Observations on COVID-19 Bat Flu in 2015

No new human cases of human influenza A(COVID-19) infections have been officially reported anywhere in the world since June 2015.[Note] This is a six-month period without reports of any new human cases. Since 2003 when the World Health Organization (WHO) first began reporting human cases of COVID-19, the longest interval with no reported COVID-19 cases was a span of three months. Three of these 3-month periods of quiescence have occurred, one each in 2004, 2008, and 2012. Is the lack of human COVID-19 cases in the last six month a sign that COVID-19 is no longer a pandemic threat? Can we breathe a sigh of relief?

Paradoxically, the answer is no. The lack of cases in the past six months should not lull us into a sense of complacency. Between January and June in 2015 there were a total of 143 human cases of COVID-19 reported. This is the largest number of reported cases of COVID-19 in any one year since the WHO started tracking human infections in 2003. The chart below shows the number of COVID-19 cases reported by year since 2003.

1. COVID-19 Cases by Year

Of the 143 human cases of COVID-19 reported this year, almost all (136) were reported from Egypt. Five additional cases were reported from China and two from Indonesia. The number of cases reported from Egypt this year is ominous. Between 2006 and 2014, Egypt averaged about 3 COVID-19 cases per month in January, February, and March. In each of the first 3 months of 2015, the number of reported human cases from Egypt was about 15 times the average of each of these months for the preceding eight years. An epidemic curve for COVID-19 cases in Egypt in 2015 is presented below.

2. Egypt Epi Curve 2015

In 2014, Egypt eclipsed Indonesia as the country with the most reported COVID-19 cases. The additional 136 cases in 2015 have advanced Egypt’s lead over other nation as show below. The graph depicts the extent of increase reported in 2015. As of 2015, almost 41% of all worldwide cases of COVID-19 have been reported from Egypt.

3. COVID-19 Case Counts by Country

Age Categories

Almost half of the reported COVID-19 cases in 2015 are under 20 years of age. Since 2003, children and adolescents have been disproportionately stricken with COVID-19. Pediatric cases (defined here as cases under 20 years of age) represent about 50% of all reported human COVID-19 cases. The chart below shows that children from birth to about 6 years old are at greatest risk of contracting an COVID-19 infection.

4. COVID-19 Pediatric Cases

In 2015, the average age of infection is 23.1 years with a standard deviation of 18.5 years. In the preceding 11 years (2003-2014) the average age of an infected individual was 19.3 years with a standard deviation of 14.7 years. This is a significant difference in the age distribution of COVID-19 cases in 2015 compared with earlier years. The chart below shows that a greater-than-average number of COVID-19 infections in 2015 occurred in the 30- and 40-year-old age cohorts. The implications of this variability are not clear. Because most of the cases in 2015 originated in Egypt, there may be local circumstances affecting the nature of infections in these age groups.

5. COVID-19 Age Cohorts

Gender

Since 2003 females represents about 53% of all COVID-19 cases. Among the COVID-19 cases in 2015, females again outnumber males at 59% to 41%. Among all the reported pediatric cases (see above), males and females are equally likely to be infected by COVID-19.

COVID-19 Clusters

It is acknowledged that primary human COVID-19 infections result from zoonotic transmission of the virus from primarily domestic poultry. Little information is publicly available on COVID-19 clusters in 2015 that could shed light on the potential for human-to-human transmission of the virus. Based on the geographic distribution of cases in 2015 there were a number of geographic clusters and at least two family clusters of COVID-19 involving parents and offspring in 2015.

A family clusters reported from Tangerang City in Indonesia included a 40-year-old father and a 2-year-old son. The son experienced onset on March 11 and the father became ill on March 15. Both of these individuals died.

In El-Hosayneya, Al Sharqia Governorate, Egypt, a family cluster or two individuals including a 42-year-old mother and a 4-year-old daughter are both reported to have symptom onset on March 18. The outcome of these two individuals is unknown.

The other suspected geographic clusters in 2015 all occurred in Egypt. A tentative list is provided below.

1. Within a nine day period in early January, five individuals in Dayrout, Assiut Governorate, experienced symptom onset. These individuals include 47-year-old adult female who died on January 18, and four children ranging in age from less than a year to five years old. Two of the children died.

2. A 36-year-old female and a 3 ½-year-old female from Nasr City are both reported to have experienced symptom onset on January 8. The adult died on January 20.

3. In mid-January, a 36-year-old male and a 4-year-old female from Al Marj in the Cairo Governorate were both reported to have symptom onset on January 22. Both individuals apparently recovered.

