolstering containment strategies.
The ideal place for rapid diagnostic kits would be at the point-of-care, rather than at national or statewide public health departments.  Though the CDC has made test kits available to state public health departments recently, with confirmation of cases still managed centrally by the CDC.
The test for diagnosis of COVID-19 relies on nucleic acid (RNA in this case) and is referred to as a real-time reverse transcriptase-polymerase chain reaction (rRT-PCR).  A sample is taken from the nasopharynx (deep nose) or oropharynx (throat) is run on a testing apparatus known as a theramal cycler.  A hyperlink to the details of the procedure.
The test often has a high sensitivity (ability to detect a true positive) and high specificity (not detecting a true negative).
The use of a chest computed tomography (CT) can be another way to determine if someone has COVID-19.  A CT can demonstrate the effects of the lung tissue from the viral infection.  When using RT-PCR resulst as a reference, the CT scan for detecting COVID-19 related pneumonia was 97% sensitive and could show disease even before the RT-PCR turned positive.
The Current Efforts 
In the last few days, several cases have been reported in the United States (e.g. California, with no clear epidemiologic connection to the original outbreak site.  Consequently, the CDC revised their criteria for a person under investigation (PUI), expanding the definition to include those with fever and cough and “no source of exposure identified.”  This leads to questions about the possibility of a smoldering epidemic already underway in some parts of the United States.
With a wider definition for PUI, it is expected that physicians will be able to test patients for COVID-19 who have more serious respiratory illnesses even without close epidemiologic connections.  They will be placed in standard, contact and airborne precautions and be isolated in special rooms that circulate the air out of the room (negative pressure), while they are being ruled out.
It is expected with a greater case burden, hospitals may be at the risk of exhausting their resources.  Presently, hospitals in the United States are coordinating efforts as entities and in conjunction with state and local health departments.  Particularly in light of the recent cases without connection to the initial outbreak area, hospitals are ramping up their vigilance in considering cases to be tested.  Signage, visual alerts and mask and alcohol sanitizer stations are placed at all entry points of the hospital.  Patients are being triaged in a way to avoid possibly infecting others in the waiting room or medical staff.
Patients who are ill with milder systems are being asked to stay home and not be seen in the clinic, rather than put others at risk for infection.
The Stock Market has been infected by COVID-19
The uncertaintly of COVID-19 has led to a paralysis and sell-off in the stock market with a decline of 12% in one week.  Investors are being encourage to wait out this volatility.  Its unclear how this strategy will be affected by the uncertainty of the COVID-19 outbreak.
Why take your chances with face-to-face meetings during the COVID-19 outbreak?  Zoom conferencing along with 3M, the makers of surgical masks, were a few of the companies that were buffered from these declines – a sign of how fears can promote company investments.  If Zoom conferencing becomes the standard for the office meeting during the COVID-19 outbreak, they will likely achieve further gains.  Anyways, at least you don’t have to shake that guy who catches his cough or sneeze with his hands – or worse get sneezed on.
It is likely that there will be economic and sociopolitical reverberations as a fallout of this outbreak for some time.


Solutions for My Extreme Sleep Deprivation

I have had insomnia all my life, but my stroke brought this problem to a new level.  I had a stroke in the brainstem which puts us to sleep and wakes us up. Since my stroke I have repeatedly had nights where I get only two hours of sleep per night.  When I did not sleep and did not feel sleepy for two days I FREAKED OUT so I got aggressive about addressing this problem.

Daytime routine.  I avoid caffeine after lunch time.  This meant changing to decaffinated iced tea for dinner and drinking water when I eat out at night.

Bedroom environment.  I sleep in a dark bedroom with no TV.  The alarm clock is placed where I cannot see it.  Sometimes I wake up and find I am sweating.  So I lowered the room temperature because a lower body temperature tells the brain to sleep.

