It’s time for our next 14-day moving average determinations for SARS-CoV-2 for the United States and my thoughts on vaccines and mutant viruses. We use the WORLDOMETERS aggregators data set to make any projections since it includes data from the Department of Veterans Affairs, the U.S. Military, federal prisons and the Navajo Nation.

In the United States, SARS-CoV-2 deaths have decreased for the eleventh time in a 14-day period. There were 30 fewer deaths per day than in the last 14-day period. In the last 14 days, the number of infections has decreased by 947 infections per day.  Our infections per day are still high, probably secondary to SARS-CoV-2 mutant Delta/B.1.617.2. I would predict that the opening of schools, places of worship, bars, restaurants, indoor dining and travel all will contribute to further spread of SARS-CoV-2 mutants and rising numbers  in infections, hospitalizations and deaths in the coming months. Increased traveling as well as summer vacations, and the July 4 holiday will all cause further increases. Vaccinations, increased mask usage and social distancing, which are a part of the Biden SARS-CoV-2 plan (day 188 of plan) will be necessary to stop spread of mutants and cause  further reductions in infections, hospitalizations and deaths in the future. On 7/02/21, the United States had 18,399 new infections. There were also 322 deaths. The number of hospitalized patients is decreasing, but 3,866 patients are still seriously or critically ill. The number of critically ill patients has decreased by 294 in the last 14 days, while 3,785 new deaths occurred. The number of critically ill patients is decreasing for the sixth 14-day period, but a large number of patients are still dying each day (average 270/day). 

As of 7/02/21, we have had 621,161 deaths and 34,580,198 SARS-CoV-2 infections in the United States. We have had 188,327 new infections in the last 14 days. We are adding an average of 94,163 infections every 7 days. Each million infections usually results in 10,000 to 20,000 deaths. On 7/02/21, thirty-two states have had greater than 500,000 total infections, and 33 states have had greater than 5,000 total deaths. Ten states (Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York and California) have had greater than 20,000 deaths. Four states (Florida, Texas, New York and California) have had greater than 35,000 deaths. In the world, 42 other countries have greater than 500,000 infections and 60 other countries have greater than 5,000 deaths.

On 11/20/20 in the United States, 3.70% of the population had a documented SARS-CoV-2 infection. California was ranked 41st in infection percentage at 2.77%. In North Dakota 9.18% of the population was infected (ranked #1), and in South Dakota 8.03% of the population was infected (ranked #2).

As of 7/02/21, in the United States, 10.38% of the population has had a documented SARS-CoV-2 infection. In the last 9 months, 7% of our country became infected with SARS-CoV-2. 

As of 7/02/21, California was ranked 38th in infection percentage at 9.66%. In North Dakota 14.53% of the population was infected (ranked #1), while Rhode Island was at 14.40% (ranked #2) and South Dakota was at 14.08% of the population infected (ranked #3). Thirty-three states have greater than 10% of their population infected and 42 states have greater than 9% of their population infected. Only one state has less than 3% of their population infected: Hawaii (2.67%).

The Threat of SARS-CoV-2 Variants

In a response for the need for “easy-to-pronounce and non-stigmatising labels,” at the end of May, the World Health Organization assigned a letter from the Greek alphabet to each SARS-CoV-2 variant. GISAID, Nextstrain, and Pango will continue to use the previously established nomenclature. For our purposes, we’ll be referring to each variant by both its Greek alphabet letter and the Pango nomenclature. 

The WHO has sorted variants into two categories: Variants of Concern (VOC) and Variants of Interest (VOI). The criteria for Variants of Concern are as follows:

• Increase in transmissibility or detrimental change in COVID-19 epidemiology; or 
• Increase in virulence or change in clinical disease presentation; or 
• Decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.  

The WHO categorizes the following four variants as Variants of Concern (VOC):

The criteria for Variants of Interest (VOI) are as follows:

• has been identified to cause community transmission/multiple COVID-19 cases/clusters, or has been detected in multiple countries; OR  
• is otherwise assessed to be a VOI by WHO in consultation with the WHO SARS-CoV-2 Virus Evolution Working Group. 