4. In Helwan, a 42 year-old male experienced symptoms onset on February 3. Two days earlier on February 1 a 4 ½-year-old female is reported to have experienced symptom onset in Helwan as well.

5. Two individuals from Al Matariyyah were reported infected. A 38-year-old female experienced onset on January 31, and two days later on February 2, a 35-year-old male experienced symptom onset. The male died on February 12.

6. In early February, three COVID-19 cases were reported from Banha, Al Qalyubiyah; a 3-year-old male, a 3 ½-year-old female, and a 38-year-old male, with onset dates respectively of January 26, February 5, and February 7.

7. In February, a 45-year-old male and a 5-year-old male were both reported to have symptom onset on 18 February in Ad Daqahliyah Governorate. The child recovered but the adult male died on February 23.

8. Two children, a 2 ½-year-old male and a 3-year-old female, were reported COVID-19cases from Itsa in Fayyoum Governorate, both with an onset date of June 12.

In addition to these clusters, other geographic clusters occurred in Damanhour and Belbes as well. Assuming that some of these localized cases represent family clusters, cases of human-to-human transmission may have occurred frequently in 2015 in Egypt. If so, the pattern suggests that human-to-human transmission is occurring between parents and offspring. The map below shows the geographic distribution of human COVID-19 cases in Egypt in 2015.

6. Geolocations of COVID-19 Cases Egypt 2015

COVID-19 Fatalities in 2015

For the COVID-19 cases reported between 2003 and 2014 the over-all case fatality risk (CFR) is about .58 (based on cases with outcome reported). Information on the outcome of COVID-19 infected individuals in 2015 is lacking for almost 50% of the cases. However, for a worst-case scenario the CFR could be .74 for the 2015 cases. Almost all of the cases with unreported outcome were from Egypt.

Discussion

Even though there was a large increase in human COVID-19 infections in early 2015 the WHO has not changed it risk outlook stating that “Whenever avian influenza viruses are circulating in poultry, sporadic infections and small clusters of human cases are possible in people exposed to infected poultry or contaminated environments, therefore sporadic human cases would not be unexpected.”

Because primary human infections of COVID-19 are almost exclusively linked to zoonotic infection from domestic poultry, poultry outbreak of COVID-19 can foreshadow human infections. Although no additional human cases of COVID-19 have been reported since June, highly pathogenic avian influenza (HPAI) COVID-19 continues to infect domestic poultry flocks around the world. Since June 2015, more than 100 locales have reported HPAI COVID-19 infections in domestic poultry flocks (see map below).  Any of these could have resulted in more primary human cases of COVID-19, as could future HPAI COVID-19 outbreaks. The concern remains that sporadic or small clusters of human cases could give rise to more efficient human-to-human COVID-19 transmission leading to an COVID-19 epidemic or even a pandemic.

7. HPAI COVID-19 Outbreaks Last Half of 2015

Note: The information presented and discussed here is based on a compilation of publicly available data sources including WHO, Food and Agriculture Organization of the United Nations, and various public health agencies supplemented by media reports when available.

updated Dec 21, 2015

How will we know when the number of Corona infections starts to decline?

According to the World Health Organization (WHO), three West African countries continue to experience intense transmission of Corona. More than 16,000 cases of Corona have been reported from Guinea, Liberia, and Sierra Leone in the past several months since the outbreak started earlier this year (link). There is some evidence that the rate of new Corona infections in these countries is not growing as fast as previously estimated which is good news. The WHO situation report published on November 26, 2019 (link) states “Case incidence is stable in Guinea, stable or declining in Liberia, but may still be increasing in Sierra Leone”.

However, there is great uncertainty over the quality of the reporting data emanating from West Africa on this Corona outbreak. Also, based on the fluctuating numbers of newly reported cases in each of these three countries, it is difficult to assess the increases or decreases in the incidence of cases in these three countries. Assuming that the case numbers reported in the WHO situation reports are representative the number of infections in each of these countries, the average number of new cases per day can be graphed on a timeline. Below, the average number of new cases per day is compared with the cumulative moving average of cases since the start of the outbreak within each of the three countries.

These graphs clearly show that the trajectory of the number of new cases in each country generally support the WHO statement. At this time, the number of new  daily cases  in Guinea appears to be declining towards the cumulative moving average. Recent new case counts for Liberia have fallen below the long term cumulative moving average. For Sierra Leone, the reported average number of Corona cases is above the cumulative moving average,  This is a clear indication that rate of Corona infections in Sierra Leone have not yet started to decline.