Preparing for bed.  If I am sleepy at 9 p.m. I go to bed.  If I wake up in the middle of the night at least I have slept for 4 or 5 hours because I went to bed early.  If I am still wide awake at 10 p.m.
I go to war.  I turn off the TV, wash my face and brush my teeth, and come back to the living room to listen to a calming CD.  If my body aches I take Tylenol.  The constant burning in my hemiplegic foot keeps me awake so I provide a competing sensation by taking a warm gel pack to bed.

Back up plans.  (1) If I lay in bed and cannot fall asleep, I get up and eat a tiny bowl of cereal with milk.  (2) If I wake up at 3 a.m. to go to the bathroom and cannot fall asleep, I get up and turn on a calming CD or a fan at a low volume for background noise.  These strategies work only IF I realize I have been lying awake for an hour or more.

From a Stroke Survivor: I’m Ain’t As Good As I’m Gonna Get, But I’m Better Than I Used To Be

I admit it. This refrain was borrowed and comes from Tim Mcgraw’s country song, Better Than I Used To Be. I love that song and realize that now, 10 years post stroke, that song could have been about mostly me. I turned the negatives that were mentioned in the song around to positive ones.
Please listen:

He sings:

Hold a grudge

I used to hold grudges–like, forever. But no more. For example, there was my his-way-or-the-highway sibling and his super-controlling wife. I realized, or pretended to imagine, that they liked to have control, but I wasn’t going to be a party to that. Or my colleagues that didn’t listen to my demands for speaking without confrontation. Or my neighbors who didn’t throw the mouse in the rubbish when it came to land in our shared driveway with my two kids playing. Having no grudges means I’m free of all that negativity and that the cliche Life Is Too Short really means something.

The hearts I’ve broke

Yes, I broke some hearts because, and as my sons say, I liked men with edge because of my sheltered past, not nice guys who would have been perfect husbands and fathers. I married an edgy guy for 18 years who threw food on the floor if he didn’t like it, broke furniture in a fit of rage, once inches away from my infant son, and threatened me countless times. The other person was simply a mistake that lasted 16 years when I should have known better. There were signs, yes. But they’re both now dead to me, the first literally, the other figuratively. I found a couple on nice ones I’m sort of interested in, but time will tell if those feelings are returned.

People I let down

Sure, I let people down, and I had reasons, albeit faulty and selfish, to do so. But show me people who don’t have any regrets in their whole lives, and I’ll show you liars. From not agreeing with contentious friends to not cooking what I said I was going to bring to a pot luck supper, I let people down, so down that they stopped speaking with me. But, come on! Over politics or Shepherd’s Pie?

There’s some dirt on me

Absolutely, there’s some but not a whole lot, like the time I used my friend’s mascara when I had an eye infection on Saturday and then two days later on Monday she found out after she used that mascara the day on Sunday the day before (ouch! that was really a bad one) or how about the time I gossiped to people I knew would spill the beans about a friend’s secret drug addiction and she didn’t get the job. I did. 

But I have one thing that wasn’t in the song. Patience! Do you know how I got patience where there wasn’t any before? From my stroke. Talk about a silver lining! It took a while to develop it, but now patience is with me all the time. People write to me occasionally to ask how I developed patience instead of constant anger and frustration. I practiced becoming patient because, in truth, it doesn’t come naturally, at least to me. You have to want it, and it will come, not right away but eventually.

Maybe, in time, I’ll become like that character from the television show My Name is Earl, a f-up who won $100,000 in the lottery and decides to correct all the wrongs from his past. Or maybe I’ll begin again in “it’s-never-too-late” fashion  to make the right decisions this time around.

Freaked Out = Home Modification

I live alone so when the electricity goes out 2 to 3 times a year I have to handle it.  My stroke took away my ability to know where vertical is unless I can see my surroundings.  So I put flashlights in every room.  My plan worked until last night when the house went completely black while I was watching TV at 10 p.m.  I reached down for the flashlight on the floor next to my couch.  I started to freak out when I could not find it.  The electricity has gone off for hours in the past and sitting on my short couch until sunrise would be awful.  I finally found the flashlight, but after the lights came back on I put the flashlight in a different location.  I moved it to the tray on my couch that holds my remote control devices.  I also moved a second flashlight to a counter directly behind the place I sit at my kitchen table.