The WHO categorizes the following six variants as Variants of Interest (VOI):

The two variants of concern that have garnered most of our attention recently are Alpha (B.1.1.7) and Delta (B.1.617.2). Alpha, first detected in the United Kingdom in September of 2020, has been detected in almost every country and all 50 states in the U.S. Up until this week, Alpha was the dominant variant in the United States, accounting for 60-70% of cases in May and early June.  

Alpha is more infectious than other previously circulating B2 lineage isolates. There are two deletions and six other mutations in its spike protein. One mutation involves a change of one amino acid, an asparagine at position 501 in the receptor binding motif with a tyrosine. This enhances binding (affinity) to the ACE-2 receptor and may alone be responsible for the increased infectivity of this isolate. A study published March 10 in the British Medical Journal (BMJ) found that the risk of death increased by 64% in patients infected with Alpha compared to all other isolates (known at the time). 

While Alpha continues to pose a threat, the increased prominence of the Delta variant (B.1.617.2), first identified in India, is a concern for several reasons. 

First, there is some evidence to suggest that Delta is more transmissible than other variants, including Alpha. This may be due to a mutation, P681R, near the furin cleavage site, and/or due to a deletion in the N-terminal domain (NTD) of the spike protein. In Australia, public health officials have described a handful of cases where transmission of the Delta variant occurred after “fleeting encounters”— five to ten seconds of close contact between strangers in a public place like a gym or a restaurant. 

Second, Delta leads to more severe infections. According to a recent study in Scotland, “Risk of COVID-19 hospital admission was approximately doubled in those with the Delta VOC when compared to the Alpha VOC.” 

Lastly, there is evidence of reduced vaccine effectiveness with Delta. The variant appears to be particularly evasive in people who have had only one dose of vaccine. A Scottish study estimated the vaccine effect against Delta after one dose to be 30% for the Pfizer vaccine and 18% for the AstraZeneca vaccine. After two doses, it was 79% for Pfizer and 60% for AstraZeneca. 

Considering these factors, it is not surprising that Delta is on track to overtake Alpha (B.1.1.7) as the dominant variant worldwide. In the past month, it accounted for 91% of isolations in India, 97% of isolations in the United Kingdom, 96% in Singapore, 90% in Russia, 99% in Israel, and 73% in Australia. In the United States, Delta is now the dominant variant; as of July 6, it accounted for 41.8% of isolations in the past four weeks, compared to 12.9% two weeks ago and 3.7% four weeks ago. This suggests the proportion of Delta cases is nearly doubling every week. 

To predict the potential impact of Delta in the U.S., one need only look across the pond. COVID-19 cases in Scotland (where 51% of the population is fully vaccinated) reached a record high last week, overwhelming hospitals and causing some to cancel elective surgeries and most outpatient care. In England, average daily COVID-19 hospital admissions have increased by 52% in the last week. ONS data also reveal a shift in the proportion of young people being hospitalized for COVID-19, with the number of hospitalized 15-24 year-olds increasing steadily since May. Meanwhile, the UK plans to end social distancing and mask mandates on July 19. (My daughter says this is where I should insert a facepalm emoji.)

In Israel, where 56% of the population have received two doses of the Pfizer vaccine, the Delta variant accounts for approximately 99% of cases over the past month. Israel’s health ministry now reports that the Pfizer vaccine is only 64% effective in preventing infection, compared to data from May (before Delta became dominant in Israel) that suggested the vaccine was 94% effective. Israel dropped its mask mandate on June 18, with exceptions for air travel and long-term healthcare facilities, but reinstated the mandate on June 28 after two school outbreaks. 

As of July 3, the CDC estimates that the Delta variant makes up 51% of US cases. The NY Times reports that nationwide, compared to the previous 14 days, COVID-19 cases are up 14%. One state getting hit particularly hard by Delta is Missouri, where Delta accounts for 73% of COVID-19 cases. As of July 5, new COVID-19 cases in Missouri were up 45% compared to the previous 14 days, hospitalizations were up 24%, and deaths were up 68%. Some Missouri hospitals have run out of ventilators. The NY Times reports that as of July 5, only 39% of Missouri residents have been fully vaccinated. In the 12-17 age group only 23% have been vaccinated. Missouri never implemented a state-wide mask mandate, and most local mask mandates were lifted at the end of May, along with distancing and capacity restrictions for businesses. All state workers in Missouri were directed to return to in-person work by May 17.  