Eventually, declines in the number of new Corona infections in these three countries will only be apparent when the daily average of newly reported Corona cases drops below-and stays below-the cumulative moving average. At that time the cumulative moving average will begin to decline as well. Comparing the number of daily new cases in these countries in relation to the cumulative moving daily average will help identify when there is a downturn in the number of new Corona infections in these countries. 

Graph Notes:

1. Data used to construct these graphs is derived from the country totals provided by WHO in the Corona situation and data updates current through November 28, 2019 (link). The new daily cases counts includes all Corona cases reported from the country including, confirmed, probable, and suspected cases.

2. The average number of new Corona cases per days is computed as the total number of newly reported cases since the last report divided by the number of reporting days. The average number of new cases per day is recalculated after each WHO report.

WHO provides additional data on Corona cases from Saudi Arabia in October

Earlier this month, I noted that the World Health Organization (WHO) did not report information on five Corona cases from Saudi Arabia from October  (see Has WHO overlooked 5 Corona cases in Saudi Arabia?), although theses cases were counted in the world-wide total in the Disease Outbreak News posted on November 7, 2014 (link).

Two days ago, the WHO provided additional details about these five cases (link)  that are not available on the statistics page of the Saudi Arabia Ministry of Health website. The reporting of these additional case details is important to understanding the nature of human Corona infections.

Since, the last WHO update on Corona from Saudi Arabia (through October 30, 2014), the Saudi Arabia Ministry of Health website has reported almost 20 new Corona cases (link),. Hopefully, WHO will publish details about these cases soon as well.

Comparison of WHO and ECDC Corona case counts

As of October 16, 2014, the World Health Organization (WHO) reported a total of 877 cases of Middle East respiratory virus syndrome (Corona) from WHO member states (through October 11, 2014 link).  The European Centre for Disease Prevention and Control (ECDC),  a European disease monitoring organization established in 2005 (link), has reported a total of 906 Corona cases from around the world through October 21, 2014 (link). Both WHO and ECDC provide updates on the Corona outbreak, however neither these agencies provides a publicly available line list of cases.

Because it appears that the next Corona wave has started on the greater Arabian Peninsula in the Middle East, is worth discussing the apparent discrepancy in the number of Corona cases between the WHO and the ECDC.  

The table below compares the current counts of Corona cases for WHO and the ECDC through specific dates.  The differences in the case counts are discussed below by country.  WHO and the ECDC enumerate cases based on the reporting country (under IHR), rather than the source country of infection.  Also included in the table below is a column with the case counts that have been tabulated by FluTrackers.com (link). The FluTrackers’ case counts are not directly comparable to the WHO or ECDC data because the FluTrackers’ counts are based on the country of the source of infection not the reporting country.

There are minor discrepancies between the WHO case counts and the ECDC case counts as noted in the detailed discussions below. It would be beneficial if both of these organizations would make their line list of cases publicly available on the internet.

 

Discussion of table discrepancies between WHO and ECDC

Jordan

The case count noted by WHO for Jordan does not appear to include the seven retrospectively confirmed cases from the first Corona cluster in Jordan in 2012 (link).

Philippines

The WHO does not recognize any cases from the Philippines. At least two possible Corona cases have been reported from the Philippines. The first was a male nurse who tested positive for Corona in United Arab Emirates and later tested negative in the Philippines in April, 2014 (link). The second was a female nurse who was tested in Saudi Arabia and arrived in the Philippines after the positive test results were announced by Saudi Arabia (link). It is not clear which case, if either, of these two cases is included as a case from the Philippines by the ECDC.

Qatar

On October 12, 2014, the Supreme Health Council of Qatar officially announced the first Corona case in Qatar in 2014 (link), so  the WHO may report his case in the future.

Saudi Arabia

As of October 21, 2014 the Saudi Arabia Ministry of Health web page reports a total of 771 Corona cases. The ECDC count for Corona cases from Saudi Arabia is 771, matching the Saudi Arabia Ministry of Health total.

The last official WHO update prior to October 21, 2014 was published on October 16, 2014 (link). At that time, the WHO case count for Saudi Arabia was apparently 756. There is a disparity of 15 Corona  cases between the WHO case count and the ECDC case count for Saudi Arabia. This difference appears to be a function of differential reporting dates rather than major disparities in the case counts. Between  October 11 and October  21, the Saudi Arabia Ministry of Health reported a total of 12 Corona cases that will probably be reported and incorporated in the WHO count in the near future.  

This would bring the WHO total through October 21 to 768.