A previous outage taught me to put a battery operated lanturn on a cart next to my bed.  I turn the lantern on by rolling on my side and pulling the cart close too me so I can feel the on switch.

Unusual problem solving after a stroke NEVER ENDS.

Patient Education: Making Sleep a Health Priority

Get the best out of your sleep

Good sleep is a necessity for the healthy functioning of the mind and body.  It is also one of the things that we can forcibly deprive ourselves.  Ideally, we spend one-third of our lives asleep.  Improving your sleep quality can be the first step toward stress resilience and  healthy decisions.

Could you imagine sleeping for 4 hours, then waking up to go to the gym to exercise, then going to work, and taking an extra cup of coffee to stay up?! If this happens to you, wouldn’t you skip the gym and maybe skip preparing a healthy meal? Without sleep, the brain has a lower threshold to develop stress, anger and impatience.  Driving a car after not sleeping well the night before is equivalent to driving under the influence of alcohol.  The system doesn’t just recalibrate the sleep deficit by sleeping in on a Saturday morning.

Sleep affects more than just the neurologic system.  Many first-time parents probably remember getting up at night because of a crying baby.  Most people recognize that sleep reduces memory and concentration and impairs judgement, but sleep also reduces the immune system, leads to weight gain and increases the risk of high blood pressure and stroke.  The endocrine, immunologic and vascular systems are regulated by sleep.

Here is a list of tips to ensure ideal sleep:

  1. Tone down technology: Silence your cellphones and other technology and put them in a different room at a set time each evening, preferably at least 2 hours before bedtime.  The screen lights can inhibit the production of melatonin, which would otherwise prepare you for sleep.
  2. Preparation: Provide yourself a 30-60 minute of winding down before lights out. Limit reading time to 20-30 minutes.
  3. Make sleep a routine: Go to bed and wake up at consistent times.  Most of the time, you will sleep for 6-8 hours naturally.  With a natural routine, you will very likely not need an alarm clock.  If you do use it, stop it and get up – don’t hit snooze 5 times.
  4. Your bed, the slumber throne. Limit activities to sex and sleep.  Watching TV, eating, working on the computer may affect your body’s ability to rest in bed.
  5. Avoid medicating to sleep: Medications to sleep should be avoided or limited to a low dose of melatonin (2-4mg nightly).  Although the medications may sometimes “work”, they come with side effects and, moreover, are not addressing the source of the problem.  The last thing you want to do is develop dependence on alcohol, benzodiazepines or ambien, etc.  and then can’t sleep without it.  As for the other side of things, avoid any intake of caffeine after noon hours.  Avoid any stimulant medications, e.g. albuterol inhalers, immediately prior to sleeping.  One interesting association of sleep apnea is the patient who drinks high levels of caffeine during the day and then takes a sleeping medication at night.
  6. Environment: Keep sleeping area dimly lit or dark.  Ambient noise should be at a minute, though white noise is acceptable.  Temperature should be on the lower side, between 60-67 degrees F.
  7. Trouble-shoot for the future: If you are having problems sleeping at night and find yourself tossing and turning, thinking too much or waiting until that magic click to start, limit time in bed to about 15-20 minutes. There is usually a reason that this has happened and it is up to you to brainstorm it.  You can sit in your chair to begin to rest, meditate and then return to your bed to sleep.  The next day, think why this happened:  It could have been that maybe you exercised too close to bedtime, took too warm of a shower before sleeping, saw a stimulating program on TV, or tried to squeeze some work on the computer too close to bedtime.

If you still have trouble sleeping after following this checklist, you should consider being evaluated for sleep apnea or other conditions (parasomnias) associated with sleeping, such as restless legs, etc.

sleep man on desk

sleep man on desk

Wuhan Coronavirus: An Emerging Global Pandemic?