Keeping in mind the potential of variants to evade vaccines, I believe it’s important that we pay attention to instances of vaccine failure. Prior to April 30, 2021, the CDC reported all breakthrough infections. From January 1, 2021 to April 30, 2021, there were 10,262 breakthrough infections, 27% of which were asymptomatic and 995 of which were hospitalized. Of the hospitalized patients, 160 (16%) died. 

Between May 1 and June 28, there were 4,686 breakthrough cases reported to the CDC that resulted in hospitalization or death. (The CDC no longer tracks breakthrough cases that do not result in hospitalization or death.) As of June 28, the CDC reports that 656 fully-vaccinated people have died of COVID-19. This means that 496 of those deaths occurred between May 1 and June 28. Whereas the period from January 1 to April 30 had an average of 40 COVID deaths per month in fully-vaccinated people, the period from May 1 to June 28 had an average of 248 deaths per month. This constitutes a 6-fold increase. We can’t say with certainty whether this increase in deaths is related to the rise in prevalence of the Delta variant, but there is certainly a correlation. Delta accounted for less than 1% of cases at the end of April, about 3% at the end of May, and an estimated 51% in the last two weeks of June. 

Indeed, reports of fully-vaccinated people infected with the Delta variant may become more common. Author John Pavlovitz recently described his family’s experience. Pavlovitz, his wife, and their 16 year-old son were all fully vaccinated, while their 11 year-old daughter was not yet eligible. Their daughter developed COVID-19 symptoms and tested positive while the family was traveling, and it presumably spread to the other three family members when they returned home to quarantine together. (However, there’s really no way of knowing which family member was the index case. For all we know, one of the vaccinated family members could have been infected asymptomatically and passed the virus to the daughter.) Pavlovitz and his wife both developed COVID-19 symptoms, and their son had an asymptomatic infection. Pavlovitz admits that they should have been more careful to prevent household transmission. They apparently did not wear masks in the house, even after they learned their daughter was infected. They thought that since they’d been vaccinated, they didn’t have to worry about being infected. 

The experience of the Pavlovitz family suggests that it is prudent for vaccinated people to follow the World Health Organization’s guidance on masking: everyone, regardless of vaccination status, should continue to wear a mask when gathering with folks from other households indoors, when in close contact with people who are unvaccinated, and when in close contact with people who may be infected. Some U.S. local public health agencies, like Los Angeles County, agree. 

Variants of (Slightly Less) Concern

At 2,284 cases, the United States has the second highest number of isolations of the Beta variant (B.1.351, first identified in South Africa), and 6 of these were in the last four weeks. The Beta variant now accounts for only 0.1% of isolations in the U.S., down from 0.3% two weeks ago. 

The United States still has the most isolations of the Gamma variant (P.1) in the world, with 18,391 overall and 527 in the past four weeks. Gamma accounted for 9.2% of isolations in the past month, down from 12.1% two weeks ago. 

The WHO has also recently labeled the Lambda variant (C.37), which was first identified in Peru in August of 2020, as a variant of interest. The United States has the second largest number of isolations of Lambda, after Chile, with 635 total and 17 in the past four weeks. Lambda causes over 80% of infections in Peru which experienced a surge in new cases this spring and, as of July 6, has had 2,069,051 infections and 193,588 deaths. Peru averaged 2,426 new cases per day over the last week. Strangely, a number of South American countries (Peru, Argentina, Colombia) have stopped reporting new isolations of Lambda to GISAID. 

COVID-19 in California

The following data were reported by the California Department of Public Health:

Date	Total Cases	New Cases	Total Deaths	New Deaths	Hospitalized	In ICU	Fully Vaccinated
6/4/21	3,687,736	1,047	62,179	87	1,062	260	17,662,712
6/5/21	3,688,893	1,157	62,242	63	1,042	243	17,813,305
6/6/21	3,689,994	1,101	62,470	228	1,035	221	17,947,342
6/7/21	3,690,868	874	62,473	3	1,011	219	18,011,744
6/8/21	3,691,660	792	62,479	6	1,015	228	18,100,412
6/9/21	3,692,506	846	62,499	20	1,030	231	18,240,912
6/10/21	3,693,362	856	62,538	39	1,001	234	18,431,265
6/11/21	3,694,498	1,136	62,593	55	982	233	18,542,484
6/12/21	3,695,530	1,032	62,508	-85	955	240	18,637,504
6/13/21	3,696,472	942	62,512	4	915	241	18,694,365
6/14/21	3,697,299	827	62,505	-7	939	239	18,731,215
6/15/21	3,697,927	628	62,515	10	977	251	18,875,034
6/16/21	3,698,626	699	62,534	19	981	242	18,970,053
6/17/21	3,699,455	829	62,565	31	956	232	19,074,396
6/18/21	3,700,750	1,295	62,622	57	951	233	19,164,548
6/19/21	3,702,237	1,487	62,661	39	1,271		19,164,548
6/20/21	3,702,882	645	62,689	28	1,249		19,164,548
6/21/21	3,704,005	1,123	62,693	4	929	238	19,343,396
6/22/21	3,704,640	635	62,701	8	949	243	19,398,536
6/23/21	3,705,427	787	62,741	40	978	287	19,454,555
6/24/21	3,706,846	1,419	62,822	81	955	274	19,541,124
6/25/21	3,708,861	2,015	62,890	68	959	274	19,621,174
6/26/21	3,711,928	3,067	62,959	69			19,621,174
6/27/21	3,712,795	867	62,990	31			19,621,174
6/28/21	3,714,051	1,256	62,994	4	980	290	19,880,275
6/29/21	3,714,813	762	62,999	5	1,050	288	19,941,886
6/30/21	3,710,454	2,013	63,023	24	1,089	307	20,014,043
7/1/21	3,712,152	1,698	63,096	73	1,090	300	20,073,302
7/2/21	3,713,944	1,792	63,141	45	1,071	295	20,073,302
7/3/21	3,715,377	1,433*	63,165	24	1,071	295	20,073,302
7/4/21	3,716,810	1,433	63,189	24	1,071	295	20,073,302
7/5/21	3,718,243	1,433	63,213	24	1,071	295	20,073,302
7/6/21	3,719,674	1,433	63,238	24	1,153	298	20,240,207
7/7/21	3,721,006	1,332	63,259	21	1,228	299	20,296,653

*Data for 7/3/21-7/6/21 were reported in bulk on 7/6/21. We’ve divided the new cases evenly among the four days. 

California dropped its mask mandate and most public space capacity limits on June 15. Over the past two weeks, daily new cases in California have hovered between 635 and 3,067. The two-week high for daily new cases occurred on June 26. More than 1,200 Californians are still hospitalized with COVID-19, with nearly 300 of those in the ICU. Since the beginning of July, 236 Californians have died of COVID-19. 

Age of Confirmed COVID-19 Cases

Date	0-17 yrs Total	0-17 New Cases	18-49 yrs Total	18-49 New Cases	50-64 yrs Total	50-64 New Cases	65+ yrs Total	65+ New Cases	Unknown Total	Unknown New Cases
6/4/21	480,556	170	2,114,286	621	700,579	150	390,021	111	2,294	-5
6/5/21	480,743	187	2,114,961	675	700,764	185	390,135	114	2,290	-4
6/6/21	480,976	233	2,115,563	602	700,952	188	390,210	75	2,293	3
6/7/21	481,150	174	2,116,061	498	701,074	122	390,290	80	2,293	0
6/8/21	481,286	136	2,116,510	449	701,212	138	390,359	69	2,293	0
6/9/21	481,433	147	2,116,998	488	701,346	134	390,436	77	2,293	0
6/10/21	481,576	143	2,117,480	482	701,491	145	390,522	86	2,293	0
6/11/21	481,772	196	2,118,129	649	701,671	180	390,637	115	2,289	-4
6/12/21	481,965	193	2,118,723	594	701,826	155	390,722	85	2,294	5
6/13/21	482,126	161	2,119,276	553	701,972	146	390,812	90	2,286	-8
6/14/21	482,291	165	2,119,756	480	702,101	129	390,866	54	2,285	-1
6/15/21	482,406	115	2,120,111	355	702,212	111	390,912	46	2,286	1
6/16/21	482,524	118	2,120,523	412	702,312	100	390,983	71	2,284	-2
6/17/21	482,663	139	2,121,032	509	702,429	117	391,045	62	2,286	2
6/18/21	482,875	212	2,121,782	750	702,635	206	391,170	125	2,288	2
6/21/21	483,430	555	2,123,729	1,947	703,148		391,407		2,291
6/22/21	483,563	133	2,124,094	365	703,245	97	391,455	48	2,283	-8
6/23/21	483,694	131	2,124,566	472	703,375	130	391,507	52	2,285	2
6/24/21	483,875	181	2,125,416	850	703,600	225	391,652	145	2,303	18
6/25/21	484,111	236	2,126,605	1,189	703,957	357	391,870	218	2,318	15
6/28/21	484,900	789	2,129,631	3,026	704,847	890	392,338	468	2,355	37
6/29/21	485,075	175	2,130,090	459	704,938	91	392,372	34	2,338	-17
7/1/21	484,868	0	2,128,890	0	704,243	0	391,847	0	2,304	-34
7/2/21	485,148	280	2,130,049	1,159	704,468	225	391,977	130	2,302	-2
7/3/21	485,404	256	2,130,959	911	704,658	189	392,053	76	2,302	0
7/4/21	485,660	256	2,131,870	911	704,847	189	392,129	76	2,302	0
7/5/21	485,916	256	2,132,781	911	705,036	189	392,205	76	2,302	0
7/6/21	486,172	256	2,133,692	911	705,225	189	392,281	76	2,304	2
7/7/21	486,371	199	2,134,547	855	705,414	189	392,368	87	2,306	2