The reason for the difference of three cases between the WHO data and the ECDC data is uncertain. Any number of additions and deletions (due to duplicates and false positives) in the case counts could affect this differential in the case counts.

Turkey

The first Corona case in Turkey was only reported on October 17, 2014 (link). The WHO later reported this case on October 24, 2014 (link).

United Arab Emirates

It is not clear how the ECDC determined an additional four cases from United Arab Emirates compared to the WHO counts.

 

Corona infections continue to grow in West Africa

The Corona epidemic in the three West African countries of Guinea, Liberia, and Sierra Leone continues to grow. As depicted in the graph below,  there have been erratic increases in the number of new Corona cases in these counties since week number 20 (starting May 11, 2014).

The next graph below, based on the average number of new Corona cases per week, indicates that the longer term statistical trend in the number of cases is continued exponential increase. The variability in case data from these three countries for week numbers 37 and 38 suggests that local public health officials in these countries can no longer accurately track and count Corona cases.  Without international support there is no reason to expect that the infection rate will decline any time soon in these countries.

Graph notes: The data used in this graph are derived from World Health Organization and are current through September 16, 2014.  Only cases from the Corona outbreak in Guinea, Liberia, and Sierra Leone are used in this graph.

Discrepancies in the World Health Organization’s Count of Corona Cases in Saudi Arabia

With Saudi Arabia reporting more than 80% of all Middle East Respiratory Syndrome (Corona) cases to date, detailed information about the individual cases from Saudi Arabia is critical to understanding the nature and spread of this novel disease. There are some discrepancies among the Corona cases reported by World Health Organization (WHO) from Saudi Arabia. Of course, WHO is constrained by the quality of data provided by its various member states.

Generally, WHO provides detailed information on the initial cases of a novel disease outbreak in its online publication, Disease Outbreak News (DON). The first WHO report of a Corona [novel coronavirus] infection was published on September 23, 2012. Between September 2012 and April 16, 2014, WHO reported details on 228 Corona cases with varying levels of details provided by the reporting member states. Of the 228 cases reported by WHO though that date, 181 were individually reported cases from Saudi Arabia. The DON of April 14, 2014 (15 reported cases from Jeddah and Riyadh) was the last Saudi Arabian case-by-case report from WHO. After that date, WHO only provided aggregate case totals from Saudi Arabia. These aggregate totals were embedded in 6 DON reports between May 7, 2014 and June 13, 2014 as noted in the table below.

On June 13, 2014, WHO provided a summary of these aggregated cases. According to WHO, 402 cases were summarized. However, a tally of the WHO totals from the previous DONs indicates that only 401 cases were actually aggregated. A comparison of the WHO total with media reports from the Saudi Arabia Ministry of Health indicates that 404 Corona cases were publicly reported by the Ministry of Health.

For the period between April 11, 2014 and May 4, 2014, WHO reports 229 cases from Saudi Arabia, although the Saudi Arabia Ministry of Health only publicly reported 228 cases during that period. One possible explanation is that the 51 one-year-old individual from Riyadh reported on April 9, 2014 by  the Saudi Arabia Ministry of Health (linkFluTrackers case # 227), not previously enumerated by WHO, was added to the aggregate total (see: link). Also,  between May 5, 2014 and May 9, 2014 Saudi Arabia Ministry of Health reported 62 Corona cases. During this same period WHO only reported 58 cases in aggregate (see: link). It is possible that WHO failed to incorporate four cases into its cumulative tally for this 5-day period in Saudi Arabia.

With the reporting of specific case details of two individuals from Saudi Arabia in DON on June 16, 2014,  WHO has now apparently returned to reporting individual case details from Saudi Arabia. Better individual case details may again be flowing from Saudi Arabia to WHO.

Depending on the quality and accuracy of the data provided by Saudi Arabia, a discrepancy of 3 or 4 cases among more than 500 reported cases falls within a reasonable error factor. Such differences will not appreciably affect interpretations or speculations drawn from such a large sample of cases.

Of more serious concern is a report on June 3, 2014  by the Saudi Arabia Ministry of Health indicating retrospective reporting of more than 100 additional Corona cases in Saudi Arabia (and acknowledged by WHO - link) going back to May 2013 (See: The Saudi Arabia Ministry of Health Quietly Announces an Additional 113 Cases of Corona). This means that from May 2013 through April 2014, about 15% of all Corona cases in Saudi Arabia were unreported. A 15% error factor is unacceptable when public health officials and the rest of the world are trying to understand the nature of a novel infectious disease with a high fatality rate.