A wave of influenza-like illness caused by a novel Coronavirus, named 2019-nCoV by the WHO, has swept through a populous area of China. Since December 31, 2019, there have been more than 830 people infected with at least 26 deaths (as of January 23rd, 2020).  Chinese authorities have placed Wuhan, a city of 11 million in the Hubei province, on lock down, or quarantine, canceling flights and not allowing public transportation into or out of the region.  This comes amid the busiest travel season in China, the Chinese New Year on January 25th.  During this time, it is projected that there will be 2.5 billion trips by land, 356 million by rail, 58 million by plane and another 43 million by sea.

Expect that anytime respiratory viruses (more easily transmissible) emerge in a populous city, there will be a high caseload.  Cases have already been confirmed in other parts of China, including Beijing, Shanghai, Macau and Hong Kong.  In the last week, countries outside of China, including Japan, South Korea, Thailand and Tawain, Singapore and Vietnam have confirmed cases. On January 21st, the first case of 2019-nCoV was confirmed in Everett, Washington, after a traveler to Wuhan arrived in Seattle-Tacoma airport on January 17th and presented a few days later.  As of Thursday, a second and third case were being evaluated in Los Angeles and Texas.

Wuhan virus map 11.1579841262468

Wuhan virus map 11.1579841262468

What are Coronaviruses?

Coronaviruses (CoV) are zoonotic RNA viruses which cause infections in a variety of animals including pigs, cows, chickens, cows, bats and humans.  It is the virus’s infection of bats from which likely was the source of severe acute respiratory syndrome (SARS-CoV) and Middle Eastern Respiratory Syndrome (MERS-CoV).  Viruses are typically host and tissue specific.  Though, a favorable mutation can cause a virus to be able to jump from animal to human and be transmitted from human to human.

While CoV generally causes mild respiratory infections overlapping the flu season, their usual behavior diverged with SARS-CoV.  From the outbreak of 2002-2003, there were a total of 8098 cases with 774 deaths, amounting to a mortality rate of 9% – even towards 50% in those older than 60.  Fortunately SARS wasn’t as easily transmissible as other respiratory viruses.

How did such a disease severity occur?  It likely relates to the effects of two types of damage: the damage caused directly by the virus infecting cells within the lining of the lungs and the damage caused by components of the immune system, such as cytokines. Some viruses can induce a greater inflammatory response and lead to a more severe presentation.

MERS-CoV was likely transmitted from its natural host camels, functioning as an intermediate host between bats and humans.  In one report in 2017, of the 660 cases of MERS in Saudi Arabia, 42% had contact with camels.  The mortality rate of this infection is approximately 30%, with the elderly and those with pre-existing illnesses at the highest risk.

The 2019-nCoV thusfar has had the greatest impact on the elderly (>60) and those with comorbid conditions, similar to the other emerged coronaviruses.  Fortunately, the mortality rate from this infection is approximately 3%, much lower than SARS and MERS.  Although there are no treatments or recognized vaccinations for this emerging coronavirus, Wuhan-based scientists have already determined the genetic sequence of 2019-nCoV, and Chinese health officials have released this information to the public.  Scientists are beginning to work toward determining a feasible future vaccine.

What is being done to prevent cases in the United States?

As a method of containing the outbreak, the CDC is screening passengers entering into the United States from Wuhan for signs of respiratory illness.  Also, the flights from Wuhan have been routed to five U.S. airports for screening:  Los Angeles’s and San Francisco’s International Airports, New York’s JFK airport,  Chicago’s O’Hare, and Atlanta’s Hartsfield-Jackson airport.

Presently, the CDC has defined those at highest risk for 2019-nCoV as Patients Under Investigation (PUI) to have these criteria:

Clinical Features & Epidemiologic Risk
Fever1 and symptoms of lower respiratory illness (e.g., cough, difficulty breathing) and In the last 14 days before symptom onset, a history of travel from Wuhan City, China.– or –

In the last 14 days before symptom onset, close contact2 with a person who is under investigation for 2019-nCoV while that person was ill.

Fever1 or symptoms of lower respiratory illness (e.g., cough, difficulty breathing) and In the last 14 days, close contact2 with an ill laboratory-confirmed 2019-nCoV patient.