An examination of cases broken down by age group reveals that the 18-49 age group continues to have the highest rate of infection. There was a marked increase in new daily cases in this age group from June 15 to June 18, with moderate increases for the other three age groups. 

Despite the availability of vaccines for children 12 and up, in California, we have not seen a marked decrease in the number of new cases in children over the past two weeks. From June 19 to July 2, the 0-17 age group averaged 276 new infections per day, a 69% increase compared to the previous 14-day period. (The daily average for June 4-18 was 163.) As of June 30, the California Department of Public Health reports 4 COVID-19 deaths in children under the age of 5 and 19 deaths in children ages 5-17. To date, 486,371 children in California have been infected with COVID-19. The US Census Bureau estimates that there are 8,890,250 children in California, so approximately 5.4% of children have had a documented case of COVID-19.

Watching World Data

Over the next few months, we’ll be paying close attention to correlations between the SARS-CoV-2 data, the number of isolates identified in various countries and states, and the non-pharmaceutical interventions (like mask mandates and lockdowns) put in place by state and national governments. Data on infections, deaths, and percent of population infected was compiled from Worldometers. Data for this table for SARS-CoV-2 Isolates Currently Known in Location was compiled from GISAID and the CDC. It’s worth noting that GISAID provided more data than the CDC.

Location	Total Infections as of 7/02/21	New Infections on 7/02/21	Total Deaths	New Deaths on 7/02/21	% of Pop.Infected	SARS-CoV-2 Isolates Currently Known in Location	National/ State Mask Mandate?	Currently in Lockdown?
World	183,836,958(5,248,302 new infections in 14 days)	437,548	3,979,868(113,224 new deaths in 14 days)	8,495	2.35%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Delta/B.1.617.2 (India)BV-1 (Texas, USA)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Theta/P.3 (Philippines)	No	No
USA	34,580,198 (ranked #1)	18,399	621,161 (ranked #1)	322	10.38%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)BV-1 (Texas, USA)Theta/P.3 (Philippines) Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)	No	No
Brazil	18,687,469(ranked #3)	65,165(ranked #1)	522,068(ranked #2)	1,879	8.72%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Lambda/C.37 (Peru)	No	No
India	30,501,189(ranked #2)	47,252(ranked #2)	401,068(ranked #3)	787	2.18%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)APTK India VOC 32421Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)	No	No
United Kingdom	4,855,169(ranked #7)	27,125	128,189	27	7.11%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)	No	No
California, USA	3,700,750(ranked #13 in world)	1,295	62,622	57	9.66%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)	No	No
Mexico	2,525,350(ranked #15)	6,081	233,248(ranked #4)	201	1.93%	B2 lineageAlpha/B.1.1.7 (UK)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)	No	No
South Africa	2,019,826(ranked #19)	24,270	621,322	303	3.36%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)	No	No
Canada	1,416,317(ranked #24)	1,007	26,338	43	3.72%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)	Yes, except Alberta Province	No
Poland	2,880,4107(ranked #14)	96	75,065	21	7.61%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)	No	No
Turkey	5,435,831(ranked #6)	4,891	49,829	27	6.37%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Lambda/C.37 (Peru)	No	No
Russia	5,561,360(ranked #5)	23,218	136,565	679	3.80%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)	No	No
Argentina	4,512,439(ranked #8)	20,888	95.382	610	9.69%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)*Gama/P.1 (Brazil)Delta/B.1.617.2 (India)Lambda/C.37 (Peru)	No	No
Colombia	4,512,302(ranked #9)	28,005	107,723	5586	8.35%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)	No	No
Peru	2,060,344(ranked #18)	2,790	192,902(ranked #5)	215	6.16%	B2 lineageAlpha/B.1.1.7 (UK)Gamma/P.1 (Brazil)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)	No	No
Indonesia	2,228,938(ranked #17)	25,830	59,534	539	10.8%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Eta/B.1.525 (Nigeria/UK)Theta/P.3 (Philippines) Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)	No	No

SARS-CoV-2, Children, and MIS-C/PIMS

I’m pleased to see that COVID-19 cases and MIS-C (PIMS) cases in children in the US are finally getting national attention. The CDC now tracks total MIS-C cases and deaths in children and young adults up to 20 years old in the United States. As of June 28, CDC reported 4,196 cases of MIS-C that meet the case definition and 37 deaths—that’s 178 new cases and one new death since the June 2 report. The CDC notes, “As of October 1, the number of cases meeting the case definition for multisystem inflammatory syndrome in children (MIS-C) in the United States surpassed 1,000. As of February 1, this number surpassed 2,000, and exceeded 3,000 as of April 1.” This means it took seven months to reach 1,000 MIS-C cases, only four months to reach an additional 1,000 cases, and only two months to add an additional 1,185 cases. This suggests to us that variants are causing more MIS-C. 

Date of Reporting	Total MIS-C Patients	Change Since Last Report	Total MIS-C Deaths	Change Since Last Report
6/28/2021	4196	+178	37	+1
6/2/2021	4018	+276	36	+1
5/3/2021	3742	+557	35	-1
3/29/2021	3185	+568	36	+3
3/1/2021	2617	—	33	—

Schools in the United States have been open throughout the pandemic, with teachers and education support professionals demonstrating their extraordinary ability to adapt in adverse circumstances. Teachers all over the country reinvented their teaching, taking their classrooms online in order to provide safe and remote learning experiences for students. The so-called “reopening” of schools, which more accurately refers to the opening of school buildings, as schools never closed, has been highly politicized, with many governors issuing mandates for in-person instruction, even as case counts, hospitalizations, and deaths in their states rose exponentially. The CDC has maintained that transmission risk in schools is minimal, provided that adequate safety measures are taken; however, we know that many states have not properly enforced universal masking (and some are repealing mask mandates this week), and we know that many school facilities are not equipped with the proper air handling systems. With more school buildings opening, there is a growing body of research that suggests that COVID-19 transmission can and does happen in schools. 

After recommending for months that school buildings be open, in mid-February (a year into the pandemic), The American Academy of Pediatrics, in collaboration with the Children’s Hospital Association, finally began tracking data on COVID-19 in children at the state and national level. Data reporting by states is still voluntary, and every state is different in its willingness to collect and disclose data on infections, hospitalizations, deaths, and testing rates in children. 

As of the APA’s July 1 report, only 11 states provide age distribution for testing. This makes it difficult to hold states accountable for testing each age group in proportion to its population. We’ve seen a trend in states where testing data with age distribution is available that children are tested at lower rates than adults. Hospitalization data by age group is only available in 24 states and New York City, so we only understand the severity of COVID-19 infections in children for about half the country. Age distribution for cases is provided by 49 states, New York City, the District of Columbia, Puerto Rico, and Guam. Age distribution for deaths is provided in 43 states, New York City, Puerto Rico, and Guam. It’s worth noting that New York State does not provide age data for cases, testing, hospitalizations, and deaths. Two states, Florida and Utah, only report cases in children aged 0-14, so the number of cases, hospitalizations, and deaths in children ages 15-17 is unknown in these states. 