How much should the general US population worry?

The disease has been traced to animal markets in Wuhan and has spread over the course of three weeks to include imported cases in neighboring and distant countries.  So far, there has been no local spread in the United States.  With heightened awareness and screening, it is with hope that the disease will not be as heavily transmitted to the general population.  Combined with a lower mortality rate than the other emerged coronavirus infections, I think the general population should not need to worry about this infection.  At this point, those with higher risk, including the elderly and those with health problems, are much more likely to be infected by influenza than 2019-nCov.

Do masks protect from this infection?

Respiratory droplets from sneezing or coughing are well contained by masks.  Given that coronaviruses are transmitted this way, it is likely that anyone infected with 2019-nCoV would prevent spread by wearing a mask.  I don’t think that everyone should get a mask at this point.  It is also important to mention that respiratory droplets containing virus can contaminate objects and the hands and then simply be ingested and cause infection.  As with any viral infection, good hand-washing and social distancing an are important part of prevention.

It is certainly too early to tell how many people will be affected by this virus – and what impact it will have.  Sometimes mortality rates can change during an epidemic, if subsequent mutations confer greater virulence (potency).  The WHO has yet to deem this a global emergency, but it certainly is looking like it may develop into a pandemic.  It is no coincidence that the virus emerged from a populous area where livestock and human meet – an animal market in Wuhan, a city in China of 11 million.

Wuhan Coronavirus:  Tips to Understanding the (Next) Pandemic


Ahmed, Anwar E. 2017.   The Predictors of 3- and 30-day Mortality in MERS-CoV patients. BMC Infec Dis. 2017; 17:615.

Fehr A, Perlman S. 2015.  Coronaviruses: An Overview of Their Replication and Pathogenesis.  Methods Mol Biol. 2017; 1282: 1-23


Summary: The 2019-2020 influenza season is off to an early start. Interestingly, the majority of cases have been associated with influenza B. With an increase in influenza-like illness identified in these last few weeks, it is possible that this season could be similar or worse than the 2017-2018 season.  Brace yourselves for an active season.

Welcome to the new year 2020.  As expected, at around the 46-48 week of 2019, we exceed the baseline of 2.5% of influenza-like illness (ILI).  The percentage of ILI has soared in the last few weeks compared to what it was last season.   Presently in United States, the seasonal influenza epidemic is widespread.  This season has been unique from others in the percentage of cases attributable to influenza B followed by H1N1.  The Centers of Disease Control (CDC) estimates approximately 64% of the flu cases are from influenza B.  Usually, influenza B cases pick up towards the second half of the season.





From the FLUVIEW CDC site (above), there has been a very high level of influenza-like activity.  Influenza has a high attack rate, affecting 5-10% of the adult population and 20-30% of the population of children.  High ILI activity suggests that there will be a high rate of transmission in those affected areas.  

The current activity in this flu season is already trending toward a higher caseload than 2017, with a steeper and earlier curve than in 2017-2018 (see red line in the graph below).  That season was the most severe season in recent years. By April 2018, more than 34 million people had the flu, about 1 million were hospitalized, and approximately 54,000 people died.    These deaths are usually from a secondary bacterial infection, complications of respiratory distress, or a cardiovascular complication attributable to influenza.  Although we have yet to see the peak of this season, should the percentage of ILI exceed those of 2017-2018, it is possible that this season will see a record number of influenza-attributable hospitalizations and deaths. 

ili curve.gif

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As a general estimate, around 5-15% of the total US population gets the flu yearly. The hospitalization rate is 1 in 100 (1%) and the death rate is 1 in 1000 (0.1%). The highest risk of mortality is seen in the 65 and older age group, but almost 60% of reported hospitalization are ages of 18-64 years. Sure, most people will get a mild case of influenza and many people will get a classic case – with rapid onset of tiredness, body aches, chills and fever with cough, fewer will need to be hospitalized and a small percentage will die. Given the sheer magnitude of those affected, this means a lot of peopleInfluenza is NOT a mild illness.