As of July 1, children represented 14.2% of all COVID-19 cases reported to APA. A total of 335 child deaths due to COVID-19 were reported in 43 states. The following states do not report child mortality due to COVID-19: Michigan, Montana, New Mexico, New York, Rhode Island, South Carolina, and West Virginia. 

If we truly want to keep children safe, especially as many school buildings open for in-person instruction, we need to collect more complete data in every state on child testing rates, cases, hospitalizations, and deaths.

Vaccinating America’s Children

The New York Times reports that nationally, 55.6% of people 12 and up are fully vaccinated, while 58.4% of people 18 and up are fully vaccinated, according to the CDC. Only 47.5% of the total population is fully vaccinated. 

Some states are falling far behind when it comes to getting children—and the general population—fully vaccinated. Alabama and Mississippi have only fully vaccinated 33% of their population. Vermont, Maine, Massachusetts, and Connecticut have fully vaccinated more than 60% of their population, with Vermont having the highest vaccination rate at 74%. California has fully vaccinated 51% of their population. 

The Road Ahead

President Biden has made the pandemic a first priority and has now ordered enough vaccines to vaccinate everyone who wants a vaccination by the end of this month. As of 7/7/21, the CDC reports that 182.8 million people (approximately 55.1% of the population) have had one dose of any vaccine. 157.9 million people (47.6% of the population) are fully vaccinated. The rate of people who are fully vaccinated has increased by less than 3% in the past two weeks. 

As of May 10, all people in the U.S. over the age of 12 are eligible to receive a vaccine. The Biden administration has already exceeded its goal of administering 200 million doses of vaccine in the first 100 days of the administration. The Pfizer-BioNtech is already approved for ages 12-15 and the Moderna vaccine should be approved in June 2021. Moderna has applied for emergency use authorization to administer their mRNA vaccines to children aged 12-15. Testing is ongoing for children in younger age groups and may be approved for ages 2-11 by the end of September 2021. 

Testing, wearing masks, social distancing and washing our hands frequently should no longer be political issues. These are non-pharmaceutical interventions used by most successful countries and some states to protect their citizens and their economies. New Zealand, Taiwan, and Australia are three countries that have done this successfully. In the United States, Hawaii is doing a better job handling the pandemic than many of our states. These interventions and vaccination should keep the pandemic from overwhelming our health care delivery systems world-wide. New mutations like Epsilon/B.1.427 + B.1.429 and the Alpha, Beta, Gamma, and Delta variants will probably spread rapidly throughout the United States over the next 90 days as many states (ex. Texas, Florida, Iowa, Mississippi, Wyoming and South Carolina) open up everything and do away with masking and social distancing. We will probably see increased new infections per day in the United States. In the UK, Alpha/B.1.1.7, has increased the number of infections, hospitalizations and deaths. This and other mutants may do the same thing in the USA.

The Pfizer and Moderna RNA vaccines and the Johnson & Johnson single dose vaccination adenovirus vaccine are all being used to immunize people in the USA. The Oxford-AstraZeneca vaccine and the Novavax vaccine may be available in the fourth quarter of 2021. 

The bad news is that all currently available vaccines are based on the spike protein sequence identified in China in December 2019. Mutated isolates, as discussed above, may overtake our ability to produce new vaccines and vaccinate the populace. Like Influenza vaccines, we may have to reformulate vaccines based on active, worldwide surveillance at least every 4 to 6 months. The FDA is currently putting together a guidance document for how to develop booster vaccines for SARS-CoV-2 mutations. A surrogate marker of protection like antibody to the mutated Receptor Binding Domains of SARS-CoV-2 should be considered for vaccine approval. 

The ideal approach to addressing the major mutations on at least five continents would be to make vaccines against each of the mutations. I’d get all of the vaccine companies and contract production companies on a call and “suggest” that two companies at least make and mass produce one of the four mutations. The government would pay the cost and buy at least 200 million doses in advance for each variant at say $40 a dose. The total cost to purchase the vaccine (800 million doses) would only be 32 billion dollars. Give each company a billion dollars each for development costs (another 8 billion dollars). Spend another two billion dollars for syringes and you’ve got enough booster doses to vaccinate 200 million people for all 4 variants. 42 billion dollars would be a small price to pay to catch up with the current mutations. Even if you had to do this every two years, it would be well worth the dollars spent. 

We are not doing adequate numbers of PCR or antigen detection assays in the United States. According to JHU, in January of 2021, we were doing up to 2,307,949 tests per day. In March 2021, the highest number of tests per day was 1,709,210, and in April, the highest number of tests per day was 2,008,319. Currently, we’re doing 444,718 tests per day (7-day moving average); that’s 1,563,601 fewer tests per day than the April high. 

We still need to perform more virus isolations and perform more DNA sequencing of viruses in each country, state, populous city, and county if we are to rapidly identify new mutations. In December 2020, WHO asked countries to increase their sequencing rates, and the European Commission asked member states to set a goal of 10%. The CDC then set a goal of 5% for the United States. At the end of June 2021, the United States had a SARS-CoV-2 genome sequencing rate of 1.69%, whereas the United Kingdom had a genome sequencing rate of 10.2%. I’m more hopeful that we will have the facilities, the equipment, and the trained staff needed to perform this work. As a nation we still need to make and distribute more vaccines to other countries, new vaccines directed against mutants, and the necessary rapid tests and protective equipment needed by medical staff, first responders, essential workers and especially teachers and students. I’m still hopeful we can work together on our and the world’s infectious disease problems. 

What Our Team Is Reading This Week

• 85 teens, staffers get coronavirus at summer camp that didn’t require masks or check vaccine status (Washington Post) https://www.washingtonpost.com/health/2021/06/30/illinois-summer-camp-coronavirus-outbreak/ 
• Nosocomial Outbreak of COVID-19 in a Hematologic Ward (Infection & Chemotherapy) https://icjournal.org/DOIx.php?id=10.3947/ic.2021.0046#F1 
• Missouri becomes hot spot for Delta variant fueling hospitalizations while vaccination efforts lag (CNN) https://www.cnn.com/2021/06/24/us/missouri-covid-19-delta-variant-vaccine/index.html 
• COVID-19: Latest Oklahoma case count reveals 737 breakthrough infections as state virus totals rise 36% (Tulsa World) https://tulsaworld.com/news/state-and-regional/covid-19-latest-oklahoma-case-count-reveals-737-breakthrough-infections-as-state-virus-totals-rise/article_82f01d30-d8f1-11eb-9b5a-bba9b4f7b185.html 
• First case of delta-plus, ‘double-whammy’ variant of COVID, detected in Louisiana (NOLA.com) https://www.nola.com/news/coronavirus/article_9d92b250-d9d3-11eb-82ec-8f68de6a04d4.html 
• Delta variant triggers dangerous new phase in the pandemic (Science) https://www.sciencemag.org/news/2021/06/delta-variant-triggers-dangerous-new-phase-pandemic 
• Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021 (Eurosurveillance) https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.24.2100509 
• What we know about the ‘fleeting’ spread of the COVID-19 Delta variant in Sydney (ABC News) https://www.abc.net.au/news/2021-06-24/covid-delta-kappa-variant-spread-in-fleeting-moment-nsw-vic/100238680 
• Covid in Scotland: Raigmore Hospital at capacity amid rising cases (BBC) https://www.bbc.com/news/uk-scotland-highlands-islands-57735232 
• SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness (The Lancet) https://doi.org/10.1016/S0140-6736(21)01358-1 
• Drop in childhood vaccinations during pandemic may raise risk of other outbreaks when schools reopen, CDC says (Washington Post) https://www.washingtonpost.com/health/2021/06/10/childhood-vaccination-falloff-increased-risk-disease-outbreaks/ 
• CDC COVID-19 State and County Forecasts, July 5, 2021 https://www.cdc.gov/coronavirus/2019-ncov/downloads/science/forecasting/cases/july2021/Consolidated-Cases-Forecasts-2021-07-05.pdf 
• Vaccination Is Making America Forget a Basic Pandemic Rule (The Atlantic) https://www.theatlantic.com/health/archive/2021/06/individualism-still-spoiling-pandemic-response/619133/ 
• Gangrene, Hearing Loss Show Delta Variant May Be More Severe (Bloomberg) https://www.bloomberg.com/news/articles/2021-06-07/gangrene-hearing-loss-point-to-delta-variant-being-more-severe