The good news is that if you have received the vaccine, you are likely to either be protected from the disease or get a milder case.  The CDC estimates the average efficacy of influenza vaccination ranges from 40 and 60%.  Other than getting a milder infection, the vaccine reduced the risk of the influenza-associated diseases, such as heart failure, respiratory failure, and secondary pneumonia.  Predictions for the 2019-2020 influenza vaccination are forthcoming.  The components for the H1N1 vaccine and usually for influenza B are more effective than the H3N2 (H1N1 (75-80%), H3N2 (20-25%)). Last season, the estimated vaccine efficacy was 47%, approximating 61% in ages 7 months to 18 years, and lower in the over 50 age group.  

The vaccinations consist of two type of influenza viruses, influenza A and B. Type A viruses are named after cell membrane (the outer layer of a virus) components – called hemagglutinin (H) and neuraminidase (N). The 2019-2020 vaccines are quadrivalent,  consisting of 2 types of A viruses (H1N1 pandemic 2009 and H3N2) and 2 The type B viruses named after lineages B/Yamagata and B/Victoria.  The influenza B cases for 2019-2020 are from the B/Victoria lineage. 

Unfortunately, unlike the measles or other childhood viruses, there is more virus differentiation — changes known as antigenic drift, when gradual, or antigenic shift, when sudden. A new vaccine has to be decided upon each year. An extensive vetting occurs involving input from multiple centers, where the most common strains are selected. Occasionally, the vaccinations do not match the years prominent strains. This year, the majority of cases have been caused by the H1N1 pdm 09. Why not 100% effective — there are enough differences from the vaccine strains and the seasonal strains (yes – it changes/re-assorts that fast) that make an immune response from the vaccination not as effective.

Below are some general questions and answers regarding influenza:

  1. Is it too late to get the vaccine if I missed earlier?  No. It is not too late to get vaccinated. The flu season usually tapers off after April. Getting a flu vaccination now would provide some protection for the remaining 2+ months. If you don’t want to make an appointment with your doctor, you can get it at many pharmacies. I would recommend the recombinant vaccination (quadrivalent) and the high-dose if you are older than 64.
  2. How is the flu spread? What are the signs and symptoms of the flu and how do these differ from the common cold.

The influenza virus can be transmitted fairly easily in both coarse/large and fine respiratory droplets – the greater density of virus is on the smaller droplets. You can breathe these droplets in or put them in your mouth. How does this happen?  1) the droplets can land on a surface and you can touch it and then put your fingers in your mouth or touch food you then eat; 2) Person-to-person a person could cover their cough and sneeze and shake your hands 3) Fomite, a person can contaminate an inanimate object, such as a doorknob, keys and a cell phone, and you can touch it and…

Unlike the common cold (rhinovirus), the symptoms for the flu come on abruptly.  There will be fatigue and muscle aches, though cough is the most common symptom.  The reason is that influenza causes varying degrees of infection in the  lungs, known as pneumonitis. Those with advanced age may have confusion or delirium along with a non-focal fever and cough. Anyone coming in with any exacerbation of chronic disease, e.g. lung disease or heart disease or even a heart attack, should be screened for seasonal influenza, given its association as an illness trigger.

3. How can I protect myself from getting the flu?

  • The influenza vaccine – Get it sooner than later.
  • Hand-washing : think about doing this more often during this time of the year -particularly when you touch a public surface or object (e.g. pen, doorknob). It might be a good time to do the fist-bump, air handshake, bowing ? or maybe just remembering to use alcohol rub if you shake someone’s hand – and wash your hands before eating.
  • Quit smoking :  Smokers have a greater risk of more severe sequellae. It may be a good time to consider quitting or seriously reducing.
  • Limit alcohol : For multiple reasons, excessive alcohol intake can affect the immune system and increase the risk of aspiration which is likely a risk factor to secondary bacterial infections in influenza. My recommendation would to limit alcohol to no more than 1 or 2 drinks a day or less.
  • Eat a healthy diet, maintain a healthy weight : Eating a variety of vegetables rife with minerals and vitamins is a great way to bolster the body’s immune system. Various vitamins such as vitamin A, D and to a lesser extent C and E have been shown to affect the immune system in deficiency states. (complexity alert) For instance Vitamin A deficiency was found in mice to impair respiratory epithelium (layer) regeneration and antibody response to influenza A. Vitamin D has been touted to be beneficial from a meta-analysis to reduce risk of infection, but there is some conflicting evidence from other studies. Nevertheless there is some biologic plausibility that Vitamin D plays a role in both adaptive (T- and B-cell) and innate (Natural killer, macrophages,etc) immunity. A prospective controlled study of 463 students 18 to 30 years old showed a benefit in the use of mega-doses of vitamin C, with a reduction in symptoms and severity (85% reduction) if taken before or after the appearance of cold or flu symptoms. A study on vitamin E in mice showed a reduction in influenza viral titer (amount), possibly linked to enhanced T helper 1 (TH1) cytokines.
  • Get plenty of sleep:   I will explore the topic of sleep and immunity on another post. Suffice it to stay, the many effector signals are involved in keeping our immune system robust and sleep is an important piece of the puzzle of why some people get more severe infections than other.
  • Exercises and keep a stress-free lifestyle
  • Obesity has come out as a new risk factor since the 2009 H1N1 pandemic flu season. One study looking at the cases of influenza showed an increase risk of hospitalization for a respiratory illness. In a person with class I obesity (BMI 30-35) the odds ratio was 1.45 and class II (BMI 35-40) and III (BMI 40-45) obesity, the odds ratio was 2.12 — for pneumonia and influenza. This fits similarly the association of more severe presentation of influenza and chronic diseases including diabetes, lung and heart disease and advanced age (impaired immunity).

4. Do omega-3 fish oils help influenza?   NO, I was asked this question recently. From my review online, fish oils may impair immune reactivity from the influenza virus (lower IgG and IgA levels) but may not have clinical impact. In one study in 1999, fish oils had anti-inflammatory properties and led to less viral clearance and some increase symptoms in mice but did not change the outcome. The possiblity of worsening the severity of influenza was suggested in another mice study

At this point, I am going with the likelihood that fish oils do not enhance one’s recovery from influenza.

5.  Are there any treatment options available for influenzaYES!  

  1.  Oseltamivir.  Oseltamivir (Tamiflu) is given twice daily over five days and is a neuraminidase inhibitor, which blocks an important step of viral progeny (new virions) leaving an infected cell to go on to infect other cells.  It likely reduces the severity and shortens the course by a few days.  Take the therapy within a day of onset.
  2.  Baloxavir is a single-dose option recently approved for this flu season (Oct 2018) and has a novel mechanism – an endonuclease inhibitor, which blocks a step needed in viral replication (“making copies”).  The important thing about these medications is that they have to be taken within 24-48 hours of the onset of flu symptoms to experience the maximal benefits, which amount to a reduction of severity and duration by a few days.

Not everyone requires treatment other than supportive care, particularly in those with mild disease.  I would recommend that anyone with an age over 60 or BMI >30 and/or with conditions such as diabetes, cirrhosis, cardiovascular or pulmonary diseases consider taking this medication to reduce the risk of severity and duration.  Patient with lymphoma and leukemia or solid organ cancer are also at higher risk of complications.  In all of these patients, I would suggest if they present with disease within 24-72 hours or are hospitalized even after this period, that they receive the therapy.

Conclusion.  Happy New Year 2020!  I hope that you have an uneventful 2019-2020 flu season.  If you are unfortunate to get it this year, I hope it is as mild for you as the common cold. There are things you can do to ensure that it is. Remember influenza can be a significant disease.  Thank you for reading this post and please share this to your friends and contacts.  If you want to stay up-to-date with future Your Health Forum posts, register your email on the the side panel.

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Patient Information: Make a Home for Your Microbiome

Your microbiome/microbiota refers to the trillions of microbes that reside inside and outside your body.  Human cells are outnumbered by the bacterial cell population.  The highest source of bacteria in the body is within the large intestines.  The status of resident bacteria has been associated with health and illness, with greater diversity being more protective.  Bacteria perform a number of functions including 1) production of certain vitamins such as Vitamin B12, B9, B2 and Vitamin K, 2) protection from infections by competing with more harmful bacteria, and 3) maintain a healthy immune system response.

Protecting your bacteria is not difficult and will likely benefit your body as a whole.  Here are some tips to maintaining a healthy microbiome:

  1. Eat mostly a plant-based, high fiber diet with low processed carbohydrates.  Limit the amount of processed carbohydrates that you consume during the meal and with snacks.  Raw plant matter may be more beneficial over cooked.  Plain yoghurt or kefir contains a healthy dose of normal gut bacteria.


  1. Avoid a significant amount of alcohol, milk, juice or sugary drinks.  Favor the fruit itself, since it will have less sugar and more fiber.  More of these substances high in alcohol and/or sugar lead to less gut diversity and GI side effects and increased inflammation.


  1. Limit the consumption of sugar and use of sugar substitutes. Sugar, processed carbohydrates (bread, pasta, white rice) in the diet has been associated with increased inflammation.


  1. Judicious Use of Antibiotics, Steroids and Proton pump inhibitors (PPI’s). Antibiotics can cause a shift in healthy gut flora and increase the risk of diff (a bacteria that causes diarrhea and colitis), yeast, Methicillin-resistant Staphylococcus aureus (MRSA).  It takes a team effort in coordination with your doctor, because antibiotics are often prescribed unnecessarily.  Prednisone can affect the immune system and cause a shift in gut flora, including increasing the risk of yeast.  PPI’s reduce acid and increase risk of more harmful bacteria populating.
  2.  Take Care of Your Health. Good sleep hygiene, exercise and low stress have all        been associated with more diverse gut microbiota.



If you have any of the following conditions, consider making a dietary adjustment to see if there is improvement, since a shift in gut microbiome, known as dysbiosis with less diversity, has been correlated either directly with these conditions or flare-ups:

  1. Gastroenterologic conditions: Peptic ulcer disease, reflux, Irritable Bowel Syndrome, Crohn’s, Small intestine bacterial overgrowth (SIBO), celiac disease
  2. Connective tissue diseases: Rheumatoid arthritis, lupus, psoriasis
  3. Skin: Atopic eczema, Rosacea, Acne
  4. Endocrine: Diabetes mellitus, Obesity
  5. Neurologic: Parkinsonism, Multiple sclerosis, other neurologic
  6. Cardiac: Coronary Artery Disease, Atherosclerosis
  7. Other: Depression, Anxiety, other mental health


Get to Know Your Gut Bacteria.  The following are general overview of the most common bacteria in the gut.  Though, an imbalance of even these bacteria could cause host effects.

Bifidobacterium and Lactobacillus help to protect the gut from harmful bacteria Plant-based foods which contain polyphenols, found in nuts, seeds, vegetables, teas, cocoa, wine and berries, feed these beneficial bacteria.  There may be a benefit in reducing inflammation in the cardiovascular system.  Bifidobacterium is associated with butyrate production, which has a protective role in the gut and anti-inflammatory effect.

Bacteroides and Firmicutes are found in a healthy gut.  Consumption of a plant-based diet with no animal fat or protein has been associated with greater populations of these bacteria.  Plant starch can also lead to a greater population of Bacteroides, also tied to obesity prevention/treatment.

Prevotella, also may favor a setting of a high fiber, plant-based diet.

Ruminococcus is more associated with a higher amount of fruit and vegetables.  These bacteria are associated with breaking down complex plant carbohydrates and producing butyrates.

Bilophila and Faecalibacterium are found in increased populations in a high saturated fat diet and may be associated with increased inflammation.



Tomova et al. The Effects of Vegetarian and Vegan Diets on Gut Microbiota.  Front Nutr. 2019; 6: 47

Refer to The Human Microbiome: Unlocking the Key to Health at YHF blog.